diff --git a/.codespellrc b/.codespellrc
new file mode 100644
index 000000000..cebf9aa26
--- /dev/null
+++ b/.codespellrc
@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,venvs
+#
+# ignore-words-list =
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 000000000..7373affc3
--- /dev/null
+++ b/.github/workflows/codespell.yml
@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+ push:
+ branches: [master]
+ pull_request:
+ branches: [master]
+
+permissions:
+ contents: read
+
+jobs:
+ codespell:
+ name: Check for spelling errors
+ runs-on: ubuntu-latest
+
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v3
+ - name: Codespell
+ uses: codespell-project/actions-codespell@v2
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 4186ac89b..590560bbe 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,3 +4,8 @@ repos:
hooks:
- id: black
language_version: python3.7
+
+- repo: https://github.com/codespell-project/codespell
+ rev: v2.2.5
+ hooks:
+ - id: codespell
diff --git a/bep028spec.md b/bep028spec.md
index 749daae10..b02c6bb37 100644
--- a/bep028spec.md
+++ b/bep028spec.md
@@ -360,7 +360,7 @@ Each Entity (as a record or a top-level entity) has the following fields:
wasGeneratedBy
|
- OPTIONAL. UUID. Identifier of the activity which generated this entity (the corresponding Activity must be defined with its own Activty record).
+ | OPTIONAL. UUID. Identifier of the activity which generated this entity (the corresponding Activity must be defined with its own Activity record).
|
@@ -555,7 +555,7 @@ An example of this can be [fMRIPrep](https://fmriprep.org/en/stable/index.html),
The most simplistic way you can think of is to have this container "black-boxed" in your workflow. You basically record the calling of this container (`command` section) and the output (see the outputs section from fMRIPrep)
-"prov:Activty": [
+"prov:Activity": [
{
diff --git a/bids_prov/afni/afni_parser.py b/bids_prov/afni/afni_parser.py
index 0980f05e1..d1ab9a7a6 100644
--- a/bids_prov/afni/afni_parser.py
+++ b/bids_prov/afni/afni_parser.py
@@ -76,10 +76,10 @@ def find_param(cmd_args_remain: list) -> dict:
for arg_remain in cmd_args_remain:
if arg_remain.startswith("-"):
if arg_remain != cmd_args_remain[-1]:
- succesor = cmd_args_remain[cmd_args_remain.index(arg_remain) + 1]
- if not succesor.startswith("-"):
- param_dic[arg_remain] = succesor
- cmd_args_remain.remove(succesor)
+ successor = cmd_args_remain[cmd_args_remain.index(arg_remain) + 1]
+ if not successor.startswith("-"):
+ param_dic[arg_remain] = successor
+ cmd_args_remain.remove(successor)
else:
param_dic[arg_remain] = True
else:
@@ -88,7 +88,7 @@ def find_param(cmd_args_remain: list) -> dict:
return param_dic
-def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
+def build_records(commands_block: list, agent_id: str, verbose: bool = False):
"""
Build the `records` field for the final .jsonld file,
from commands lines grouped by stage (e.g. `Registration`, `Post-stats`)
@@ -96,7 +96,7 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
Parameters
----------
- commands_bloc : list of str
+ commands_block : list of str
all commands extracted from afni file
agent_id : int
random uuid for software agent (here afni)
@@ -115,7 +115,7 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
bloc_act = []
- for (bloc, cmd) in commands_bloc:
+ for (block, cmd) in commands_block:
cmd_s = re.split(" |=", cmd)
a_name = cmd_s[0]
cmd_args_remain = cmd_s[1:]
@@ -232,7 +232,7 @@ def build_records(commands_bloc: list, agent_id: str, verbose: bool = False):
# "derivedFrom": input_id,
}
)
- bloc_act.append((bloc, activity["@id"]))
+ bloc_act.append((block, activity["@id"]))
records["Activities"].append(activity)
if verbose:
@@ -294,23 +294,23 @@ def readlines(input_file: str) -> list:
# commands = [cmd for cmd in commands if not any(
# cmd.startswith(begin) for begin in dropline_begin)]
- regex_bloc = re.compile(r'# =+ ([^=]+) =+')
- commands_bloc = []
- bloc = ""
+ regex_block = re.compile(r'# =+ ([^=]+) =+')
+ commands_block = []
+ block = ""
for cmd in commands:
if cmd.startswith("# ==="):
- bloc = regex_bloc.match(cmd).groups()[0] if regex_bloc.match(cmd) is not None else "bloc ..."
+ block = regex_block.match(cmd).groups()[0] if regex_block.match(cmd) is not None else "block ..."
if not any(cmd.startswith(begin) for begin in dropline_begin):
- commands_bloc.append((bloc, cmd))
+ commands_block.append((block, cmd))
- commands_bloc = [(bloc, re.sub(r"\s+", " ", cmd))
- for (bloc, cmd) in commands_bloc] # drop multiple space between args
+ commands_block = [(block, re.sub(r"\s+", " ", cmd))
+ for (block, cmd) in commands_block] # drop multiple space between args
- commands_bloc = [(bloc, cmd)
- for (bloc, cmd) in commands_bloc if cmd] # drop empty commands
+ commands_block = [(block, cmd)
+ for (block, cmd) in commands_block if cmd] # drop empty commands
- return commands_bloc
+ return commands_block
def get_activities_by_ids(graph, ids):
@@ -425,7 +425,7 @@ def get_extern_entities_from_activities(graph, activities, id_fusion_activity):
def afni_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None,
- soft_ver='afni24', indent=2, verbose=True, with_blocs=True) -> bool:
+ soft_ver='afni24', indent=2, verbose=True, with_blocks=True) -> bool:
"""
afni parser
@@ -438,55 +438,55 @@ def afni_to_bids_prov(filename: str, context_url=CONTEXT_URL, output_file=None,
output_file : str
name of output parsed file with extension json.ld
soft_ver:str
- version of sofware afni
+ version of software afni
indent : int
number of indentation in jsonld
verbose : bool
True to have more verbosity
- with_blocs : bool
+ with_blocks : bool
To retrieve or not the results of the parser in block mode and not only for each command
Returns
-------
bool
Write the json-ld to the location indicated in output_file.
- If `with_blocs` is True, it generates the file to the location indicated in output_file.
+ If `with_blocks` is True, it generates the file to the location indicated in output_file.
"""
- commands_bloc = readlines(filename)
+ commands_block = readlines(filename)
graph, agent_id = get_default_graph(label="AFNI", context_url=context_url, soft_ver=soft_ver)
- records, bloc_act = build_records(commands_bloc, agent_id, verbose=verbose)
+ records, bloc_act = build_records(commands_block, agent_id, verbose=verbose)
graph["Records"].update(records)
compute_sha_256_entity(graph["Records"]["Entities"])
- if with_blocs:
+ if with_blocks:
bl_name = list(OrderedDict.fromkeys(bl for (bl, id) in bloc_act))
- blocs = [{
+ blocks = [{
"bloc_name": bl,
"act_ids": [id_ for (b, id_) in bloc_act if b == bl]} for bl in bl_name]
- graph_bloc = copy.deepcopy(graph)
- activities_blocs = []
- entities_blocs = []
- for bloc in blocs:
- activities = get_activities_by_ids(graph_bloc, bloc["act_ids"])
- fus_activities = fusion_activities(activities, bloc["bloc_name"])
+ graph_block = copy.deepcopy(graph)
+ activities_blocks = []
+ entities_blocks = []
+ for block in blocks:
+ activities = get_activities_by_ids(graph_block, block["act_ids"])
+ fus_activities = fusion_activities(activities, block["bloc_name"])
ext_entities = get_extern_entities_from_activities(
- graph_bloc, activities, fus_activities["@id"])
+ graph_block, activities, fus_activities["@id"])
for ent in ext_entities:
- if ent["@id"] not in entities_blocs:
- entities_blocs.append(ent)
+ if ent["@id"] not in entities_blocks:
+ entities_blocks.append(ent)
for ent_used in fus_activities["Used"]:
if ent_used not in [id_["@id"] for id_ in ext_entities]:
fus_activities["Used"].remove(ent_used)
- activities_blocs.append(fus_activities)
+ activities_blocks.append(fus_activities)
- graph_bloc["Records"]["Activities"] = activities_blocs
- graph_bloc["Records"]["Entities"] = entities_blocs
+ graph_block["Records"]["Activities"] = activities_blocks
+ graph_block["Records"]["Entities"] = entities_blocks
- return writing_jsonld(graph_bloc, indent, output_file)
+ return writing_jsonld(graph_block, indent, output_file)
return writing_jsonld(graph, indent, output_file)
diff --git a/bids_prov/fsl/fsl_parser.py b/bids_prov/fsl/fsl_parser.py
index 0da509751..29315854d 100644
--- a/bids_prov/fsl/fsl_parser.py
+++ b/bids_prov/fsl/fsl_parser.py
@@ -37,7 +37,7 @@
]
)
-# tags used to detect outputs from cammand lines
+# tags used to detect outputs from command lines
# eg. convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat
OUTPUT_TAGS = frozenset(
[
@@ -141,14 +141,14 @@ def readlines(filename: str) -> Mapping[str, List[str]]:
# return None
-def _get_kwarg(serie, with_value=True):
+def _get_kwarg(series, with_value=True):
"""
- Get the named arguments (kwarg) from a column ("Used", "GeneratedBy", "ParametersValue" or "ParametersNoValue" ) of the dataframe coming frome in description_functions.json
+ Get the named arguments (kwarg) from a column ("Used", "GeneratedBy", "ParametersValue" or "ParametersNoValue" ) of the dataframe coming from in description_functions.json
Parameters
----------
- serie : pandas series
+ series : pandas series
A list of the command arguments description.
with_value : boolean
A bool to specify if values are expected or not, in order to dicrimine "ParametersValue" (with_value=True), and "ParametersNoValue" (with_value=False)
@@ -162,7 +162,7 @@ def _get_kwarg(serie, with_value=True):
arg_list = []
add_argument_list = []
- for u_arg in serie:
+ for u_arg in series:
if type(u_arg) == dict:
# parser.add_argument(u_arg["name"], nargs='+', action='append')
if "Nargs" in u_arg:
@@ -199,14 +199,14 @@ def _get_kwarg(serie, with_value=True):
return add_argument_list, arg_list
-def _get_arg(serie, arg_rest):
+def _get_arg(series, arg_rest):
"""
- Get the ordinal arguments from a column ("Used", "GeneratedBy") of the dataframe coming from in description_functions.json. _get_arg shoud be used when all named arguments are removed from the initial command.
+ Get the ordinal arguments from a column ("Used", "GeneratedBy") of the dataframe coming from in description_functions.json. _get_arg should be used when all named arguments are removed from the initial command.
Parameters
----------
- serie : pandas series
+ series : pandas series
A list of the command arguments description.
arg_rest : string of the command, (without all the named argument used in description_functions.json)
@@ -217,7 +217,7 @@ def _get_arg(serie, arg_rest):
arg_list = []
arg_purge = [arg for arg in arg_rest if not arg.startswith("-")]
- for u_arg in serie:
+ for u_arg in series:
if type(u_arg) == int:
# print("arg_purge", type(arg_purge), arg_purge, u_arg)
if u_arg < len(arg_purge):
diff --git a/bids_prov/tests/test_afni_parser.py b/bids_prov/tests/test_afni_parser.py
index a7f040a0a..265674a80 100644
--- a/bids_prov/tests/test_afni_parser.py
+++ b/bids_prov/tests/test_afni_parser.py
@@ -63,7 +63,7 @@ def test_readlines():
"3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D"
]
- commands = [cmd.strip() for (bloc, cmd) in commands]
+ commands = [cmd.strip() for (block, cmd) in commands]
# Replace multi (>=2 ) blank space to one
commands = [re.sub(r"\s{2,}", " ", cmd) for cmd in commands]
expected_commands = [cmd.strip() for cmd in expected_commands]
diff --git a/code_of_conduct.md b/code_of_conduct.md
index 7354b4b9a..8557d0506 100644
--- a/code_of_conduct.md
+++ b/code_of_conduct.md
@@ -5,7 +5,7 @@
We as members, contributors, and leaders pledge to make participation in our
community a harassment-free experience for everyone, regardless of age, body
size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
nationality, personal appearance, race, religion, or sexual identity
and orientation.
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
index 6dd965aca..b5381c892 100644
--- a/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
+++ b/examples/from_parsers/afni/afni_alt_onesided_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "@id": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:b3ac12f5-d164-4144-89f6-67daadcf23ac",
+ "@id": "urn:ec251330-d3c1-4154-8da1-e690bdf5e956",
"Label": "Make directory",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:9eca7ae7-6ffe-446a-8603-7137fd4e4ee9",
+ "@id": "urn:0d388f61-9111-482b-8107-7545ebbec4cb",
"Label": "Make directory",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:df0f3c2c-5569-4f68-b81d-0a334275b3d2",
+ "@id": "urn:e2b59a11-aa0a-47a5-9bc6-a727eb7145a8",
"Label": "cp",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:680f5096-e37f-4ec7-b010-2dae5b5a44fd",
- "urn:8596c632-de2b-47b7-b261-0bcc1b11efb4"
+ "urn:329d09d5-6a12-4729-a722-c6dc26a2fbe5",
+ "urn:e6da214d-7f37-4bda-a731-0c7458945ec7"
]
},
{
- "@id": "urn:d17f25f0-c1e6-432f-9d55-370e965b4514",
+ "@id": "urn:9284e0b5-0ecb-4842-9411-923f3e87928f",
"Label": "3dcopy",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:16bf4939-3694-4686-af30-f2acf3976d7b"
+ "urn:7f4d9ddc-df59-4c9d-a7ad-d520e12afd9a"
]
},
{
- "@id": "urn:137dfd65-b714-4d68-91d7-4b5c61d6653e",
+ "@id": "urn:3c6eaf78-bf2e-4231-a5e7-82ef6217fe8c",
"Label": "3dTcat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:12d262d4-d471-4599-a49d-b4cc3e0afab2"
+ "urn:2d7fbb57-9060-4d9b-88e3-daacd0134d99"
]
},
{
- "@id": "urn:426ecd4c-c844-4216-95ee-fdea203c4ac7",
+ "@id": "urn:7f84ea18-06fe-4c30-89d2-ddfcf648b295",
"Label": "3dToutcount",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:af357576-8640-45a8-b66f-ea5b863776aa"
+ "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8"
]
},
{
- "@id": "urn:4c94d596-d066-4fae-b4ac-31bd8a4eb431",
+ "@id": "urn:fae06d9d-613d-46ce-83dd-84b396a4e7df",
"Label": "cat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:35ff0a25-7087-4dde-92e3-84a2069160fa"
+ "urn:2bcdf477-8b44-4542-9267-198f2aae6231"
]
},
{
- "@id": "urn:994296a3-49bb-4c51-a3b9-96095c772750",
+ "@id": "urn:3ba5cd1f-fdfc-400a-a1ae-227bdfe70c50",
"Label": "3dTshift",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:af357576-8640-45a8-b66f-ea5b863776aa"
+ "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8"
]
},
{
- "@id": "urn:dbf6e423-b7f4-467c-99e7-f781accfb665",
+ "@id": "urn:e6575988-076c-4dac-868c-1cba20f3c597",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:66c6f4a5-e5db-46b2-b07c-e741461d17cd",
- "urn:a6816927-efa4-41b8-9288-3137c8b366a0"
+ "urn:183fa34a-9df4-4380-85c5-75f4e62fa9cc",
+ "urn:231abdc8-7275-44f3-86b3-b8cd318f4207"
]
},
{
- "@id": "urn:f76d19e5-b0b5-45bc-a574-b35b52c5604a",
+ "@id": "urn:86a2c39f-8c70-46ea-a91d-e12263267963",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:47364376-8009-46b5-9c2c-50f39f9aa7b7",
- "urn:656ab567-c679-4a66-9a7e-b12940a77924"
+ "urn:4d5696da-b769-4e33-9d69-07fac85ea539",
+ "urn:65603e13-f0b7-4788-91a0-dff5363681c9"
]
},
{
- "@id": "urn:2b13402b-a51c-4043-8706-ad2728b1668d",
+ "@id": "urn:b9ea35db-d498-431f-88a6-0669481d8bd2",
"Label": "cat_matvec",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:1bccfb06-3514-411e-bc4d-7d5021d773b8"
+ "urn:07f5df79-08d1-431a-afd0-fcdb6563121f"
]
},
{
- "@id": "urn:70b358c7-8ce7-49a4-b5f1-2256b0311124",
+ "@id": "urn:fd4b3e64-5e6c-48aa-b561-2bea00747104",
"Label": "3dvolreg",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:816045b3-2730-4afa-9cce-255578e9966f"
+ "urn:95e22684-0144-4cce-af19-97b1623d1b90"
]
},
{
- "@id": "urn:65e5b8ec-8793-4d1a-9626-73a770621fea",
+ "@id": "urn:b2f7ad57-5a5b-442e-9c5b-2c0072ba9c85",
"Label": "3dcalc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:816045b3-2730-4afa-9cce-255578e9966f"
+ "urn:95e22684-0144-4cce-af19-97b1623d1b90"
]
},
{
- "@id": "urn:1584680b-a5c4-45be-94be-7b696c8e2397",
+ "@id": "urn:fa8342fe-9330-4fbe-8c69-740405630269",
"Label": "cat_matvec",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:1bccfb06-3514-411e-bc4d-7d5021d773b8"
+ "urn:07f5df79-08d1-431a-afd0-fcdb6563121f"
]
},
{
- "@id": "urn:e4dbc681-d344-4eb1-ac0c-12733bcdbb55",
+ "@id": "urn:f1ae068f-bd6c-4f5e-990f-bc158d798aa4",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:42d9c5ac-c680-4d9a-ad99-b824a3b0f394",
- "urn:816045b3-2730-4afa-9cce-255578e9966f",
- "urn:db266899-a1e3-4ced-ac54-5e9fc8e925ff"
+ "urn:8b0df28d-d3ef-4a15-9789-745572110d2a",
+ "urn:95e22684-0144-4cce-af19-97b1623d1b90",
+ "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
]
},
{
- "@id": "urn:9c79005b-4a9a-49e5-9b9e-e8bfd5752c8e",
+ "@id": "urn:3474c8cd-db1d-499b-a758-30039fb6ad37",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:42d9c5ac-c680-4d9a-ad99-b824a3b0f394",
- "urn:867c3f3e-61a4-4e15-868f-d6f881110e8b",
- "urn:db266899-a1e3-4ced-ac54-5e9fc8e925ff"
+ "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
+ "urn:8b0df28d-d3ef-4a15-9789-745572110d2a",
+ "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
]
},
{
- "@id": "urn:fe6d6a5a-eb3e-4181-805e-a2e2fe4fec50",
+ "@id": "urn:fb5b492a-60c2-449b-8413-fd136b506cd7",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:3e1fcf67-d0c6-41ce-b2d4-494232f1d5fe"
+ "urn:f1ebdf2e-24f8-49fd-8cf4-c135b087159d"
]
},
{
- "@id": "urn:da70a0c2-17ec-4c1c-9942-adf20b85a387",
+ "@id": "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e",
"Label": "cat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:b5cd528a-7c8f-4f15-ab9f-0bd7bca967ca"
+ "urn:0723034d-fc73-4fc4-9deb-605b9add0ee7"
]
},
{
- "@id": "urn:abf58822-094d-478e-8a84-f7519450b542",
+ "@id": "urn:0134c831-73b9-47b6-80a6-41535abaf825",
"Label": "3dcopy",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:209a7ec7-d866-4295-a415-a6b5798cc3de"
+ "urn:64b3106f-d986-42e5-bea5-ad79de7eed00"
]
},
{
- "@id": "urn:52844cb7-c62b-41ef-bc17-de747ef73c6c",
+ "@id": "urn:086568a2-e38c-44a5-ac87-7bbb46fb1215",
"Label": "3dcalc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:23e29248-772c-45f4-8176-869d5bb08030",
- "urn:b7e9d248-a3aa-4de7-bd2a-0c2db25f4d01"
+ "urn:76f8224d-55bf-46a5-bc7f-2973c300c08f",
+ "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15"
]
},
{
- "@id": "urn:4dd0b74d-0f56-46f4-a431-38c65782ceb7",
+ "@id": "urn:b5d49317-69e9-4232-b911-58eab6897675",
"Label": "3dcopy",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:db266899-a1e3-4ced-ac54-5e9fc8e925ff"
+ "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
]
},
{
- "@id": "urn:e8a448c0-04d3-4137-bc5d-41cee7d54402",
+ "@id": "urn:7271accf-6874-4774-8e77-f2c8317f2b9b",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:43dca89a-d0f3-4707-b491-9bf44284d9a6"
+ "urn:d4191393-3201-4f9e-aa33-65310f13e2d2"
]
},
{
- "@id": "urn:707144f1-53d3-42ec-ba6f-542f54333737",
+ "@id": "urn:5a59dd20-8346-4538-8661-9396d02224d7",
"Label": "3dmerge",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:3949d23a-4ffc-49cf-90b3-b9af6d0ecad5",
- "urn:f8fccd8c-a469-43b6-a102-7923558cdb83"
+ "urn:4dc466e1-b429-43bb-b880-add7232b7347",
+ "urn:f33a292b-a905-408f-ba76-441a2058a27b"
]
},
{
- "@id": "urn:3d2b1791-0c11-4d49-a9c6-abd1f5374040",
+ "@id": "urn:dda87c51-4f5a-49b0-928d-a53c9b3c47f6",
"Label": "3dAutomask",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8b407455-a555-4fa6-bcda-746acc712cf2"
+ "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c"
]
},
{
- "@id": "urn:8552e2e6-e17e-4c59-a484-215e804f9bc9",
+ "@id": "urn:c3acf82f-0adc-4874-bd69-b28b507542c7",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:c2144b4f-8b0f-4584-863a-cb9f06b98711",
+ "@id": "urn:b5c075e3-f245-4bc9-8cc4-d55eec21091e",
"Label": "3dresample",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257",
- "urn:db266899-a1e3-4ced-ac54-5e9fc8e925ff"
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
]
},
{
- "@id": "urn:9c267539-9f5e-4c6a-820b-652610506db1",
+ "@id": "urn:1a0a3bff-cc42-4522-8a1b-0ec281a16e51",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:fe43eb18-b0fc-4dfc-9d79-e154b0bf1b40"
+ "urn:920dddce-28c6-421c-882c-9a68550b6b34"
]
},
{
- "@id": "urn:8d8b1a81-efd4-4ec8-9f8c-f8bd29768886",
+ "@id": "urn:7437f41a-5203-4d70-ac17-53d387d4947b",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1d0b4ab1-9c00-460b-a339-d7f4602a8644",
- "urn:f96391da-8ad6-4968-90fc-e3e5e9d1f810"
+ "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee",
+ "urn:aca48b64-0f58-44c1-bf54-eb7e9089f5b9"
]
},
{
- "@id": "urn:5b079aab-bbe2-4c2c-bf2a-b67914b572b1",
+ "@id": "urn:31571f6d-d8ca-4c66-a64a-c2a2a88753d4",
"Label": "3ddot",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1d0b4ab1-9c00-460b-a339-d7f4602a8644",
- "urn:f96391da-8ad6-4968-90fc-e3e5e9d1f810"
+ "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee",
+ "urn:aca48b64-0f58-44c1-bf54-eb7e9089f5b9"
]
},
{
- "@id": "urn:f82eb87b-862d-408e-b96c-a142427057ff",
+ "@id": "urn:924f0baf-a156-4e39-835b-4b9974948de2",
"Label": "3dresample",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257",
- "urn:4a586b50-9b84-4d1c-ae6a-04112b3056b3"
+ "urn:5c0e3a05-6e09-4bc9-bb52-e8c4c019ce22",
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee"
]
},
{
- "@id": "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1",
+ "@id": "urn:9d7031f9-b790-4f40-b4db-a36f7f1cdd18",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:99a72a05-324e-47a9-a72f-17d952a1b355"
+ "urn:09ebc5dc-0466-4923-bd49-13831d041c86"
]
},
{
- "@id": "urn:cbd8f7a7-e0a6-4c73-84e3-22dd6e13c348",
+ "@id": "urn:d816bf62-f91e-4d89-af7d-9078d2f8bc45",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8b407455-a555-4fa6-bcda-746acc712cf2"
+ "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c"
]
},
{
- "@id": "urn:820e1ce0-2ab6-4f10-b95c-96faec0c975a",
+ "@id": "urn:8abe0474-66d5-4e8d-b799-4ca935562832",
"Label": "3dcalc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:73dc9b49-8e2c-44bc-a868-f4864e9d45bd",
- "urn:8b407455-a555-4fa6-bcda-746acc712cf2",
- "urn:b7e9d248-a3aa-4de7-bd2a-0c2db25f4d01"
+ "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15",
+ "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c",
+ "urn:a05bcc8c-767e-4ef9-ad52-82fdcf352918"
]
},
{
- "@id": "urn:0aabb59a-ee81-4df8-8921-da60f4c7f23a",
+ "@id": "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:521a1422-bf72-4868-a196-36ea32e32333"
+ "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97"
]
},
{
- "@id": "urn:1fdbba0a-7cc5-4a61-a176-47060d3ec405",
+ "@id": "urn:32ee6bc3-7996-47c5-ba5d-ad3dae831538",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:521a1422-bf72-4868-a196-36ea32e32333"
+ "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97"
]
},
{
- "@id": "urn:b6f3d426-8b9e-4890-bdfe-fd4ff7add62d",
+ "@id": "urn:a85d6e1c-9519-48a0-9494-5592eb2b8506",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:521a1422-bf72-4868-a196-36ea32e32333"
+ "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97"
]
},
{
- "@id": "urn:5f30236b-7177-4396-8dc1-f5273c7647d9",
+ "@id": "urn:9734bf62-20af-427c-a298-49437e993740",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:7f7e32bd-8c96-4db8-a1c2-6dce6a2dd739"
+ "urn:8f862f58-0135-443a-84b8-7d315d0751e5"
]
},
{
- "@id": "urn:22577639-ce6b-4c30-91e9-2c95f8eab904",
+ "@id": "urn:dbb688bc-e370-4644-9913-9ae6f2e86ecb",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:9e33b686-c0c9-443c-b09a-e260a466da80"
+ "urn:8683b331-474b-43db-938a-3fb2df8077ff"
]
},
{
- "@id": "urn:ca3ac5a5-7b11-4707-8113-dddff04409ce",
+ "@id": "urn:7cf453df-7e7b-4f99-8439-7859bdc17e52",
"Label": "3dTcat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:7f7e32bd-8c96-4db8-a1c2-6dce6a2dd739"
+ "urn:8f862f58-0135-443a-84b8-7d315d0751e5"
]
},
{
- "@id": "urn:036f2b82-0e8d-46c3-bc57-1f2f0456e364",
+ "@id": "urn:67cafc9e-cf08-49e6-ab5b-e48caba9edf8",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:517a16eb-aa7f-4d32-8cd0-19db3ce2d355"
+ "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a"
]
},
{
- "@id": "urn:18bd9c7d-706e-46b0-9ef8-d845970d2f31",
+ "@id": "urn:678f852c-890c-4abc-bf0a-1e737c5189bc",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:a00d33e9-976c-4da2-bfd5-c323f5de4e6d"
+ "urn:203b180e-1762-40ec-80d2-0e9ec0447898"
]
},
{
- "@id": "urn:58eb8130-38d3-46cc-8a21-e4b5ff740ae4",
+ "@id": "urn:8cb47f6b-5181-4500-9572-0906eac7e750",
"Label": "3dcalc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:1050fa11-dffe-4880-bdee-9ad82afbd4dc",
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257",
- "urn:9a8c6a5d-e331-49ee-9cbf-7aae85f6c449"
+ "urn:2fd43732-f606-4c9b-a9f0-74885d47be97",
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "urn:8c858fbe-04ee-48dc-bab5-c1ae2ef9159c"
]
},
{
- "@id": "urn:5174fcd8-825d-46ed-a9f2-6b364163d866",
+ "@id": "urn:df27cd3b-d715-4b02-b53b-a3b58ad15509",
"Label": "3dTnorm",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:b0783160-cc25-4f90-87b0-62ea91dd364e"
+ "urn:1d06d47e-8469-4b81-9404-fbc57017ad23"
]
},
{
- "@id": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
+ "@id": "urn:cb1c0160-0e2f-4a93-b70f-8f61530cdb27",
"Label": "3dmaskave",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:a4a72b44-266e-4cf8-843b-40c5956df505",
+ "@id": "urn:5fee107f-6a26-4850-849e-b57806b77df2",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:2eace7c1-48d7-42d0-8a53-9cd10b219f30"
+ "urn:03b235ce-bedb-404b-8ea4-83225a07fb37"
]
},
{
- "@id": "urn:5b26ef30-7cf9-4d67-9818-95e38cea6091",
+ "@id": "urn:46e28345-fd6e-4493-8d14-61325dd2787f",
"Label": "3dcalc",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd",
- "urn:9f20d7ff-f5a0-46d0-8829-cf585dd6a6ba"
+ "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2",
+ "urn:906a7e97-4954-4db4-90a8-66b1d76cd022"
]
},
{
- "@id": "urn:1aa7103f-ebf2-4568-be03-f2d1e223af21",
+ "@id": "urn:30a127a0-5da6-41e9-b18f-b0d0213d8bad",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:9c84233e-4c3f-40e2-8828-b10d5fc0b1ef"
+ "urn:e73ff039-8349-4916-94b3-209aa86d7a3f"
]
},
{
- "@id": "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
+ "@id": "urn:3f99163c-feeb-4ddf-b9a3-98fbe5c4c030",
"Label": "1dcat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a"
+ "urn:54de5eb3-f9ac-4833-886e-bf68285dca2b"
]
},
{
- "@id": "urn:b390c087-192d-44fe-8042-1bcca38ab6ae",
+ "@id": "urn:af4526e8-a45d-47d0-9556-d2eccbaa0079",
"Label": "1dcat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:c17bb85f-17c1-41eb-9367-0ee3a76060b5"
+ "urn:a3f63c7e-f657-4071-82d5-23c6f12857a3"
]
},
{
- "@id": "urn:71135527-0811-46d0-887d-1b56a42edc2e",
+ "@id": "urn:0a6241b6-2152-4e5b-8113-cc6c69d9197b",
"Label": "3dTstat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:1ebe5cf2-e3de-4260-b209-df16e3768d62"
+ "urn:5420810d-a31a-49fd-acd7-8b299036cc1f"
]
},
{
- "@id": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
+ "@id": "urn:fa5adf0f-a40a-43dc-b563-398664d6a64e",
"Label": "1dcat",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:1ebe5cf2-e3de-4260-b209-df16e3768d62"
+ "urn:5420810d-a31a-49fd-acd7-8b299036cc1f"
]
},
{
- "@id": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
+ "@id": "urn:ab91b3fd-d259-4e35-917b-15e7f7eb5390",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257"
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee"
]
},
{
- "@id": "urn:63a6fef4-fa62-4df6-8328-87f0bddf63b2",
+ "@id": "urn:f4ad58dc-3808-48a2-ab28-b91512eceeb8",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257"
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee"
]
},
{
- "@id": "urn:640db747-51b4-4c85-a15e-94117c886ae4",
+ "@id": "urn:b1cc91c7-f921-41c1-8be7-392416eeeb13",
"Label": "3dClustSim",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:3c0180cc-d6d3-4ccc-8f38-fe8174ca9257"
+ "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee"
]
},
{
- "@id": "urn:7a512ed2-ad13-49f5-a0dd-1b83659fa35f",
+ "@id": "urn:a2736bdd-b58b-4fd5-b985-64805c68ad20",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:2eb30742-cf34-4fe0-8ac9-40a44a229224"
+ "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0"
]
},
{
- "@id": "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d",
+ "@id": "urn:0b2038d7-d9aa-47f4-9a7c-4fcf52ee799b",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:a045e7a9-d02f-4c07-9480-ef691c027817",
+ "AssociatedWith": "urn:4a83669a-6fc8-4866-a4cb-b74c48b8c2f5",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:ac6fc9f2-1d1f-4612-ad97-fb964bfe01e8",
+ "@id": "urn:84a2fd0f-cef6-4ec3-a2b4-defce849f38f",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:b3ac12f5-d164-4144-89f6-67daadcf23ac",
+ "GeneratedBy": "urn:ec251330-d3c1-4154-8da1-e690bdf5e956",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:cb4c5056-c449-472b-b206-0576b5edec2b",
+ "@id": "urn:992191e6-cd54-483e-90d3-3b177bf40e12",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:9eca7ae7-6ffe-446a-8603-7137fd4e4ee9"
+ "GeneratedBy": "urn:0d388f61-9111-482b-8107-7545ebbec4cb"
},
{
- "@id": "urn:680f5096-e37f-4ec7-b010-2dae5b5a44fd",
+ "@id": "urn:329d09d5-6a12-4729-a722-c6dc26a2fbe5",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_one_sided_t_test/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
- "@id": "urn:8596c632-de2b-47b7-b261-0bcc1b11efb4",
+ "@id": "urn:e6da214d-7f37-4bda-a731-0c7458945ec7",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_one_sided_t_test/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
- "@id": "urn:9e80f43e-0a65-4409-8521-93ce44d2a2f8",
+ "@id": "urn:d809c990-23f3-4601-80f6-06be25447e95",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:df0f3c2c-5569-4f68-b81d-0a334275b3d2"
+ "GeneratedBy": "urn:e2b59a11-aa0a-47a5-9bc6-a727eb7145a8"
},
{
- "@id": "urn:16bf4939-3694-4686-af30-f2acf3976d7b",
+ "@id": "urn:7f4d9ddc-df59-4c9d-a7ad-d520e12afd9a",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
},
{
- "@id": "urn:77134def-200f-4e91-bf5b-5beae8522368",
+ "@id": "urn:905e675b-0242-43eb-9763-4908abbe7de9",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:d17f25f0-c1e6-432f-9d55-370e965b4514"
+ "GeneratedBy": "urn:9284e0b5-0ecb-4842-9411-923f3e87928f"
},
{
- "@id": "urn:12d262d4-d471-4599-a49d-b4cc3e0afab2",
+ "@id": "urn:2d7fbb57-9060-4d9b-88e3-daacd0134d99",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
}
},
{
- "@id": "urn:b723daf9-7d1e-4070-a15b-11cbabd9f404",
+ "@id": "urn:868803d2-f2c9-45ad-98ae-215da048aed3",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:137dfd65-b714-4d68-91d7-4b5c61d6653e"
+ "GeneratedBy": "urn:3c6eaf78-bf2e-4231-a5e7-82ef6217fe8c"
},
{
- "@id": "urn:af357576-8640-45a8-b66f-ea5b863776aa",
+ "@id": "urn:b9336d7f-7863-4a9c-bda6-7cfde4a6b9e8",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
}
},
{
- "@id": "urn:d9e0442e-5d73-4c85-8e4d-66f08337e10b",
+ "@id": "urn:7f9d7885-1d14-424b-8008-2888ebe51bba",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:426ecd4c-c844-4216-95ee-fdea203c4ac7",
+ "GeneratedBy": "urn:7f84ea18-06fe-4c30-89d2-ddfcf648b295",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
},
{
- "@id": "urn:35ff0a25-7087-4dde-92e3-84a2069160fa",
+ "@id": "urn:2bcdf477-8b44-4542-9267-198f2aae6231",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
}
},
{
- "@id": "urn:e69315ec-55c8-4cf6-aaaf-52ba92d2ec31",
+ "@id": "urn:e44fb4cb-778d-41e7-9cbc-5d6cc1a73c68",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:4c94d596-d066-4fae-b4ac-31bd8a4eb431",
+ "GeneratedBy": "urn:fae06d9d-613d-46ce-83dd-84b396a4e7df",
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}
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{
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@@ -702,7 +702,7 @@
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@@ -710,16 +710,16 @@
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@@ -727,7 +727,7 @@
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@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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@@ -760,34 +760,34 @@
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@@ -795,16 +795,16 @@
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -846,16 +846,16 @@
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@@ -863,16 +863,16 @@
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@@ -880,7 +880,7 @@
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@@ -888,34 +888,34 @@
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@@ -923,7 +923,7 @@
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@@ -931,7 +931,7 @@
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@@ -939,25 +939,25 @@
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@@ -965,16 +965,16 @@
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@@ -982,16 +982,16 @@
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@@ -999,7 +999,7 @@
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@@ -1007,7 +1007,7 @@
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@@ -1015,16 +1015,16 @@
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@@ -1032,25 +1032,25 @@
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@@ -1058,34 +1058,34 @@
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{
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"AtLocation": "motion_deriv.1D",
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{
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+ "@id": "urn:8f862f58-0135-443a-84b8-7d315d0751e5",
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"AtLocation": "pb04.$subj.r*.scale+tlrc.HEAD",
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@@ -1093,25 +1093,25 @@
}
},
{
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"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:5f30236b-7177-4396-8dc1-f5273c7647d9",
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{
- "@id": "urn:f281a192-9bc5-4c8e-891f-f639659c098a",
+ "@id": "urn:49b19b62-af92-47fa-8c77-2337c2f05775",
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"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:ca3ac5a5-7b11-4707-8113-dddff04409ce",
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}
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{
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+ "@id": "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a",
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"digest": {
@@ -1119,16 +1119,16 @@
}
},
{
- "@id": "urn:ec085929-3a73-462c-837f-7b8ada04bdf4",
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"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:036f2b82-0e8d-46c3-bc57-1f2f0456e364",
+ "GeneratedBy": "urn:67cafc9e-cf08-49e6-ab5b-e48caba9edf8",
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{
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+ "@id": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
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"digest": {
@@ -1136,16 +1136,16 @@
}
},
{
- "@id": "urn:f1e10c64-fe4a-4263-b044-ebe6c840ffbf",
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"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:18bd9c7d-706e-46b0-9ef8-d845970d2f31",
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{
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"digest": {
@@ -1153,7 +1153,7 @@
}
},
{
- "@id": "urn:1050fa11-dffe-4880-bdee-9ad82afbd4dc",
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"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1161,16 @@
}
},
{
- "@id": "urn:1e1b8b6a-4f33-4ce5-b008-9056f9eade30",
+ "@id": "urn:4eec28c2-77b1-4e2a-b5ad-a4bf544143f9",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:58eb8130-38d3-46cc-8a21-e4b5ff740ae4",
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{
- "@id": "urn:b0783160-cc25-4f90-87b0-62ea91dd364e",
+ "@id": "urn:1d06d47e-8469-4b81-9404-fbc57017ad23",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1178,25 @@
}
},
{
- "@id": "urn:fffdce39-1022-4364-aa1b-182e4f764878",
+ "@id": "urn:ef4d92a2-528c-4884-9e55-9b6f0f020e18",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:5174fcd8-825d-46ed-a9f2-6b364163d866",
+ "GeneratedBy": "urn:df27cd3b-d715-4b02-b53b-a3b58ad15509",
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}
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{
- "@id": "urn:9f20d7ff-f5a0-46d0-8829-cf585dd6a6ba",
+ "@id": "urn:906a7e97-4954-4db4-90a8-66b1d76cd022",
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"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
+ "GeneratedBy": "urn:cb1c0160-0e2f-4a93-b70f-8f61530cdb27",
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{
- "@id": "urn:2eace7c1-48d7-42d0-8a53-9cd10b219f30",
+ "@id": "urn:03b235ce-bedb-404b-8ea4-83225a07fb37",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:3318f2f4-021e-4945-ac68-a79194eece86",
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"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:a4a72b44-266e-4cf8-843b-40c5956df505",
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{
- "@id": "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd",
+ "@id": "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2",
"Label": "rm.errts.unit",
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@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:0cc3f639-004a-4d2d-af86-b5c8d36f74bf",
+ "@id": "urn:9138c461-25d9-4077-b2c2-acf0e0cef1fd",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:5b26ef30-7cf9-4d67-9818-95e38cea6091",
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{
- "@id": "urn:9c84233e-4c3f-40e2-8828-b10d5fc0b1ef",
+ "@id": "urn:e73ff039-8349-4916-94b3-209aa86d7a3f",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:cd671150-53fa-415a-ad4f-d28f69a46244",
+ "@id": "urn:9f27626b-b95b-4840-a3d2-3c61d7d614f9",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:1aa7103f-ebf2-4568-be03-f2d1e223af21",
+ "GeneratedBy": "urn:30a127a0-5da6-41e9-b18f-b0d0213d8bad",
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"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a",
+ "@id": "urn:54de5eb3-f9ac-4833-886e-bf68285dca2b",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:4dde7fde-d83c-4871-9581-a2f80c237204",
+ "@id": "urn:8ef8df32-6435-4171-a299-d223d76c6c6e",
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"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
+ "GeneratedBy": "urn:3f99163c-feeb-4ddf-b9a3-98fbe5c4c030",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:c17bb85f-17c1-41eb-9367-0ee3a76060b5",
+ "@id": "urn:a3f63c7e-f657-4071-82d5-23c6f12857a3",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:66c4a64b-24fb-4355-b6f0-745d29806e79",
+ "@id": "urn:5418c0a4-9327-411b-9e4c-8e07ad6b9045",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:b390c087-192d-44fe-8042-1bcca38ab6ae",
+ "GeneratedBy": "urn:af4526e8-a45d-47d0-9556-d2eccbaa0079",
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}
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{
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+ "@id": "urn:5420810d-a31a-49fd-acd7-8b299036cc1f",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:f9294378-917d-4969-b1ea-e82eef53f208",
+ "@id": "urn:3a301cd9-25da-471b-8223-bad090c7347d",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:71135527-0811-46d0-887d-1b56a42edc2e",
+ "GeneratedBy": "urn:0a6241b6-2152-4e5b-8113-cc6c69d9197b",
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"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:60f84ff1-e701-4e52-8dbe-dca9e99a1c2f",
+ "@id": "urn:b552aaae-f3a6-43f9-a28e-2adaa38edc2c",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
+ "GeneratedBy": "urn:fa5adf0f-a40a-43dc-b563-398664d6a64e",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:e502668a-42ab-4093-9bf5-a7a57645e2ad",
+ "@id": "urn:98af3652-a864-476a-b2d5-059404150cbd",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
+ "GeneratedBy": "urn:ab91b3fd-d259-4e35-917b-15e7f7eb5390",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:a4807546-b85f-4467-b4e1-5302e8f0d87c",
+ "@id": "urn:bdbf17fa-bfef-4bd5-90d8-f02ac4320a78",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:63a6fef4-fa62-4df6-8328-87f0bddf63b2",
+ "GeneratedBy": "urn:f4ad58dc-3808-48a2-ab28-b91512eceeb8",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:53043b2a-cb9b-43cc-8521-29127997d9dc",
+ "@id": "urn:99e36abe-ae11-4401-99aa-a5ddc3092b09",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:640db747-51b4-4c85-a15e-94117c886ae4",
+ "GeneratedBy": "urn:b1cc91c7-f921-41c1-8be7-392416eeeb13",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:2eb30742-cf34-4fe0-8ac9-40a44a229224",
+ "@id": "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:907b32a8-d868-44e1-9252-fa126deb550f",
+ "@id": "urn:8339701c-d6f7-49d6-8d0e-657dc2e062cc",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d",
+ "GeneratedBy": "urn:0b2038d7-d9aa-47f4-9a7c-4fcf52ee799b",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
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diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc.png b/examples/from_parsers/afni/afni_alt_onesided_proc.png
index b4e99b12f..0f82f2954 100644
Binary files a/examples/from_parsers/afni/afni_alt_onesided_proc.png and b/examples/from_parsers/afni/afni_alt_onesided_proc.png differ
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
new file mode 100644
index 000000000..c12baaeca
--- /dev/null
+++ b/examples/from_parsers/afni/afni_alt_onesided_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:cbb044da-cc8b-4ef7-977c-2c3794c9027a",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_one_sided_t_test/tone_counting_onset_times.txt ./afni_one_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:ad6afb1f-16c3-42d2-b5c1-ed7709d5baf8",
+ "urn:fec2d381-36fb-4e79-af50-fb87c41fb116",
+ "urn:9df834a4-e7db-4a93-b135-78a21e8af4cf"
+ ]
+ },
+ {
+ "@id": "urn:519e09f7-3485-43b6-bbe5-d045cfa8a316",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:a03334c1-a3eb-4f6e-8950-27ed8c34fe59"
+ ]
+ },
+ {
+ "@id": "urn:e4f1c0c1-d62c-4d95-9f6a-2dc7252f0873",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:03f18f63-6da0-4cef-bc7c-af56235662fa",
+ "urn:22967322-3dec-480a-a8aa-40245b9baa07"
+ ]
+ },
+ {
+ "@id": "urn:fcf71ded-26d2-4518-a3e8-bb58b66bdb22",
+ "Label": "tshift",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:03f18f63-6da0-4cef-bc7c-af56235662fa"
+ ]
+ },
+ {
+ "@id": "urn:4fe9ad80-620c-406c-a242-7f323181a475",
+ "Label": "align",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:8ad2f8c8-b192-4c41-9949-ae52df0c39f4",
+ "urn:f3da51a8-5835-48b7-b300-aa60d22b491a"
+ ]
+ },
+ {
+ "@id": "urn:5c602888-1bca-4c78-8710-3274acc87d5e",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:8bde6cef-d597-4805-a798-f881ef0ce6da",
+ "urn:b8ebf28b-6cc9-4040-851b-6784925385f7",
+ "urn:e1e7caef-17a4-4cc0-9292-7012723265a8"
+ ]
+ },
+ {
+ "@id": "urn:a054bb26-df1e-4d57-bb67-aac6b5241eb0",
+ "Label": "volreg",
+ "AssociatedWith": "urn:92a9d09b-f1f1-45e6-8d0a-7b0bc87efa44",
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+ "@id": "urn:c99b701f-4e3e-42c7-9395-6f2c2ba4e03f",
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+ "AtLocation": "blur.errts.1D",
+ "GeneratedBy": "urn:ba63f369-bdcf-4064-8aef-f45a16a720c4",
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+ "sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
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+ {
+ "@id": "urn:dbcf467f-1db2-4626-a77a-4ff116e8eff2",
+ "Label": "ClustSim",
+ "AtLocation": "ClustSim",
+ "GeneratedBy": "urn:ba63f369-bdcf-4064-8aef-f45a16a720c4",
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+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:c57f3b03-6b8b-4a49-91ad-10414a5bb1f6",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
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+ {
+ "@id": "urn:f4175f7f-1672-46eb-aba1-2ec74d8ac766",
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+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
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+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_alt_onesided_proc_block.png b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png
new file mode 100644
index 000000000..59f9064b0
Binary files /dev/null and b/examples/from_parsers/afni/afni_alt_onesided_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
index 199793c34..52bff0c8a 100644
--- a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
+++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "@id": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:fb8aec64-0092-4cf1-afe3-07ed664020c4",
+ "@id": "urn:a3e80646-9e6a-421f-9d5d-36a21303d503",
"Label": "Make directory",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:c0281cc6-41ae-4afb-8712-bdddf923860a",
+ "@id": "urn:62721fb4-d252-4369-bdba-ca764ea274af",
"Label": "Make directory",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:8e8d84c6-ac64-47ec-8655-dbebf6578a78",
+ "@id": "urn:c5dfced5-481c-431e-9aa4-58913f7adba2",
"Label": "cp",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:27cbef79-02e5-4f56-a288-ea546ba6a2b1",
- "urn:f13883ba-2f4e-4780-b5f6-a5542c1ab6a6"
+ "urn:28adcfaf-736c-4b8b-8bc3-d265bf0eba90",
+ "urn:3864259f-5550-45d1-b33a-9df348637636"
]
},
{
- "@id": "urn:f9655809-f177-40cc-84aa-562f4ab32877",
+ "@id": "urn:01fb4cd3-71f1-4d76-86fb-813344b065d1",
"Label": "3dcopy",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:52020508-61e6-4dfe-a196-64f7e40dc726"
+ "urn:638257a8-0895-48d4-8016-cc60c84f7b3e"
]
},
{
- "@id": "urn:077324da-6b60-44f7-925b-9c45937d10db",
+ "@id": "urn:b134ff18-cea0-4fd7-ba7c-462a43576f99",
"Label": "3dTcat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:cb896b82-c1f6-4b6e-8517-e6b9b39074f0"
+ "urn:7798a257-63de-4a1e-9e79-f2c54807c99f"
]
},
{
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"Label": "3dToutcount",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:1cbd5316-e669-4ad5-8a60-7933b80ed67c"
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]
},
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"Label": "cat",
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+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:6efa21e0-6d91-4904-86e8-79b259347c7f"
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]
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+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
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]
},
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+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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]
},
{
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"Label": "@auto_tlrc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
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]
},
{
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"Label": "cat_matvec",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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"Parameters": {},
"Used": [
- "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162"
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]
},
{
- "@id": "urn:a02c3dfa-efee-4642-a8db-093fed35d380",
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"Label": "3dvolreg",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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"Parameters": {},
"Used": [
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]
},
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- "@id": "urn:643c3f61-e81e-440d-9d0a-da03147eb483",
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"Label": "3dcalc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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"Parameters": {},
"Used": [
- "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24"
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]
},
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"Label": "cat_matvec",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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]
},
{
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"Label": "3dAllineate",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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},
{
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"Label": "3dAllineate",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
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]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
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"Used": [
- "urn:6fb270cb-246a-489a-9655-358899756167"
+ "urn:81b58bf8-24f5-4583-852e-b7717232a36c"
]
},
{
- "@id": "urn:b13a8837-4e83-4ffe-8583-44ad77c778bf",
+ "@id": "urn:c1e1e658-7814-4772-9a8e-1f78cc2304f6",
"Label": "cat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:c2a01973-43c7-40c2-9965-0854e22d0f72"
+ "urn:fcb23b68-034c-4168-9337-6bdcb3c5554c"
]
},
{
- "@id": "urn:d8969622-62e2-4899-b5bc-b94a3a671e93",
+ "@id": "urn:3be0b06d-d28f-40c3-ae8f-7e5ee3a243bc",
"Label": "3dcopy",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3"
+ "urn:c458d0e0-760b-477e-ba6e-3738fb12899d"
]
},
{
- "@id": "urn:330d4fc2-a9cb-4bec-a07d-d6330eba562c",
+ "@id": "urn:3ed53110-62f4-4afb-b4d4-e532ba05c06d",
"Label": "3dcalc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:7c985012-41b6-48aa-8ae4-c809eb06bb31",
- "urn:86081194-0636-47f1-9e3b-b68114def1d2"
+ "urn:630c11dd-1330-4b11-acf6-38a25866bf9b",
+ "urn:9d1166fb-e484-48db-a28a-5096b6f510ac"
]
},
{
- "@id": "urn:f71aba7e-cfbf-475d-a938-f89e03affa34",
+ "@id": "urn:7b132978-d935-41d5-8649-09988bf6e150",
"Label": "3dcopy",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:327b460c-e751-42b0-855a-b65d10971e57"
+ "urn:8c94882f-3654-445d-a224-864aff7c65de"
]
},
{
- "@id": "urn:6bb2f2da-6e50-4376-958c-d807ba9130f4",
+ "@id": "urn:794a1586-eeca-42d4-bd17-209350f2dca7",
"Label": "3dAllineate",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:42c4bd6e-e9ad-4e7d-a0c2-4e7992d3bc12"
+ "urn:53a89cdd-70b9-4db2-b069-8c90ee557888"
]
},
{
- "@id": "urn:d351d30f-a4e9-40b2-9de0-e697ad8f4e22",
+ "@id": "urn:351af4c6-0a25-41b8-a04a-f7a9e1fbe0f4",
"Label": "3dmerge",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:8273d1cf-36af-4d5a-b308-a5d717a67b33",
- "urn:eb232e1e-58ae-4077-b3ad-87d1feb35b6c"
+ "urn:7ade7234-672e-4949-8cac-ddb7c085f8e3",
+ "urn:c6d90bd6-3dfb-4883-8769-e2c8ee94f629"
]
},
{
- "@id": "urn:968c32d6-2eb2-4c77-9682-582fcb20b7b3",
+ "@id": "urn:e0f7df09-b3b6-46ed-bb81-f50f98b456b3",
"Label": "3dAutomask",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:df9d2191-8a3a-45c5-9650-403521b23e4d"
+ "urn:ecb26611-af49-4f77-9041-82a002d7c2d5"
]
},
{
- "@id": "urn:556ef24d-95ef-4bd6-9ece-befd90da3730",
+ "@id": "urn:37563603-83e1-4a1b-b5fd-3e44180f457c",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:cab660e8-ac9e-485b-9138-7d11f33d718e",
+ "@id": "urn:bce0e9d4-45fc-4c6f-9aa7-73b7ed67b6d6",
"Label": "3dresample",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:327b460c-e751-42b0-855a-b65d10971e57",
- "urn:cf470468-8935-47d3-9691-08ad68075642"
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34",
+ "urn:8c94882f-3654-445d-a224-864aff7c65de"
]
},
{
- "@id": "urn:64d8d399-2f2a-45b7-b2f1-35d4a6bd86d0",
+ "@id": "urn:b968a2b7-1ab3-4918-a943-f019e88bf502",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:e0ebcb86-cf35-4440-ac64-822e3534baa4"
+ "urn:70d7aa44-9486-4d80-a553-314541d0689f"
]
},
{
- "@id": "urn:5fb6a9ff-927f-44f5-bf62-36f29f8bc963",
+ "@id": "urn:52930724-156d-4201-a99f-92d0664a5726",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:861e89e6-1845-4582-a116-5e03e9fcc252",
- "urn:f3d3c8eb-359a-40e9-8d1b-d12c2819bbfe"
+ "urn:3ae6d58b-af74-4aba-b551-beafc94b9403",
+ "urn:4d776027-1b79-454d-b119-8be7428aa40a"
]
},
{
- "@id": "urn:cefd6c7b-e87e-4af7-b301-5f5251f4cf59",
+ "@id": "urn:7229a79a-35b5-414f-bbef-a80c6a0aa382",
"Label": "3ddot",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:861e89e6-1845-4582-a116-5e03e9fcc252",
- "urn:f3d3c8eb-359a-40e9-8d1b-d12c2819bbfe"
+ "urn:3ae6d58b-af74-4aba-b551-beafc94b9403",
+ "urn:4d776027-1b79-454d-b119-8be7428aa40a"
]
},
{
- "@id": "urn:5ef09dd0-e649-4deb-b02f-8328d272ded4",
+ "@id": "urn:85f8c26a-fb6e-4a28-b689-84fc0a73caa9",
"Label": "3dresample",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:85c3ce0a-f7b8-45ed-91e7-a7a671050994",
- "urn:cf470468-8935-47d3-9691-08ad68075642"
+ "urn:056dd331-56c7-4481-9025-6a972c52f7af",
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34"
]
},
{
- "@id": "urn:02936a64-481f-4382-8b6b-948a05e2ee63",
+ "@id": "urn:3da27e70-7531-4071-b13c-dfa3d43a7765",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:f5e4ae76-a5a0-4b3d-876d-4183e80d5a95"
+ "urn:b85723e2-2634-41a2-b745-ce014c138e48"
]
},
{
- "@id": "urn:2486fe67-6767-4b41-ad86-0d8b7dd40624",
+ "@id": "urn:42662c59-30f0-487c-b0cc-2d69743b66b6",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:df9d2191-8a3a-45c5-9650-403521b23e4d"
+ "urn:ecb26611-af49-4f77-9041-82a002d7c2d5"
]
},
{
- "@id": "urn:26c558ba-8b6d-4b5c-bf5b-936db5ea9a5f",
+ "@id": "urn:95e20196-ea50-47d2-85d2-5ca1fceaeb1e",
"Label": "3dcalc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:7c985012-41b6-48aa-8ae4-c809eb06bb31",
- "urn:b7b77d81-1384-436c-80a5-7f0f62115948",
- "urn:df9d2191-8a3a-45c5-9650-403521b23e4d"
+ "urn:5634518e-8272-499c-ab40-b15f1a0d7d8a",
+ "urn:630c11dd-1330-4b11-acf6-38a25866bf9b",
+ "urn:ecb26611-af49-4f77-9041-82a002d7c2d5"
]
},
{
- "@id": "urn:52b5a16d-e063-4b0b-828e-c4143d18e14d",
+ "@id": "urn:82d0c2a5-8bef-434d-b2ec-a87aa9951889",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:cc379f28-99f7-4692-87e4-3b93193bcb89"
+ "urn:375c7dcd-2880-43fb-8f1b-194947fd0df1"
]
},
{
- "@id": "urn:7891b04d-79c7-490c-b5ae-53a2d9225899",
+ "@id": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:cc379f28-99f7-4692-87e4-3b93193bcb89"
+ "urn:375c7dcd-2880-43fb-8f1b-194947fd0df1"
]
},
{
- "@id": "urn:f825b81b-a359-4837-9ddd-1c429b57df18",
+ "@id": "urn:b4d4a49d-8698-4991-92f7-6ded6f8f4ab8",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:cc379f28-99f7-4692-87e4-3b93193bcb89"
+ "urn:375c7dcd-2880-43fb-8f1b-194947fd0df1"
]
},
{
- "@id": "urn:53bc14bc-0fc7-4b7d-9de3-3ec77f7da912",
+ "@id": "urn:5fb06023-e8e1-439e-9746-ceaedfd29f11",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:ec3fde1b-e382-4f29-a2ba-e04bbd8c559b"
+ "urn:0b8198b6-4d60-44c0-9caa-24b1b282aced"
]
},
{
- "@id": "urn:ada01202-ea7b-4b88-b337-d7350ee0a693",
+ "@id": "urn:ceb18837-f089-46e0-8d15-f53ebe8394c7",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:3fad8090-cbbc-4f6f-a231-9b8a6bbe5b50"
+ "urn:7abc0423-3682-48cf-8806-fee1a3fb186c"
]
},
{
- "@id": "urn:b346cab9-5b54-40ea-9de7-c8b74a75c790",
+ "@id": "urn:01b68f11-7d17-4160-ba1b-f1fbd37d9835",
"Label": "3dTcat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:ec3fde1b-e382-4f29-a2ba-e04bbd8c559b"
+ "urn:0b8198b6-4d60-44c0-9caa-24b1b282aced"
]
},
{
- "@id": "urn:ee9fc801-0cec-47c2-b99d-60a01df64f52",
+ "@id": "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:59855331-85db-49d2-b637-e7f573189444"
+ "urn:6db2c440-a1c5-4be4-be37-c75b9faba368"
]
},
{
- "@id": "urn:a85a4a11-bd99-4e4a-b3dc-e021689042d4",
+ "@id": "urn:ff48f871-b123-4c72-b715-2253a677865a",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:d8335e2a-2948-4271-a9f9-e4b5155b8a41"
+ "urn:8dc86011-0121-48e3-945d-edfafd138b17"
]
},
{
- "@id": "urn:0d27f1fd-4f17-4470-bcec-00f31d32585c",
+ "@id": "urn:b01d3376-c72d-48d5-8d9b-624e86c64704",
"Label": "3dcalc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:c0e2232b-3121-49e4-9765-abca3e931e90",
- "urn:cf470468-8935-47d3-9691-08ad68075642",
- "urn:e3fa7976-f584-405e-adc8-f130bfa9a62d"
+ "urn:05033224-1bed-4f2e-904f-113e6309a493",
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34",
+ "urn:58675ac0-241a-40e0-8600-1775c2221c7b"
]
},
{
- "@id": "urn:9256a39d-9dd7-4cc1-9cf9-d82a3e799545",
+ "@id": "urn:cc9700cd-65ba-4289-bd45-05989e9f1060",
"Label": "3dTnorm",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:7caef081-9c3e-4cb6-b7db-69e7470b5478"
+ "urn:e3fada0d-7fcf-4eb8-9901-c8a9e6d0cb11"
]
},
{
- "@id": "urn:cd69bdd6-87b9-4324-8e15-9dfa7d9948bc",
+ "@id": "urn:610c8f66-d08d-4279-8b6a-ea432da642c9",
"Label": "3dmaskave",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:1163e644-4c67-4a4a-8632-fef54fc43897",
+ "@id": "urn:15a73dc4-e916-465e-a7f7-1cdfe5c68626",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:98813b04-86b8-43e8-b7c1-7b79dc16b682"
+ "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd"
]
},
{
- "@id": "urn:32da1042-3bfe-4549-b418-b69a601dbad5",
+ "@id": "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
"Label": "3dcalc",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:64ce8c11-0547-45c6-9800-a2a392488900",
- "urn:88b6394b-ab36-4212-ada9-3823354cec18"
+ "urn:4ba80317-1444-4c5a-a247-982471301cb6",
+ "urn:a6a7d9c7-b476-48d8-b50d-0884eb184eb3"
]
},
{
- "@id": "urn:332fb2ea-36f4-43c9-baea-0b38ef2a2179",
+ "@id": "urn:03124019-a030-437d-a028-c6cde009e15f",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:fcac9d40-80b9-4b4b-83e3-a11d7f74a441"
+ "urn:ac9f2384-a0e0-4065-aa27-51ffe9369655"
]
},
{
- "@id": "urn:02fb5596-8669-4c2a-9df6-600488e892b5",
+ "@id": "urn:44e2aed7-c604-4e4d-8be6-5ac2defa313e",
"Label": "1dcat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:c8b07e4a-29df-4360-bb6b-0d4b76d035a2"
+ "urn:a824a15d-3234-4f76-9f95-bb38ecf3ba84"
]
},
{
- "@id": "urn:1320e946-ac94-4740-9e0c-b6f97ad0d99b",
+ "@id": "urn:d9f85d96-c33c-411a-8cfa-c8de426d250a",
"Label": "1dcat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:8db107d7-034d-4963-a81d-edf6a4c19ab2"
+ "urn:e928214a-6a3c-469d-9739-b94b422c1976"
]
},
{
- "@id": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "@id": "urn:576ad643-bad3-45b6-a625-e9823c45c0af",
"Label": "3dTstat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:d867fd7f-631d-420b-900e-78f8937f4436"
+ "urn:340ac867-6732-4a1b-a9db-70fd07d8285f"
]
},
{
- "@id": "urn:10f8b075-1fca-472e-b140-189ba027fbad",
+ "@id": "urn:48aae18d-fcff-4f4d-bbd4-d8262dc89ce4",
"Label": "1dcat",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:d867fd7f-631d-420b-900e-78f8937f4436"
+ "urn:340ac867-6732-4a1b-a9db-70fd07d8285f"
]
},
{
- "@id": "urn:d3ee1eb9-ba34-4c1b-be52-8fb9737bcae5",
+ "@id": "urn:48863a0d-1cea-4233-887c-2754a9ff4167",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:cf470468-8935-47d3-9691-08ad68075642"
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34"
]
},
{
- "@id": "urn:29e1c19f-538c-4342-9e76-a6866ccd580f",
+ "@id": "urn:0bf8d61a-569e-48a0-a2d0-a44e6e87a32f",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:cf470468-8935-47d3-9691-08ad68075642"
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34"
]
},
{
- "@id": "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31",
+ "@id": "urn:aa9cdb8e-969f-44a3-b463-a59c7ba99855",
"Label": "3dClustSim",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:cf470468-8935-47d3-9691-08ad68075642"
+ "urn:3fa86845-cc78-4a61-9b14-b2b6cd058b34"
]
},
{
- "@id": "urn:2fc6ed9f-b90f-4833-a80d-770788678427",
+ "@id": "urn:c506f2c2-9750-4694-a22c-9a59dc47c6cd",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:51597196-e9da-4265-8d9f-85e8e2c7d6cb"
+ "urn:69de28c5-0c0c-45ce-8afb-bd975bea590c"
]
},
{
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+ "@id": "urn:19e29262-d365-463f-971e-ea6537b869f9",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:dbfafcd8-f88e-479d-94c2-8cfba84e19a9",
+ "AssociatedWith": "urn:74badce5-1fae-46aa-b055-750279abb84b",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
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+ "@id": "urn:93b166eb-4469-4dae-9d65-435cb8462de2",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:fb8aec64-0092-4cf1-afe3-07ed664020c4",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:c0281cc6-41ae-4afb-8712-bdddf923860a"
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+ "@id": "urn:3864259f-5550-45d1-b33a-9df348637636",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
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{
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_bi_sided_t_test/tone_counting_probe_duration.txt",
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@@ -617,13 +617,13 @@
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:8e8d84c6-ac64-47ec-8655-dbebf6578a78"
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{
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+ "@id": "urn:638257a8-0895-48d4-8016-cc60c84f7b3e",
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"AtLocation": "sub-01_T1w.nii.gz",
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@@ -631,13 +631,13 @@
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:f9655809-f177-40cc-84aa-562f4ab32877"
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"Label": "sub-01_task-tonecounting_bold.nii.gz",
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@@ -645,13 +645,13 @@
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:077324da-6b60-44f7-925b-9c45937d10db"
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@@ -659,16 +659,16 @@
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{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:2956e891-bc2d-4540-acbf-aa3927057795",
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+ "@id": "urn:6b5d0405-4cd3-4e91-b83e-54bfc4060735",
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"AtLocation": "outcount.r*.1D",
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@@ -676,25 +676,25 @@
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{
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+ "@id": "urn:6fd8cde4-416a-4eef-bb49-901f85a600f3",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:48807715-825b-46b4-b198-c4820efdf562",
+ "GeneratedBy": "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:9af51269-2e27-4c5d-959d-c8ffae1ee4d9",
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+ "@id": "urn:032573f6-5228-40f3-aa2f-e69f7d20428b",
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"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
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{
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+ "@id": "urn:aa535b62-3124-47ac-be27-a5c5b047ea68",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
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@@ -710,16 +710,16 @@
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{
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"AtLocation": "_al_junk",
- "GeneratedBy": "urn:1cb0b710-db77-4b58-aaa5-ad2f0c1455fb",
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+ "@id": "urn:07255a93-153e-49f8-9bc0-72c6b0ffbe4f",
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"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +727,7 @@
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{
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"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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+ "@id": "urn:53a89cdd-70b9-4db2-b069-8c90ee557888",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:f2905fa3-7c8d-4629-bc94-3108b1af34f2",
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@@ -760,34 +760,34 @@
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"AtLocation": "mat.r$run.warp.aff12.1D",
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@@ -795,16 +795,16 @@
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@@ -1136,16 +1136,16 @@
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"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:88b6394b-ab36-4212-ada9-3823354cec18",
+ "@id": "urn:4ba80317-1444-4c5a-a247-982471301cb6",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:cd69bdd6-87b9-4324-8e15-9dfa7d9948bc",
+ "GeneratedBy": "urn:610c8f66-d08d-4279-8b6a-ea432da642c9",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:98813b04-86b8-43e8-b7c1-7b79dc16b682",
+ "@id": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:49a2c107-7e29-4508-b66a-759397b637be",
+ "@id": "urn:aaa7b906-ee6a-4c9e-ad92-0f42cec51ab8",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:1163e644-4c67-4a4a-8632-fef54fc43897",
+ "GeneratedBy": "urn:15a73dc4-e916-465e-a7f7-1cdfe5c68626",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:64ce8c11-0547-45c6-9800-a2a392488900",
+ "@id": "urn:a6a7d9c7-b476-48d8-b50d-0884eb184eb3",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:8dc7b7dd-1c2d-4de6-af43-49413cef05bf",
+ "@id": "urn:27be58c6-0756-4473-ba14-a13d5c6ab920",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:32da1042-3bfe-4549-b418-b69a601dbad5",
+ "GeneratedBy": "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:fcac9d40-80b9-4b4b-83e3-a11d7f74a441",
+ "@id": "urn:ac9f2384-a0e0-4065-aa27-51ffe9369655",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:c933e975-7f89-4ed1-8131-48cef7b2aa42",
+ "@id": "urn:915a73a0-d2c9-476c-bb2b-55f6b431b745",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:332fb2ea-36f4-43c9-baea-0b38ef2a2179",
+ "GeneratedBy": "urn:03124019-a030-437d-a028-c6cde009e15f",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:c8b07e4a-29df-4360-bb6b-0d4b76d035a2",
+ "@id": "urn:a824a15d-3234-4f76-9f95-bb38ecf3ba84",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:12132d02-f825-4fad-a4be-15d0cf2a31f1",
+ "@id": "urn:88191880-daa5-4212-ac56-8abe766fdafa",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:02fb5596-8669-4c2a-9df6-600488e892b5",
+ "GeneratedBy": "urn:44e2aed7-c604-4e4d-8be6-5ac2defa313e",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:8db107d7-034d-4963-a81d-edf6a4c19ab2",
+ "@id": "urn:e928214a-6a3c-469d-9739-b94b422c1976",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:59ad2686-bf03-4c54-ab58-52d3e36e159d",
+ "@id": "urn:b8cb0ff5-5460-47f8-90c4-248b45cac8b7",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:1320e946-ac94-4740-9e0c-b6f97ad0d99b",
+ "GeneratedBy": "urn:d9f85d96-c33c-411a-8cfa-c8de426d250a",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:d867fd7f-631d-420b-900e-78f8937f4436",
+ "@id": "urn:340ac867-6732-4a1b-a9db-70fd07d8285f",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:065fd0da-dec5-43b9-89bd-2e28490b2920",
+ "@id": "urn:6a233baf-1b6c-47eb-9adc-255967269d82",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "GeneratedBy": "urn:576ad643-bad3-45b6-a625-e9823c45c0af",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:4f8e64ff-f2e7-4b80-b21d-aab197e3b643",
+ "@id": "urn:4f72060b-abb0-4451-8860-7302be4ce10c",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:10f8b075-1fca-472e-b140-189ba027fbad",
+ "GeneratedBy": "urn:48aae18d-fcff-4f4d-bbd4-d8262dc89ce4",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:f6388f61-a430-4ddb-8dc8-558e2ef8b0ac",
+ "@id": "urn:88f837ec-5247-4166-9aa2-585f997c9666",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:d3ee1eb9-ba34-4c1b-be52-8fb9737bcae5",
+ "GeneratedBy": "urn:48863a0d-1cea-4233-887c-2754a9ff4167",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:b30a0c58-4263-4d7f-be30-876f71d4d2d0",
+ "@id": "urn:e0dc27be-7b70-47b6-a296-855e0078ebb2",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:29e1c19f-538c-4342-9e76-a6866ccd580f",
+ "GeneratedBy": "urn:0bf8d61a-569e-48a0-a2d0-a44e6e87a32f",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:e255be3b-54f2-4438-a0c3-73a0866a113e",
+ "@id": "urn:6fb6a185-0f0e-4cc2-a182-ea48fedca732",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31",
+ "GeneratedBy": "urn:aa9cdb8e-969f-44a3-b463-a59c7ba99855",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:51597196-e9da-4265-8d9f-85e8e2c7d6cb",
+ "@id": "urn:69de28c5-0c0c-45ce-8afb-bd975bea590c",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:e1e59516-0eed-4c3c-84d8-68271d7d9ac8",
+ "@id": "urn:0e752515-4b43-4951-829f-65da8aa40859",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:92706503-83a5-42fd-b68e-7dba8a30c693",
+ "GeneratedBy": "urn:19e29262-d365-463f-971e-ea6537b869f9",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png
index c94731604..fbb2e8dc6 100644
Binary files a/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc.png differ
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
new file mode 100644
index 000000000..93faa79d7
--- /dev/null
+++ b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:68a18c08-3b1d-4a17-92bf-7211f35d75f9",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_bi_sided_t_test/tone_counting_onset_times.txt ./afni_bi_sided_t_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:8e150d04-ca7e-48c8-a1fb-f2105218cd3f",
+ "urn:cb2c6935-c344-43e3-8766-cf55331e5fdb",
+ "urn:d11257eb-c99b-4d61-bdfe-3106a9771062"
+ ]
+ },
+ {
+ "@id": "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:36267516-ae53-4c72-80b2-9670e20b5dc5"
+ ]
+ },
+ {
+ "@id": "urn:98b17263-9c83-441a-8036-eae0e019e728",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:d15f5078-43d1-4fc8-8cf4-3841b62016a6",
+ "urn:8275d440-30cc-4e5c-8c5a-b01e135fe60d"
+ ]
+ },
+ {
+ "@id": "urn:31afdc2f-30f8-4682-a3d6-58f886590e75",
+ "Label": "tshift",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:d15f5078-43d1-4fc8-8cf4-3841b62016a6"
+ ]
+ },
+ {
+ "@id": "urn:13612015-a8d2-4871-b508-f4bb94ecc89b",
+ "Label": "align",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:919fe30c-bd24-48b2-8300-e9c516a5a2e5",
+ "urn:ccfa074a-7374-482d-904c-32d16b9beb96"
+ ]
+ },
+ {
+ "@id": "urn:27c5e77b-c388-49ac-8e7c-da3fd292e0ae",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:04d86c72-4729-4d2f-b96e-5528baeb3bb0",
+ "urn:b1c9ffd2-83cd-4e5a-8786-87ce83c590c4",
+ "urn:348bd625-237d-483a-8b51-01dd412cc2b5"
+ ]
+ },
+ {
+ "@id": "urn:39d91d05-0337-4cde-8b33-86c43a213344",
+ "Label": "volreg",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:8fbe36bf-d9b2-4847-aeae-94e8a4899d5f",
+ "urn:8fbe36bf-d9b2-4847-aeae-94e8a4899d5f",
+ "urn:348bd625-237d-483a-8b51-01dd412cc2b5",
+ "urn:8fbe36bf-d9b2-4847-aeae-94e8a4899d5f",
+ "urn:e9b77b89-e773-4cef-aa43-7eadf239cd96",
+ "urn:06e46abc-0511-45ce-8e29-17bdba176c6a",
+ "urn:e9b77b89-e773-4cef-aa43-7eadf239cd96",
+ "urn:e5f95aaf-ca43-46a3-9cdc-ec7221aae50d",
+ "urn:f86a6c6f-3ced-4686-8ed9-79c1377c287a",
+ "urn:9d505fad-bfb4-4d42-9041-d332f14f09ef",
+ "urn:87b3d43b-7d89-4e8b-a598-0662190f537f",
+ "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6",
+ "urn:e9b77b89-e773-4cef-aa43-7eadf239cd96",
+ "urn:692441c6-99ea-4157-8677-cd88be27b858"
+ ]
+ },
+ {
+ "@id": "urn:e1032fac-1238-49eb-a651-fe0ae2e8d155",
+ "Label": "blur",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:af541e75-5edd-41d5-a5d7-1876d5f8873e",
+ "urn:b33646b2-646b-45ae-a449-43a0c28b1a6d"
+ ]
+ },
+ {
+ "@id": "urn:226bd3cb-3e0d-4c85-82cc-7baa47c0f26e",
+ "Label": "mask",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:75bdbb93-ecf8-4707-b568-3acb8cd49ddc",
+ "urn:3ca35147-dc66-46af-bd2a-ca466dc5c4f9",
+ "urn:e9b77b89-e773-4cef-aa43-7eadf239cd96",
+ "urn:0aefca75-8457-4b37-9220-9065a676cc39",
+ "urn:103b9c6b-fbc7-40be-8757-146bebb0be8c",
+ "urn:7b40b911-8757-4a00-bae1-fb3d68382e7b",
+ "urn:103b9c6b-fbc7-40be-8757-146bebb0be8c",
+ "urn:7b40b911-8757-4a00-bae1-fb3d68382e7b",
+ "urn:0cac31cc-159f-4927-b0dd-f1a7166d6614",
+ "urn:3ca35147-dc66-46af-bd2a-ca466dc5c4f9",
+ "urn:2c73cf58-a76c-4b38-8157-b945a6fc64be"
+ ]
+ },
+ {
+ "@id": "urn:8465e4d8-80f6-4f0f-b165-cb30f2704a4d",
+ "Label": "scale",
+ "AssociatedWith": "urn:b83b346d-bbf3-4ad0-bf40-e52d3ebfca17",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:75bdbb93-ecf8-4707-b568-3acb8cd49ddc",
+ "urn:75bdbb93-ecf8-4707-b568-3acb8cd49ddc",
+ "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a",
+ "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6"
+ ]
+ },
+ {
+ "@id": "urn:27efb73c-c0cf-4c10-9047-b4ff9de6bad4",
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+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:cb3177ed-bc4b-431f-a111-dee5794e9478",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png
new file mode 100644
index 000000000..4658c933b
Binary files /dev/null and b/examples/from_parsers/afni/afni_bi_sided_t_test_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
index 2225617eb..af7cada6a 100644
--- a/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
+++ b/examples/from_parsers/afni/afni_clustconn_18_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "@id": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:c3fef51d-5762-42e0-b208-60c41cb88f9e",
+ "@id": "urn:9f20d7ff-f5a0-46d0-8829-cf585dd6a6ba",
"Label": "Make directory",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:acda275a-b3d5-4117-b8e2-02e26364ba33",
+ "@id": "urn:2eace7c1-48d7-42d0-8a53-9cd10b219f30",
"Label": "Make directory",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:0b2b92bb-d5a0-481b-b286-f5524c5174c7",
+ "@id": "urn:5b26ef30-7cf9-4d67-9818-95e38cea6091",
"Label": "cp",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:8730a528-9da2-4da2-86d6-74a3e33e67aa",
- "urn:ddec23dd-7280-4054-9869-d0c3d53b0adf"
+ "urn:680c6102-4992-41dd-bc1f-da0ab18255f0",
+ "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd"
]
},
{
- "@id": "urn:1b9550df-d2e5-4b1a-b614-4a6e123b2c9b",
+ "@id": "urn:1aa7103f-ebf2-4568-be03-f2d1e223af21",
"Label": "3dcopy",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:da476eb4-c8f5-4aba-b5cd-3b7836110dcc"
+ "urn:9c84233e-4c3f-40e2-8828-b10d5fc0b1ef"
]
},
{
- "@id": "urn:0b1a99ce-3115-4f96-b2c8-98f09202047a",
+ "@id": "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77",
"Label": "3dTcat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:714f6651-d049-41fc-87e3-69c7f1b1a912"
+ "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a"
]
},
{
- "@id": "urn:f6057a4e-833e-48c2-8171-e0b1bc7c8bec",
+ "@id": "urn:b390c087-192d-44fe-8042-1bcca38ab6ae",
"Label": "3dToutcount",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:eb31f484-923d-463e-b2d9-c7fca7e7817c"
+ "urn:c17bb85f-17c1-41eb-9367-0ee3a76060b5"
]
},
{
- "@id": "urn:68ebae99-927e-455f-b2a6-5123f2ef2fba",
+ "@id": "urn:71135527-0811-46d0-887d-1b56a42edc2e",
"Label": "cat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:a011f4d3-bcb4-49b9-92b5-60d54964a1d2"
+ "urn:1ebe5cf2-e3de-4260-b209-df16e3768d62"
]
},
{
- "@id": "urn:5b07097b-74e7-4377-be56-e02e611bc43f",
+ "@id": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
"Label": "3dTshift",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:eb31f484-923d-463e-b2d9-c7fca7e7817c"
+ "urn:c17bb85f-17c1-41eb-9367-0ee3a76060b5"
]
},
{
- "@id": "urn:4274fe0d-59d1-4526-b361-8143401dfa7e",
+ "@id": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:db7eedc2-2f44-4a6c-9028-5188d14b7b88",
- "urn:ec3a19d9-9a5a-4b83-a471-89e8fce3eadc"
+ "urn:18e70cc0-08a9-4e53-b907-377ca9e96d82",
+ "urn:e502668a-42ab-4093-9bf5-a7a57645e2ad"
]
},
{
- "@id": "urn:8b592887-7f42-4141-995d-d6d0ce67d10a",
+ "@id": "urn:ab84bc1d-9e74-4e20-ac76-6c921f79d5ec",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:559ab88d-a226-41c0-aee7-6b3c5cfbe790",
- "urn:8e023450-0935-49bf-8dd0-7bb4196fbdf4"
+ "urn:640db747-51b4-4c85-a15e-94117c886ae4",
+ "urn:a4807546-b85f-4467-b4e1-5302e8f0d87c"
]
},
{
- "@id": "urn:6cfef149-6cf9-489a-b7d2-fb11d514c35a",
+ "@id": "urn:29409d41-a531-4b0b-a6ff-7d8bb83a2d57",
"Label": "cat_matvec",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:5ba2fd1c-e80f-42b6-8553-5bb99fd8c06a"
+ "urn:53043b2a-cb9b-43cc-8521-29127997d9dc"
]
},
{
- "@id": "urn:00125f77-6342-48bb-963c-4dae68613589",
+ "@id": "urn:2eb30742-cf34-4fe0-8ac9-40a44a229224",
"Label": "3dvolreg",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:323dfd98-0e23-4cd6-bca7-da37bd766307"
+ "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d"
]
},
{
- "@id": "urn:37a9d9ad-1722-4d7b-a9fd-2cd6c084801b",
+ "@id": "urn:6418fb3a-4697-42cb-844f-98221898c9a4",
"Label": "3dcalc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:323dfd98-0e23-4cd6-bca7-da37bd766307"
+ "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d"
]
},
{
- "@id": "urn:b3d8f618-85a4-422f-8deb-58d93c99b3c6",
+ "@id": "urn:fea42141-8ffc-435c-bab7-a16e244425dc",
"Label": "cat_matvec",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:5ba2fd1c-e80f-42b6-8553-5bb99fd8c06a"
+ "urn:53043b2a-cb9b-43cc-8521-29127997d9dc"
]
},
{
- "@id": "urn:e5200db4-26eb-4575-bc6d-d3297eadb4f1",
+ "@id": "urn:11a44ba1-105e-4ecd-ad59-a75e07367e7d",
"Label": "3dAllineate",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:323dfd98-0e23-4cd6-bca7-da37bd766307",
- "urn:5bb841a2-ccbb-4a7a-8b72-a203131c444e",
- "urn:5e9bf653-542a-4ed6-96a4-f8edeb95cda8"
+ "urn:5931aa32-07bf-4032-a21d-cf78b7684d58",
+ "urn:d0dbc87f-48a6-4316-8b9e-dee1b99104a4",
+ "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d"
]
},
{
- "@id": "urn:940a024f-3e2f-4682-85f1-a12ff1028ab6",
+ "@id": "urn:9a8178c0-e37c-46d4-97cf-dcb710a6c585",
"Label": "3dAllineate",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
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- "urn:5bb841a2-ccbb-4a7a-8b72-a203131c444e",
- "urn:5e9bf653-542a-4ed6-96a4-f8edeb95cda8"
+ "urn:3fd2d4d5-677d-469b-bae5-9d764bd9e696",
+ "urn:5931aa32-07bf-4032-a21d-cf78b7684d58",
+ "urn:d0dbc87f-48a6-4316-8b9e-dee1b99104a4"
]
},
{
- "@id": "urn:189beb08-e9a2-4516-9240-a715584e0031",
+ "@id": "urn:75b7b742-134c-4743-b2c6-7783513975e0",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:bfc775c7-b23c-4f34-a471-608d47d69d7e"
+ "urn:41107f04-1af4-41a4-81c7-4e597cd0c7d7"
]
},
{
- "@id": "urn:91c12036-fc30-427f-aa13-e71430011001",
+ "@id": "urn:cacb4e68-b84c-40a7-8f92-26fd5ff055a9",
"Label": "cat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:ff2a2443-83b2-4529-a30f-d2d858c75ea9"
+ "urn:772e9d5e-658c-470c-864a-5c2ca5163b82"
]
},
{
- "@id": "urn:e4185d45-0bcd-48f6-91a2-839587f71001",
+ "@id": "urn:1a587f9b-fc4a-4277-9fb0-9f79e2d2db5d",
"Label": "3dcopy",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:e750f6bc-d97a-4a51-ac11-ae1720f99d12"
+ "urn:2651517a-d223-43a6-8156-df647cf71859"
]
},
{
- "@id": "urn:5023c995-0b5c-4c5d-8e82-318ef6c185f8",
+ "@id": "urn:c3c6543b-54bc-42b7-9412-951ebc52f6b4",
"Label": "3dcalc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:2bd63b48-4475-4f80-9b48-bceab9a6454c",
- "urn:cd671cbd-c42d-4719-81c8-0a9e3e044d7b"
+ "urn:731707e8-ab6e-4f05-ad4b-e7145f2957bb",
+ "urn:f0039bc0-40e7-4b50-bf95-40e5d7fa3bb4"
]
},
{
- "@id": "urn:4a8f29c1-4ba1-4ea3-a128-eccc5bc20519",
+ "@id": "urn:7b0e85df-6682-4dd4-b97d-04aadce54c0d",
"Label": "3dcopy",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:5e9bf653-542a-4ed6-96a4-f8edeb95cda8"
+ "urn:d0dbc87f-48a6-4316-8b9e-dee1b99104a4"
]
},
{
- "@id": "urn:7446de50-5f1d-49d2-bbe6-26e5cecd4100",
+ "@id": "urn:8647e6ec-4a8a-426b-a5fa-679949689216",
"Label": "3dAllineate",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:b979651c-e069-41c3-9435-6a7efa49c0f1"
+ "urn:7a512ed2-ad13-49f5-a0dd-1b83659fa35f"
]
},
{
- "@id": "urn:fd337a81-c20c-4ebe-85a4-29f828dcba40",
+ "@id": "urn:1e0b2ec0-5b80-47ba-ad3c-5b8cd6caa41c",
"Label": "3dmerge",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:85df3309-7274-417c-818b-db0e65a74b46",
- "urn:a3127220-c9fb-4c52-99d6-9a7bfb95a855"
+ "urn:4f23fee2-dbc5-4548-8c36-f9da7b4b6e9a",
+ "urn:b3504581-2806-4e1d-814e-0f0ba71c883e"
]
},
{
- "@id": "urn:11aca076-ca97-4e8f-8c73-205ea9d1bd0a",
+ "@id": "urn:16e56703-dac3-4c6f-b5bb-6421103ed9de",
"Label": "3dAutomask",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:bd3cda7f-ebb1-4668-8946-9c8ecc7be163"
+ "urn:838961dc-199d-4121-88e2-2675adb60b37"
]
},
{
- "@id": "urn:7ae1bda0-f7e4-4f14-a7f4-a922b1efd5eb",
+ "@id": "urn:1f2447f7-73a4-4261-90bd-3f92589a700f",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:301eb051-62cc-44d8-a38f-abdeb3a57511",
+ "@id": "urn:bfddd750-a372-43d1-ae2a-a023348e8b54",
"Label": "3dresample",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:5e9bf653-542a-4ed6-96a4-f8edeb95cda8",
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c"
+ "urn:d0dbc87f-48a6-4316-8b9e-dee1b99104a4",
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2"
]
},
{
- "@id": "urn:5b04f058-84b0-4900-86d8-ba5bda1ed793",
+ "@id": "urn:3f226f39-dc7a-4f5f-8051-c1aad4d78f23",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:9dcd837c-b805-482e-ada6-bc351c6279b5"
+ "urn:2cca56e2-0ca3-40d3-8b46-288d3ee06214"
]
},
{
- "@id": "urn:d235363a-c2f2-4f62-9687-c7df80999bb0",
+ "@id": "urn:1f7d23d2-5467-4a69-9915-466cc446167b",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:693a8ebf-4876-42b8-b3e6-39bc58fb9175",
- "urn:db08eb96-49ca-4fa9-bfb8-b3dc3e4c4f79"
+ "urn:3ccddd9f-ea57-4ce6-9092-ca4b5a77eac7",
+ "urn:61be43c2-2b91-4045-88de-c723a6db4e88"
]
},
{
- "@id": "urn:0fd3b96b-ed78-45b9-aaf3-91d34f33e91b",
+ "@id": "urn:ece6e4e5-9e5a-42e6-a7e9-b10e1fd24153",
"Label": "3ddot",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:693a8ebf-4876-42b8-b3e6-39bc58fb9175",
- "urn:db08eb96-49ca-4fa9-bfb8-b3dc3e4c4f79"
+ "urn:3ccddd9f-ea57-4ce6-9092-ca4b5a77eac7",
+ "urn:61be43c2-2b91-4045-88de-c723a6db4e88"
]
},
{
- "@id": "urn:72d6dd2f-3315-4dc9-90e9-175008e98179",
+ "@id": "urn:e84cd6af-ea9f-41f5-826b-f4076d21fd1e",
"Label": "3dresample",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c",
- "urn:929a3f98-4314-480f-b888-01bdcf215560"
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2",
+ "urn:dc43357b-0d1e-4e30-a9ee-8be5fcb5feb2"
]
},
{
- "@id": "urn:f2e84dd6-35d9-45be-bd69-95e73d210f05",
+ "@id": "urn:2c85290f-b3f2-431b-91c4-402a54caa3b8",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:b377a62c-0136-42c9-bc3b-33bf283478b4"
+ "urn:de46ce68-4f74-457e-9cf6-0025743ec8ee"
]
},
{
- "@id": "urn:a31aaad2-d520-4981-96e1-11371b1fc426",
+ "@id": "urn:c6df2258-37b7-44c3-93a9-668c7ca69446",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:bd3cda7f-ebb1-4668-8946-9c8ecc7be163"
+ "urn:838961dc-199d-4121-88e2-2675adb60b37"
]
},
{
- "@id": "urn:4fd31fdf-5476-4077-ba9e-36bbeef52970",
+ "@id": "urn:7770962b-a499-4159-9e68-1276c1c6a1d7",
"Label": "3dcalc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:bd3cda7f-ebb1-4668-8946-9c8ecc7be163",
- "urn:bfdaeecc-9a20-4732-acf7-ebc9e8c2d4c1",
- "urn:cd671cbd-c42d-4719-81c8-0a9e3e044d7b"
+ "urn:731707e8-ab6e-4f05-ad4b-e7145f2957bb",
+ "urn:838961dc-199d-4121-88e2-2675adb60b37",
+ "urn:b31016e4-d131-4b54-b8bb-8ffb95e1235a"
]
},
{
- "@id": "urn:b4dbacf5-4b0e-469b-90b1-49e7d3a155cd",
+ "@id": "urn:24298056-18a6-4dd6-895e-60079ab7a1df",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:f083169d-392f-4543-a4f8-a09c7293f427"
+ "urn:7328ba94-9c2f-4c40-ac01-9f1f0a322c34"
]
},
{
- "@id": "urn:f8fc8443-30d8-4435-8ef5-98fd326b0325",
+ "@id": "urn:f5a56707-32a3-4cd0-9a54-dd077cd0af99",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:f083169d-392f-4543-a4f8-a09c7293f427"
+ "urn:7328ba94-9c2f-4c40-ac01-9f1f0a322c34"
]
},
{
- "@id": "urn:965a2ebc-918d-4d0d-b318-6856a499fe16",
+ "@id": "urn:d2b680dd-23d5-4966-8455-b411d2fcfba5",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:f083169d-392f-4543-a4f8-a09c7293f427"
+ "urn:7328ba94-9c2f-4c40-ac01-9f1f0a322c34"
]
},
{
- "@id": "urn:196eab7a-3e2b-410e-a4c3-89f706ae8db3",
+ "@id": "urn:1aee3f47-2397-4b97-92ab-90d2167edbca",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:93adf029-3670-4112-a2a2-66bb7b20a01a"
+ "urn:b37df0c3-3a26-4307-b6d2-36d0294c8502"
]
},
{
- "@id": "urn:0c860fc3-fbed-464c-a458-8e2221e88652",
+ "@id": "urn:e2038ef4-ff24-4366-bfc1-1a9a292de9a3",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:bc1d54d7-90b4-444e-8ad4-93948efd48fd"
+ "urn:955da2fc-77e8-4752-8215-2a0149f99377"
]
},
{
- "@id": "urn:fe3e4131-9b71-4cde-ae30-0c848b08a6d6",
+ "@id": "urn:6fb2e193-f4ca-40ee-80b8-e26e32ee95eb",
"Label": "3dTcat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:93adf029-3670-4112-a2a2-66bb7b20a01a"
+ "urn:b37df0c3-3a26-4307-b6d2-36d0294c8502"
]
},
{
- "@id": "urn:b5ef5827-8b9c-420a-ba5d-ff074a4816e4",
+ "@id": "urn:d8b2dc52-ca26-4227-aff0-f19085500225",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:2c2a2a5f-12d9-443d-8307-038476e05738"
+ "urn:a876f85d-2556-4f1c-bc99-507e89425058"
]
},
{
- "@id": "urn:b3d8eda4-b9f9-403e-a4c2-21b5fb08c82e",
+ "@id": "urn:ccd926fc-64ca-4ced-957e-43a0c16005a6",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:c32b3dea-3bb5-460f-836b-f0d37c0c92f4"
+ "urn:aaa58822-55d3-41ef-936e-040f81bc9bfd"
]
},
{
- "@id": "urn:bcca5728-ee7a-4910-b04e-4afe1f0100d4",
+ "@id": "urn:b53dd96f-c6f3-4f09-aba0-44ae517c9a93",
"Label": "3dcalc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:1e06fa49-f568-4a8d-95b1-1b00344d42c2",
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c",
- "urn:a3f2f8a1-7fef-44a9-9328-c23a6932e226"
+ "urn:09a35bda-f038-4046-a2ba-bdf2ec4a47d8",
+ "urn:74b17bd8-cbc5-4d4f-87c3-abd4546fdc05",
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2"
]
},
{
- "@id": "urn:dd59d2c2-9e43-4dac-b1d2-71a3db038952",
+ "@id": "urn:5212afa6-9451-4b1b-96ff-74703db15b8e",
"Label": "3dTnorm",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2"
+ "urn:05815c41-2723-4765-8fd7-5f156da7ab3d"
]
},
{
- "@id": "urn:7a60ceed-9253-40d3-ab98-9dbcceac5361",
+ "@id": "urn:fd0c1922-3af4-4ff4-9e43-e101e9894067",
"Label": "3dmaskave",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:b000ce49-ee34-4b4a-a104-841943e9bc11",
+ "@id": "urn:3c30a42c-7e7d-40e2-9996-3e7fb6731876",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:c49d5a06-0a28-4dff-8d3f-b322c4f36291"
+ "urn:b9670e8d-db9b-4147-b470-a0ebb2231289"
]
},
{
- "@id": "urn:fac26c4d-38f9-49b0-9faf-062fe892a8ff",
+ "@id": "urn:c17b2fce-6992-45ca-8529-7c2ff62a9b35",
"Label": "3dcalc",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:308e722d-3011-4493-b217-f569373f2c39",
- "urn:95ca1050-f815-482f-a5d5-50df9eb5fcc6"
+ "urn:25e272ce-bbb9-472b-a887-0fa02eaaae18",
+ "urn:732bc20d-caa6-4a38-a847-b070eab25f26"
]
},
{
- "@id": "urn:9e7316c6-b46b-4b93-b667-1785f7503f51",
+ "@id": "urn:3fb1a61e-f38c-4b78-96e1-aa7016017e06",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:c153fb7f-09ea-4050-a6df-7fb63bcfa826"
+ "urn:2db5a491-8578-4336-b566-e4d28726d7ec"
]
},
{
- "@id": "urn:9293b57e-bed7-40ac-b1e7-d6552e21881c",
+ "@id": "urn:adba2e9e-51d0-43c3-9c18-93620dc310b5",
"Label": "1dcat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522"
+ "urn:aae97d91-c38d-4bad-a44f-266f2980278e"
]
},
{
- "@id": "urn:3dbc753d-ec5f-4933-816b-b57d17bdb32d",
+ "@id": "urn:083011da-8332-4224-8b04-3e446b1d0565",
"Label": "1dcat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:9f51d912-394a-4bb7-8858-1674aed5be7c"
+ "urn:e73688be-08fe-432e-be79-af3c6e4d3fcb"
]
},
{
- "@id": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "@id": "urn:ce136485-f2cb-4219-86c1-c4706b2d5e23",
"Label": "3dTstat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:5c3a9cf4-7f25-47ac-a792-27f8c421ff6d"
+ "urn:d4257f34-69b5-4910-a169-f8a8325c1191"
]
},
{
- "@id": "urn:041f3508-d4c5-4ef0-947d-4fc6d5de0a0f",
+ "@id": "urn:f42e9433-2e8b-4418-985e-0e729a4b9011",
"Label": "1dcat",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:5c3a9cf4-7f25-47ac-a792-27f8c421ff6d"
+ "urn:d4257f34-69b5-4910-a169-f8a8325c1191"
]
},
{
- "@id": "urn:48c32de6-d8cc-4932-9033-005392de7601",
+ "@id": "urn:76f34313-4036-4758-aeb7-417bdfa5b93a",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c"
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2"
]
},
{
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+ "@id": "urn:088f075e-c210-425a-a867-c66589f1c2c4",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c"
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2"
]
},
{
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+ "@id": "urn:015e9618-f2b6-44d9-8ebf-d24749832865",
"Label": "3dClustSim",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:83d9775b-d095-4fa1-9c97-3eb1ccbcc82c"
+ "urn:dbd3b92d-80ca-4cdb-9a6a-e46c1bd4baf2"
]
},
{
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+ "@id": "urn:f7b7e56c-dc14-4d84-aa56-ff1cfc542fb6",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:e6787718-533c-4ee0-9c8b-804f603f9942"
+ "urn:632d059b-7317-409b-bc33-1129e0fb3384"
]
},
{
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+ "@id": "urn:3a654753-b045-43d9-91af-47a534e1ddf0",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:053445f1-731c-4b12-ad78-83c800e44f52",
+ "AssociatedWith": "urn:6918cf06-5b73-4345-8163-3633a24242b4",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
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{
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+ "@id": "urn:a4a72b44-266e-4cf8-843b-40c5956df505",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:c3fef51d-5762-42e0-b208-60c41cb88f9e",
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{
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+ "@id": "urn:3318f2f4-021e-4945-ac68-a79194eece86",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:acda275a-b3d5-4117-b8e2-02e26364ba33"
+ "GeneratedBy": "urn:2eace7c1-48d7-42d0-8a53-9cd10b219f30"
},
{
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+ "@id": "urn:96b92e44-3256-4d88-85cd-4eed25cd88cd",
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"AtLocation": "./afni_cluster_nn2/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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+ "@id": "urn:680c6102-4992-41dd-bc1f-da0ab18255f0",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn2/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
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+ "@id": "urn:0cc3f639-004a-4d2d-af86-b5c8d36f74bf",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:0b2b92bb-d5a0-481b-b286-f5524c5174c7"
+ "GeneratedBy": "urn:5b26ef30-7cf9-4d67-9818-95e38cea6091"
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{
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+ "@id": "urn:9c84233e-4c3f-40e2-8828-b10d5fc0b1ef",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
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{
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"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:1b9550df-d2e5-4b1a-b614-4a6e123b2c9b"
+ "GeneratedBy": "urn:1aa7103f-ebf2-4568-be03-f2d1e223af21"
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{
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+ "@id": "urn:d14b7740-d4ad-41e7-8204-c7cb9f0d331a",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
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{
- "@id": "urn:a20c4998-341d-444f-8893-454db53c472c",
+ "@id": "urn:4dde7fde-d83c-4871-9581-a2f80c237204",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:0b1a99ce-3115-4f96-b2c8-98f09202047a"
+ "GeneratedBy": "urn:1459fb22-3e8e-4f90-898a-d1defbf3be77"
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{
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"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
}
},
{
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+ "@id": "urn:66c4a64b-24fb-4355-b6f0-745d29806e79",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:f6057a4e-833e-48c2-8171-e0b1bc7c8bec",
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}
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{
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+ "@id": "urn:1ebe5cf2-e3de-4260-b209-df16e3768d62",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
}
},
{
- "@id": "urn:005f3bf8-1933-45c3-b283-155aa5cd92fe",
+ "@id": "urn:f9294378-917d-4969-b1ea-e82eef53f208",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:68ebae99-927e-455f-b2a6-5123f2ef2fba",
+ "GeneratedBy": "urn:71135527-0811-46d0-887d-1b56a42edc2e",
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}
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+ "@id": "urn:60f84ff1-e701-4e52-8dbe-dca9e99a1c2f",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:5b07097b-74e7-4377-be56-e02e611bc43f",
+ "GeneratedBy": "urn:2159c5ee-3437-45f6-ba8e-e352b535e409",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
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+ "@id": "urn:18e70cc0-08a9-4e53-b907-377ca9e96d82",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
}
},
{
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+ "@id": "urn:e502668a-42ab-4093-9bf5-a7a57645e2ad",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +710,16 @@
}
},
{
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+ "@id": "urn:63a6fef4-fa62-4df6-8328-87f0bddf63b2",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:4274fe0d-59d1-4526-b361-8143401dfa7e",
+ "GeneratedBy": "urn:b8e6f38b-bdf3-4d81-9788-8890b5877ee1",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:8e023450-0935-49bf-8dd0-7bb4196fbdf4",
+ "@id": "urn:a4807546-b85f-4467-b4e1-5302e8f0d87c",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +727,7 @@
}
},
{
- "@id": "urn:559ab88d-a226-41c0-aee7-6b3c5cfbe790",
+ "@id": "urn:640db747-51b4-4c85-a15e-94117c886ae4",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
}
},
{
- "@id": "urn:5ba2fd1c-e80f-42b6-8553-5bb99fd8c06a",
+ "@id": "urn:53043b2a-cb9b-43cc-8521-29127997d9dc",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +743,16 @@
}
},
{
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+ "@id": "urn:7a512ed2-ad13-49f5-a0dd-1b83659fa35f",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6cfef149-6cf9-489a-b7d2-fb11d514c35a",
+ "GeneratedBy": "urn:29409d41-a531-4b0b-a6ff-7d8bb83a2d57",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
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{
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+ "@id": "urn:ecd29557-0d0a-4e07-b160-323fcdaf374d",
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"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +760,34 @@
}
},
{
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"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:00125f77-6342-48bb-963c-4dae68613589",
+ "GeneratedBy": "urn:2eb30742-cf34-4fe0-8ac9-40a44a229224",
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{
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+ "@id": "urn:8c844809-356a-415e-bce7-a1036132d1eb",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:37a9d9ad-1722-4d7b-a9fd-2cd6c084801b",
+ "GeneratedBy": "urn:6418fb3a-4697-42cb-844f-98221898c9a4",
"digest": {
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{
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+ "@id": "urn:5931aa32-07bf-4032-a21d-cf78b7684d58",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:b3d8f618-85a4-422f-8deb-58d93c99b3c6",
+ "GeneratedBy": "urn:fea42141-8ffc-435c-bab7-a16e244425dc",
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{
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+ "@id": "urn:d0dbc87f-48a6-4316-8b9e-dee1b99104a4",
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"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +795,16 @@
}
},
{
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+ "@id": "urn:d1982c0f-816a-4e2d-8d0d-c5a1c170463f",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:e5200db4-26eb-4575-bc6d-d3297eadb4f1",
+ "GeneratedBy": "urn:11a44ba1-105e-4ecd-ad59-a75e07367e7d",
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}
},
{
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+ "@id": "urn:3fd2d4d5-677d-469b-bae5-9d764bd9e696",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +812,16 @@
}
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{
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+ "@id": "urn:e23efce6-e63a-4362-b5a0-1a7040a484cf",
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"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:940a024f-3e2f-4682-85f1-a12ff1028ab6",
+ "GeneratedBy": "urn:9a8178c0-e37c-46d4-97cf-dcb710a6c585",
"digest": {
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}
},
{
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+ "@id": "urn:41107f04-1af4-41a4-81c7-4e597cd0c7d7",
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"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +829,16 @@
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},
{
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+ "@id": "urn:93400375-d710-4879-8f2b-74ac3a72470d",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:189beb08-e9a2-4516-9240-a715584e0031",
+ "GeneratedBy": "urn:75b7b742-134c-4743-b2c6-7783513975e0",
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}
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{
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+ "@id": "urn:772e9d5e-658c-470c-864a-5c2ca5163b82",
"Label": "dfile.r*.1D",
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"digest": {
@@ -846,16 +846,16 @@
}
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{
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+ "@id": "urn:7328ba94-9c2f-4c40-ac01-9f1f0a322c34",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:91c12036-fc30-427f-aa13-e71430011001",
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{
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+ "@id": "urn:2651517a-d223-43a6-8156-df647cf71859",
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"digest": {
@@ -863,16 +863,16 @@
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{
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- "GeneratedBy": "urn:e4185d45-0bcd-48f6-91a2-839587f71001",
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{
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"digest": {
@@ -880,7 +880,7 @@
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"digest": {
@@ -888,34 +888,34 @@
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{
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@@ -965,16 +965,16 @@
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@@ -1015,16 +1015,16 @@
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@@ -1093,25 +1093,25 @@
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@@ -1255,16 +1255,16 @@
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@@ -1272,16 +1272,16 @@
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"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:7a75f677-aee4-4241-bc66-2169ae57d63d",
+ "@id": "urn:074a948e-c6ba-4b28-9d5e-92965faea971",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "GeneratedBy": "urn:ce136485-f2cb-4219-86c1-c4706b2d5e23",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:a7de91f4-6659-4288-9fa1-daeb0fd5f01b",
+ "@id": "urn:655ab22b-c4d4-4588-8cec-545096d5cb2b",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:041f3508-d4c5-4ef0-947d-4fc6d5de0a0f",
+ "GeneratedBy": "urn:f42e9433-2e8b-4418-985e-0e729a4b9011",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:172bd5a5-991c-451d-826c-b88c1cc58855",
+ "@id": "urn:5e26136f-5604-4340-8c7b-44216fd86348",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:48c32de6-d8cc-4932-9033-005392de7601",
+ "GeneratedBy": "urn:76f34313-4036-4758-aeb7-417bdfa5b93a",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:9409d309-6e12-4b1c-94b2-7bee390b752e",
+ "@id": "urn:ba768bfc-8d83-41b6-a165-99c6551f22ac",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:83b8a0a0-af45-4d8f-9a2e-35c24bcb3c0c",
+ "GeneratedBy": "urn:088f075e-c210-425a-a867-c66589f1c2c4",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:837c6c1f-5c41-4ce9-8bf6-5ee96151ec45",
+ "@id": "urn:31054834-2460-4ad5-bfa8-309f871874ae",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:a0e4adbb-6344-4a60-991e-336d5f663b71",
+ "GeneratedBy": "urn:015e9618-f2b6-44d9-8ebf-d24749832865",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:e6787718-533c-4ee0-9c8b-804f603f9942",
+ "@id": "urn:632d059b-7317-409b-bc33-1129e0fb3384",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:7e90b8aa-1787-46fb-88cf-ae5ddc1b0750",
+ "@id": "urn:ec10785b-703e-4c62-94ac-128617692f13",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:33c75be3-aa4e-406c-baeb-c6b0c73dd6e4",
+ "GeneratedBy": "urn:3a654753-b045-43d9-91af-47a534e1ddf0",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
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diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc.png b/examples/from_parsers/afni/afni_clustconn_18_proc.png
index 93ff3d3f9..88e64ac98 100644
Binary files a/examples/from_parsers/afni/afni_clustconn_18_proc.png and b/examples/from_parsers/afni/afni_clustconn_18_proc.png differ
diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
new file mode 100644
index 000000000..196014a07
--- /dev/null
+++ b/examples/from_parsers/afni/afni_clustconn_18_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:678c01d1-55b3-48e4-80a7-50bd58e40b65",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_cluster_nn2/tone_counting_onset_times.txt ./afni_cluster_nn2/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
+ "urn:c79be97e-b015-4120-b508-621e5bd01049",
+ "urn:22644854-5b21-46b9-8f42-4e730f48909b"
+ ]
+ },
+ {
+ "@id": "urn:1a3eab84-6a4d-46a9-9d8e-4f75db8644f4",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:5599d82d-e9dc-49b9-ba3d-62d2fef3c704"
+ ]
+ },
+ {
+ "@id": "urn:0409ad06-cf22-4cc1-b3e0-933604ab29b5",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:7a540544-90c6-42f9-9ca4-3ccb8a141ace",
+ "urn:045c8348-5186-4209-9572-bd0dcd050d80"
+ ]
+ },
+ {
+ "@id": "urn:97c24bcb-3fcd-4a5e-bd82-05e213699d99",
+ "Label": "tshift",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:7a540544-90c6-42f9-9ca4-3ccb8a141ace"
+ ]
+ },
+ {
+ "@id": "urn:d5f274be-3cda-4bfc-bca6-4afcd1622e19",
+ "Label": "align",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:7bcc4566-fca1-49a5-88eb-00f9726c62a7",
+ "urn:d0b5d93b-5323-4075-9d8b-c8da048aee8d"
+ ]
+ },
+ {
+ "@id": "urn:1858825f-50b4-4f73-9b5a-28e9ce1dc88f",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:1acb59f0-d174-4fd6-add7-3662f9b53c07",
+ "urn:8bd3d219-0c10-4cb1-997c-d64dfbc7aaea",
+ "urn:ee1cb0d3-c3d2-45c5-9798-ac85e16ec0e7"
+ ]
+ },
+ {
+ "@id": "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a",
+ "Label": "volreg",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:44ca55e2-233d-49f0-b27c-c1bbae75800c",
+ "urn:44ca55e2-233d-49f0-b27c-c1bbae75800c",
+ "urn:ee1cb0d3-c3d2-45c5-9798-ac85e16ec0e7",
+ "urn:44ca55e2-233d-49f0-b27c-c1bbae75800c",
+ "urn:bfdf23b1-84f5-493b-af60-ac30b7f045e3",
+ "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "urn:bfdf23b1-84f5-493b-af60-ac30b7f045e3",
+ "urn:d56be92e-40d9-463a-9e7e-2b14886091df",
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+ ]
+ },
+ {
+ "@id": "urn:f5777f7f-afef-49f9-be4a-a93d2a957623",
+ "Label": "blur",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:d66f2975-367e-471e-b934-9427c9784ed2",
+ "urn:f5deb909-5717-4cc7-abdc-3b6ef5b1e1d0"
+ ]
+ },
+ {
+ "@id": "urn:5f1265e6-ae5c-49cc-825c-cfc8fb60e870",
+ "Label": "mask",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:d839cce9-09a1-4f7f-98a1-1111d118824c",
+ "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "urn:bfdf23b1-84f5-493b-af60-ac30b7f045e3",
+ "urn:9f9a7b54-8e6c-416f-9fde-1ef0401fb67a",
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+ "urn:711c3b2d-51b7-457e-af1a-8d07e299e9b9"
+ ]
+ },
+ {
+ "@id": "urn:4d3e09b8-a6d1-4cae-ab6e-518c9140be14",
+ "Label": "scale",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:d839cce9-09a1-4f7f-98a1-1111d118824c",
+ "urn:04b2b95f-4706-4a8e-be80-12e76066f1b1",
+ "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "urn:d839cce9-09a1-4f7f-98a1-1111d118824c"
+ ]
+ },
+ {
+ "@id": "urn:7ba4e7c7-b024-4437-89fb-12b9fd6d684e",
+ "Label": "regress",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
+ "Used": [
+ "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
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+ "urn:8456e1f8-f2ca-4e15-ba7d-728b19b628b1",
+ "urn:a436f385-0f2b-4f63-9e9f-3fc989a38ba4",
+ "urn:1493a23b-141b-40c4-8fce-42e43fa48cab",
+ "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "urn:89dafdd6-e4c2-414e-8682-1fff8940a2aa",
+ "urn:be104b26-6320-4707-bd15-ad1549f178d7",
+ "urn:286200ad-d727-41c1-9a52-8425ccd365e5",
+ "urn:6eadba50-fb9c-4d7e-bf72-1b88f1ca5a88",
+ "urn:e05cbe53-170e-4a16-85f7-af70818b0819",
+ "urn:d6d5a8d3-4d08-467c-b393-de558c52d4f0",
+ "urn:fb2f5584-9e8c-454b-83ee-e6ba10178c44",
+ "urn:6b074efa-a20c-49fa-a8c6-75535054c1d1",
+ "urn:3d5d9307-5d13-47ee-beab-a43df5d0d8e8",
+ "urn:3d5d9307-5d13-47ee-beab-a43df5d0d8e8"
+ ]
+ },
+ {
+ "@id": "urn:bc261f1d-b44d-4663-8826-2438b4367d0b",
+ "Label": "blur estimation",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
+ "Used": [
+ "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c"
+ ]
+ },
+ {
+ "@id": "urn:9a5ec82b-4187-43d9-9c8e-a2884b7f56c6",
+ "Label": "auto block: generate review scripts",
+ "AssociatedWith": "urn:5a94b1ea-6185-4724-82e8-6a994f8b40e5",
+ "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
+ "Used": [
+ "urn:4d0b4182-47ba-4a78-bd74-e3f99493f451"
+ ]
+ }
+ ],
+ "Entities": [
+ {
+ "@id": "urn:1d5fc7c1-5967-451b-9074-9ecff2ec0f09",
+ "Label": "tone_counting_onset_times.txt",
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diff --git a/examples/from_parsers/afni/afni_clustconn_18_proc_block.png b/examples/from_parsers/afni/afni_clustconn_18_proc_block.png
new file mode 100644
index 000000000..8a84a8890
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index 420b0e25d..3a866c957 100644
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"Label": "3dToutcount",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:c05383d4-1b77-4993-8d08-0684a1484222"
+ "urn:f0e04c2e-44e8-4aff-aab5-a7e1ee98098f"
]
},
{
- "@id": "urn:e7b2e4af-beef-4f6a-8237-0d0680e02e9a",
+ "@id": "urn:e2c6602c-92d2-4b70-b934-693f7eb32861",
"Label": "cat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:6f328faa-8b2a-4820-83bc-b21ef00175a5"
+ "urn:17768148-44d0-425b-84d0-501f2fcfeed7"
]
},
{
- "@id": "urn:434be8cd-9929-453f-8644-d42a0ecab635",
+ "@id": "urn:13bfb68d-6090-4f83-a70e-3f46774397ec",
"Label": "3dTshift",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:c05383d4-1b77-4993-8d08-0684a1484222"
+ "urn:f0e04c2e-44e8-4aff-aab5-a7e1ee98098f"
]
},
{
- "@id": "urn:e77ccb11-2453-4a71-8c6a-7aa8acf1a8ad",
+ "@id": "urn:a12f67fa-445a-4453-bfea-0530ee29ab2d",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:505b3ba1-3f18-4073-b8cf-0761605c222b",
- "urn:b09f1df1-7eef-43ab-b856-44362156042d"
+ "urn:394709cb-79e2-416f-bb26-838d0473f728",
+ "urn:83c18660-6b2b-43ef-9001-34ec53eb6663"
]
},
{
- "@id": "urn:bad1b199-f926-4892-9e5d-b40f8fbd3997",
+ "@id": "urn:c7199008-6f75-4762-a1e8-cf1323e12c40",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:8111caba-eb40-4a7e-bdba-a17cdf324f75",
- "urn:94e688ae-2361-4473-8e64-a7c826738680"
+ "urn:2070ae2f-3560-47c0-ac79-34a688f24a9a",
+ "urn:9f29816e-b4da-4f57-bad3-cb44b7169a34"
]
},
{
- "@id": "urn:ee130f6b-a062-46b2-b51d-4a1e42d71915",
+ "@id": "urn:6fb154ac-656d-4ec4-b52c-ba5f3a2cb810",
"Label": "cat_matvec",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:b2670328-db1e-4674-90cb-13fcc914f630"
+ "urn:2f10fe24-4e6d-4509-8f66-a7f2ef7f6913"
]
},
{
- "@id": "urn:4448454e-d15c-4499-8c25-12bb3e6fe805",
+ "@id": "urn:1c51ee27-d1e8-4e43-a40f-6ccd1b31dc4d",
"Label": "3dvolreg",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:82256fe2-87d2-4e98-ab6a-4c27b73a2e44"
+ "urn:c630db8e-9100-44ca-9a60-53fd57a1b4b5"
]
},
{
- "@id": "urn:3d32c7eb-ba23-4b67-a36c-c499e9d77732",
+ "@id": "urn:78ed0f4d-6f99-449e-a8c8-4eefb0449abd",
"Label": "3dcalc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:82256fe2-87d2-4e98-ab6a-4c27b73a2e44"
+ "urn:c630db8e-9100-44ca-9a60-53fd57a1b4b5"
]
},
{
- "@id": "urn:09b2ca30-3c1a-4e49-9157-1698e71f13b0",
+ "@id": "urn:9e0641d9-7808-4496-99b0-0b3b57c641fa",
"Label": "cat_matvec",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:b2670328-db1e-4674-90cb-13fcc914f630"
+ "urn:2f10fe24-4e6d-4509-8f66-a7f2ef7f6913"
]
},
{
- "@id": "urn:d8cb9afd-8dc9-4f9a-8770-c49d73892b8b",
+ "@id": "urn:f2550307-1615-4358-8769-d61fcd43cd75",
"Label": "3dAllineate",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:23a692d8-75aa-4033-a468-aa0e65da9c36",
- "urn:82256fe2-87d2-4e98-ab6a-4c27b73a2e44",
- "urn:aece4d2b-0460-4251-8c7f-126fce456814"
+ "urn:27891055-5aed-4c5b-97cc-85ba345b94d4",
+ "urn:699957e1-c0b1-455a-ac1e-4d72da9755be",
+ "urn:c630db8e-9100-44ca-9a60-53fd57a1b4b5"
]
},
{
- "@id": "urn:754ec45e-6b37-49ed-8902-ae1b5b9610bd",
+ "@id": "urn:08ce5ea2-6664-46f5-ae28-cb7521a7776d",
"Label": "3dAllineate",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:23a692d8-75aa-4033-a468-aa0e65da9c36",
- "urn:7e3a9ab1-40eb-4692-b0a6-da89e21fe018",
- "urn:aece4d2b-0460-4251-8c7f-126fce456814"
+ "urn:27891055-5aed-4c5b-97cc-85ba345b94d4",
+ "urn:699957e1-c0b1-455a-ac1e-4d72da9755be",
+ "urn:72715ec1-d45e-4385-a39a-2e81fe95c12b"
]
},
{
- "@id": "urn:a3198397-f5bd-445e-9b58-1981dd0a6dba",
+ "@id": "urn:5f3b06ec-bc29-436d-b9b9-286e16290002",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:bab2ae80-8942-4f06-84a4-3a82ba65b210"
+ "urn:7ad3059d-8206-4ed1-a834-9bb3cfcb85e0"
]
},
{
- "@id": "urn:a0665740-7578-4953-a5d8-2febc139b4c8",
+ "@id": "urn:dcd723bd-d6ae-4392-95d7-d8de7cf0552a",
"Label": "cat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:a9b86e5d-509c-4128-917c-3441d311007a"
+ "urn:7638c2af-8a37-4b27-9b47-40735fced5d7"
]
},
{
- "@id": "urn:cb9ad31a-ff52-4fc0-9e45-c50f04ad7dd1",
+ "@id": "urn:60c5a807-5f6b-42c2-91ef-82e58d0c1fb6",
"Label": "3dcopy",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:4a27a7a8-d862-4a7d-9875-6f60deecb583"
+ "urn:ca5ab9bf-eb66-4b0a-90e7-eec0cc934c5e"
]
},
{
- "@id": "urn:7d205378-c584-45cd-a840-ce5eb3edceba",
+ "@id": "urn:f8579074-adae-4f6c-8795-99bf5647aa6e",
"Label": "3dcalc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:03330031-ed4b-4c42-9765-1ce0737c19e1",
- "urn:2d8c3fda-3c56-479a-9328-deb5fc80e1e9"
+ "urn:cd9a5684-f24c-48d7-9be2-e01e71cabb42",
+ "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
]
},
{
- "@id": "urn:136d77c7-32b6-4e25-8112-3cb9c4cbdb46",
+ "@id": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
"Label": "3dcopy",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:aece4d2b-0460-4251-8c7f-126fce456814"
+ "urn:699957e1-c0b1-455a-ac1e-4d72da9755be"
]
},
{
- "@id": "urn:dec7cd8d-b963-4546-b3e6-5a63b61ef300",
+ "@id": "urn:42c7cfa6-3436-47fc-9b0e-0efd39381912",
"Label": "3dAllineate",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:afb4482f-41f7-48c4-8884-81f04334d619"
+ "urn:cd9873c3-d9ba-4e4e-a33a-017011561abf"
]
},
{
- "@id": "urn:61891cc9-48c2-4693-8cb8-8cbc53fabbf6",
+ "@id": "urn:1077cd25-b4bf-47ce-b006-37f8dec7d4ac",
"Label": "3dmerge",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:6beedc47-df31-4025-9be0-977a2f2980fe",
- "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b"
+ "urn:5ad4f4c3-0369-486a-a649-2860f71566eb",
+ "urn:9b462dc8-9807-4841-b48f-e9b74eed7a81"
]
},
{
- "@id": "urn:b7a893d5-a985-4693-b6c6-2f732211170d",
+ "@id": "urn:849de179-0714-449c-972c-9bd0385b606a",
"Label": "3dAutomask",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:d0c0bd35-a9bc-471a-90c8-51581635290c"
+ "urn:d43dafc3-339c-4c4d-818a-dfa1b4c67e05"
]
},
{
- "@id": "urn:df4f0286-cff5-4533-8b9d-da7083d40de2",
+ "@id": "urn:41da3ae7-d09c-401e-8d9f-c440dcdfc993",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:6a7a3359-9111-448c-8d33-d9e86321c801",
+ "@id": "urn:d5c50b91-bf99-44fc-8817-638474bc5ed8",
"Label": "3dresample",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7",
- "urn:aece4d2b-0460-4251-8c7f-126fce456814"
+ "urn:699957e1-c0b1-455a-ac1e-4d72da9755be",
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae"
]
},
{
- "@id": "urn:c8e777cc-a609-4c27-a92d-c46856ae9e17",
+ "@id": "urn:b44ee1b6-ca32-4efe-b5b2-2295397c29f9",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:7424fdd6-0e84-4e65-8552-14c9c1e6a56b"
+ "urn:075cb241-654e-4dad-8f85-643caa9ad2d8"
]
},
{
- "@id": "urn:32ca3d5b-761b-4903-b0a1-49daa50ee44d",
+ "@id": "urn:57bd302c-cbfd-4a43-a6e6-1604de3d3428",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:3f6ebb09-33c2-450f-a017-1aba59644f2e",
- "urn:f7f2f055-f692-42dd-b871-eb23b1fa7842"
+ "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
+ "urn:d38ceba6-3dd6-445f-8989-59b9378fdb02"
]
},
{
- "@id": "urn:2e5c9e5f-35b0-41e0-832d-b95799f3925a",
+ "@id": "urn:dd8157e4-5f84-4055-8577-d34fe317c4c9",
"Label": "3ddot",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:3f6ebb09-33c2-450f-a017-1aba59644f2e",
- "urn:f7f2f055-f692-42dd-b871-eb23b1fa7842"
+ "urn:31e0a47f-bd71-463f-8e81-315d673c0f72",
+ "urn:d38ceba6-3dd6-445f-8989-59b9378fdb02"
]
},
{
- "@id": "urn:40f457bf-fbab-4594-8373-c6a3665036e7",
+ "@id": "urn:1d60fb80-4134-40ee-a4a7-9fec8e81944a",
"Label": "3dresample",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:19ca205d-a4a5-46a2-8920-bfedeae3ad91",
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7"
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae",
+ "urn:b1207d77-5b40-4bd8-b6a6-55ac3138df83"
]
},
{
- "@id": "urn:be636df1-e671-4fc0-b305-d3a0366578bf",
+ "@id": "urn:150bb5a4-2723-4470-8249-b8a11cf37033",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:153fa781-92e7-4922-ad3d-98ee7ca75991"
+ "urn:d1a7cf1e-a9fe-46eb-b700-3db0ecdbd36e"
]
},
{
- "@id": "urn:0d259108-198a-403f-b1d3-bba09529827d",
+ "@id": "urn:a6b3758d-de35-4810-bd31-118109b7fc63",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:d0c0bd35-a9bc-471a-90c8-51581635290c"
+ "urn:d43dafc3-339c-4c4d-818a-dfa1b4c67e05"
]
},
{
- "@id": "urn:2f679b50-65f1-46d1-9294-aba74a8d3c0c",
+ "@id": "urn:f4e177a7-c607-494d-a39c-faacc2b24ddd",
"Label": "3dcalc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:2d8c3fda-3c56-479a-9328-deb5fc80e1e9",
- "urn:3cb3b1c6-e903-4569-a9fb-c6c5b3e5c4c5",
- "urn:d0c0bd35-a9bc-471a-90c8-51581635290c"
+ "urn:a1fccbf8-9cdb-4933-9e66-288648dedef9",
+ "urn:d43dafc3-339c-4c4d-818a-dfa1b4c67e05",
+ "urn:f2e2545b-dc53-4ac0-8a68-40994b1b2d60"
]
},
{
- "@id": "urn:7821235c-3bfa-4236-abb0-1b9543708a70",
+ "@id": "urn:5d425601-5d7e-4ed9-9377-d968237a7bc4",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:bec94431-e6e6-49b1-9844-70ed437c5011"
+ "urn:61ad5e58-0713-429a-9ed7-a5bbfa9bea59"
]
},
{
- "@id": "urn:10441440-f68c-4a5f-b183-f563d2e794c3",
+ "@id": "urn:19fbe20a-d53a-4526-a882-a3fe0e9e8bea",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:bec94431-e6e6-49b1-9844-70ed437c5011"
+ "urn:61ad5e58-0713-429a-9ed7-a5bbfa9bea59"
]
},
{
- "@id": "urn:2c547239-06b0-4d02-bc5c-fb786699f884",
+ "@id": "urn:f542fa6c-2d9f-427c-86d8-d9a9a2ba5436",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:bec94431-e6e6-49b1-9844-70ed437c5011"
+ "urn:61ad5e58-0713-429a-9ed7-a5bbfa9bea59"
]
},
{
- "@id": "urn:223a4067-5f9c-4c22-88f3-a4a2c47ed665",
+ "@id": "urn:a3c9a40b-6244-4a75-a576-433e5217bf0a",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:3f4994fb-b29d-46be-80da-ba384b45215f"
+ "urn:ec1e16aa-96dd-498e-b63c-edbe048ab155"
]
},
{
- "@id": "urn:5d191212-57cc-456b-85cd-85783c7fe6b9",
+ "@id": "urn:cc93b360-37bb-4882-b87b-548637050754",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:31b4e687-2c8a-4111-864c-e9c49ea12643"
+ "urn:c05383d4-1b77-4993-8d08-0684a1484222"
]
},
{
- "@id": "urn:056d59d8-964b-4d0f-bb91-9a8707d359dc",
+ "@id": "urn:6f328faa-8b2a-4820-83bc-b21ef00175a5",
"Label": "3dTcat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:3f4994fb-b29d-46be-80da-ba384b45215f"
+ "urn:ec1e16aa-96dd-498e-b63c-edbe048ab155"
]
},
{
- "@id": "urn:045b5f7d-291b-4fa3-9c79-73625dc7cf0c",
+ "@id": "urn:5fec2cf3-fa6a-4cd0-9306-fa3ba9543c53",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:33d046bd-be2f-4413-a576-ac8b265651df"
+ "urn:daed513b-1d35-403b-a28f-b4555092af97"
]
},
{
- "@id": "urn:f1f79801-0474-444d-9932-f7e5d0d51daf",
+ "@id": "urn:b09f1df1-7eef-43ab-b856-44362156042d",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:89482764-88d8-4c62-a56d-1411b5ccfdee"
+ "urn:505b3ba1-3f18-4073-b8cf-0761605c222b"
]
},
{
- "@id": "urn:3a9caa74-65f8-4212-8dfb-9f6105f65c2c",
+ "@id": "urn:bad1b199-f926-4892-9e5d-b40f8fbd3997",
"Label": "3dcalc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:65b903a1-5eeb-488d-b160-9bbf997f6387",
- "urn:6c62078a-2203-4119-9ef8-6f736b6b4888",
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7"
+ "urn:8111caba-eb40-4a7e-bdba-a17cdf324f75",
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae",
+ "urn:94e688ae-2361-4473-8e64-a7c826738680"
]
},
{
- "@id": "urn:827ed196-545b-4a41-ba1b-fbb5e32fad7d",
+ "@id": "urn:afb4482f-41f7-48c4-8884-81f04334d619",
"Label": "3dTnorm",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:f6e491b8-c07b-4a3f-87c8-7454d74ed5f7"
+ "urn:4448454e-d15c-4499-8c25-12bb3e6fe805"
]
},
{
- "@id": "urn:f6a7d888-b32e-41fd-986d-4a7ced3524ee",
+ "@id": "urn:f53199d2-d78d-4610-ba41-c25c2fed43d4",
"Label": "3dmaskave",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:0cd1409b-fa23-4fa9-b126-4875a72d4205",
+ "@id": "urn:cfe72aec-bd1a-4ee1-a000-f14251902181",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:15b1634e-9051-43c0-a06f-29a9d5f199c1"
+ "urn:bd6c8246-39c9-4521-a578-2fbd75723ccf"
]
},
{
- "@id": "urn:35a1ea29-a6a9-4480-935b-60a9ed7fb806",
+ "@id": "urn:7bcf3122-e120-44d2-8fb2-8e67537b56b3",
"Label": "3dcalc",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:16569afa-e9a2-4485-bc9f-6d2049cda352",
- "urn:777b0433-6ebc-4e4d-8c6b-040c2b716fee"
+ "urn:23a692d8-75aa-4033-a468-aa0e65da9c36",
+ "urn:3d32c7eb-ba23-4b67-a36c-c499e9d77732"
]
},
{
- "@id": "urn:ec6ed868-0e75-4970-907a-8803c2f75303",
+ "@id": "urn:a5e6e3c8-5a2d-4230-b3ae-7d5cc1e7afb8",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:555f05f3-dbaf-4f5f-ba7e-7c35d5f9ee07"
+ "urn:ccb973ca-2141-47aa-a525-6ea2a3e49c50"
]
},
{
- "@id": "urn:0f534eba-dacb-4931-bba9-6c47154c0249",
+ "@id": "urn:754ec45e-6b37-49ed-8902-ae1b5b9610bd",
"Label": "1dcat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:26e3d878-ff09-4d57-83a2-45bf6fe593cc"
+ "urn:5b84a168-7b3e-4a42-939c-6ddace47728b"
]
},
{
- "@id": "urn:57d24b1c-57b6-4a34-b8ed-55ac1bfcf2b1",
+ "@id": "urn:cc96af70-469a-46be-bda8-7dd0836370b8",
"Label": "1dcat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:045b52c8-7cb0-4b15-98eb-a7a12321b4c6"
+ "urn:8c6633c0-1445-454f-9af8-3f73d297d9d1"
]
},
{
- "@id": "urn:03fee530-1ea7-404f-a470-3f22a2e8998c",
+ "@id": "urn:bab2ae80-8942-4f06-84a4-3a82ba65b210",
"Label": "3dTstat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:1fd80f42-e522-4b86-bb22-5df3ece23840"
+ "urn:011a8821-2375-46f5-be9c-b2fe24d4eedb"
]
},
{
- "@id": "urn:fe9b261f-86e1-42ae-8c4e-90a11247319a",
+ "@id": "urn:a9b86e5d-509c-4128-917c-3441d311007a",
"Label": "1dcat",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:1fd80f42-e522-4b86-bb22-5df3ece23840"
+ "urn:011a8821-2375-46f5-be9c-b2fe24d4eedb"
]
},
{
- "@id": "urn:910fd52b-fc9e-4525-99f8-715d9edf7896",
+ "@id": "urn:4a27a7a8-d862-4a7d-9875-6f60deecb583",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7"
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae"
]
},
{
- "@id": "urn:67468386-08fe-4518-8aff-be434d2e335d",
+ "@id": "urn:03330031-ed4b-4c42-9765-1ce0737c19e1",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7"
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae"
]
},
{
- "@id": "urn:3591baa3-31c7-47f7-978d-4a5246174400",
+ "@id": "urn:136d77c7-32b6-4e25-8112-3cb9c4cbdb46",
"Label": "3dClustSim",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:8151d2f2-5ad5-434d-863a-7e01c98263b7"
+ "urn:926a47a6-ea55-4ad2-9e72-15447c30aeae"
]
},
{
- "@id": "urn:9b34c8c7-5d6f-44a8-b84f-cda8e8f97f40",
+ "@id": "urn:dec7cd8d-b963-4546-b3e6-5a63b61ef300",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:734caeea-8af0-4599-9908-c08308cc9452"
+ "urn:d2f4881f-3117-40fd-8b8d-cf002001b831"
]
},
{
- "@id": "urn:32d0c5a2-4cd2-4aff-a9e0-4a0bd2f7e626",
+ "@id": "urn:487a68cf-1b53-49f7-9891-e4ba3dd75314",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:6035c3dd-8696-43dc-971f-e8ef69b32e66",
+ "AssociatedWith": "urn:95f75c97-0fac-44dd-a66b-ad1a188906a5",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:4b562a15-6bf7-4e4d-aa40-ce2850c3ad1e",
+ "@id": "urn:589b66e0-ab84-4130-8846-006b115bfb26",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:f4e177a7-c607-494d-a39c-faacc2b24ddd",
+ "GeneratedBy": "urn:65519446-a0d5-4e2f-99ae-44bf766cc3df",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:71ab96a6-c63f-4d51-9ba5-44e05d4a6bff",
+ "@id": "urn:1cbc6101-33d2-4015-8b31-5647416620dd",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:a1fccbf8-9cdb-4933-9e66-288648dedef9"
+ "GeneratedBy": "urn:757e1873-4676-46d2-a92f-5b67fb687b7c"
},
{
- "@id": "urn:5d425601-5d7e-4ed9-9377-d968237a7bc4",
+ "@id": "urn:92acfa7c-8df3-461e-8e54-89c8affe431a",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
- "@id": "urn:442c7bb5-4110-445a-becc-73c99a9b4c58",
+ "@id": "urn:2fa4fb99-2391-410c-a805-a4f4476069d3",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_nn3/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
- "@id": "urn:7ee58b52-0d8d-455d-bd78-b48d8d308cb5",
+ "@id": "urn:d50cffba-0a06-4acb-83ec-fef24b78dfda",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5e833f79-5816-4ba7-aba6-6aa5c0860121"
+ "GeneratedBy": "urn:026881b3-e898-4f69-a75e-48c164c99568"
},
{
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@@ -631,13 +631,13 @@
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@@ -645,13 +645,13 @@
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@@ -659,16 +659,16 @@
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@@ -676,25 +676,25 @@
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@@ -702,7 +702,7 @@
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{
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@@ -710,16 +710,16 @@
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@@ -727,7 +727,7 @@
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@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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@@ -760,34 +760,34 @@
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@@ -795,16 +795,16 @@
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{
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -846,16 +846,16 @@
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@@ -863,16 +863,16 @@
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@@ -880,7 +880,7 @@
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@@ -888,34 +888,34 @@
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@@ -923,7 +923,7 @@
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@@ -931,7 +931,7 @@
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{
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@@ -939,25 +939,25 @@
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@@ -965,16 +965,16 @@
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@@ -982,16 +982,16 @@
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{
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@@ -999,7 +999,7 @@
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@@ -1007,7 +1007,7 @@
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+ "urn:6a7a3359-9111-448c-8d33-d9e86321c801",
+ "urn:dc4ce4e5-21bb-442b-9dc3-fa387ea90bbb",
+ "urn:aee873fe-d817-466b-8d31-98fcb45222d3"
+ ]
+ },
+ {
+ "@id": "urn:f6c58562-64eb-4875-b481-83d9e0a584b8",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:9dbd4acf-480e-4f44-9312-2ba368f1eefb"
+ ]
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+ {
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+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:f7f2f055-f692-42dd-b871-eb23b1fa7842",
+ "urn:48605004-13de-4ff6-9ce3-a22c66dbfeef"
+ ]
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+ "Label": "tshift",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:f7f2f055-f692-42dd-b871-eb23b1fa7842"
+ ]
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+ "Label": "align",
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+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:02b3cea2-0b28-44c1-844a-f3f9f6b33325",
+ "urn:153fa781-92e7-4922-ad3d-98ee7ca75991"
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+ "Label": "tlrc",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:2f679b50-65f1-46d1-9294-aba74a8d3c0c",
+ "urn:97d913aa-b73f-4d76-9c34-a50085ef0573",
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+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
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+ "urn:7821235c-3bfa-4236-abb0-1b9543708a70",
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+ "Label": "blur",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:1174c647-6787-4ce9-8047-d006125b1459",
+ "urn:ec6ed868-0e75-4970-907a-8803c2f75303"
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+ "Label": "mask",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:11818376-0d68-4f56-9f44-084b77b5f1be",
+ "urn:3f4994fb-b29d-46be-80da-ba384b45215f",
+ "urn:c9a2a664-d761-4a85-b582-3d8cf5cf2c6b",
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+ "Label": "scale",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
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+ "urn:11818376-0d68-4f56-9f44-084b77b5f1be",
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+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
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+ "urn:6c62078a-2203-4119-9ef8-6f736b6b4888",
+ "urn:6c62078a-2203-4119-9ef8-6f736b6b4888",
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+ "Label": "blur estimation",
+ "AssociatedWith": "urn:d2fd03b5-32f2-4d3f-9a7e-91a684205c9b",
+ "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
+ "Used": [
+ "urn:c9a2a664-d761-4a85-b582-3d8cf5cf2c6b",
+ "urn:c9a2a664-d761-4a85-b582-3d8cf5cf2c6b",
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+ "Label": "auto block: generate review scripts",
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+ "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
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+ "digest": {
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+ "GeneratedBy": "urn:354e747f-12b7-48c2-a27f-7d8d56e137e0"
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+ "Label": "sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
+ "digest": {
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diff --git a/examples/from_parsers/afni/afni_clustconn_26_proc_block.png b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png
new file mode 100644
index 000000000..ff1a87755
Binary files /dev/null and b/examples/from_parsers/afni/afni_clustconn_26_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_con_f_proc.jsonld b/examples/from_parsers/afni/afni_con_f_proc.jsonld
index e661007e2..24cf90eec 100644
--- a/examples/from_parsers/afni/afni_con_f_proc.jsonld
+++ b/examples/from_parsers/afni/afni_con_f_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "@id": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
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{
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+ "@id": "urn:c9fd7c76-2ae4-45b3-878b-40d9bad11085",
"Label": "Make directory",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
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"Parameters": {},
"Used": []
},
{
- "@id": "urn:116e0cb2-5547-433d-9b0a-cd59c277c6b8",
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"Label": "Make directory",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
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"Parameters": {},
"Used": []
},
{
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"Label": "cp",
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- "urn:fee3ecea-2b2c-433e-bb26-e3e78eea72fd"
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]
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- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
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]
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},
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+ "@id": "urn:bbdd547f-1200-4863-9dda-efa4d1e55184",
"Label": "3dcalc",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:4206f70c-3207-4464-a93b-1094b5e556ce"
+ "urn:70787460-c0e9-4624-a974-df03ea059fd7"
]
},
{
- "@id": "urn:e4fd13bd-1c92-4e3b-9674-25ec45487409",
+ "@id": "urn:0c6b3aeb-06f8-4e6b-b3ed-88acdbf9e0e6",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:da7d2044-3bd8-4f27-88cd-f87a8407fdb0"
+ "urn:3b785f19-73bf-4c34-a038-7a9b4396a169"
]
},
{
- "@id": "urn:9e9057eb-e197-4c3e-b411-5cc092df19e5",
+ "@id": "urn:cfc270b2-011d-4313-9bf2-42cf99099862",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4",
- "urn:4206f70c-3207-4464-a93b-1094b5e556ce",
- "urn:57519ad5-a5ee-4b54-95a1-995405cbc897"
+ "urn:63697e02-287b-45a2-bb20-41e265601261",
+ "urn:70787460-c0e9-4624-a974-df03ea059fd7",
+ "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247"
]
},
{
- "@id": "urn:0807935a-9ab8-477e-8608-b44b647607cf",
+ "@id": "urn:eba38419-a546-4321-8e0a-8f3a41271a29",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4",
- "urn:57519ad5-a5ee-4b54-95a1-995405cbc897",
- "urn:6a7c684d-98df-4535-be47-fcf9e2eda67d"
+ "urn:63697e02-287b-45a2-bb20-41e265601261",
+ "urn:bcdad7b0-1900-445e-a58d-7cdbd0dd9cfc",
+ "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247"
]
},
{
- "@id": "urn:6b71e692-ec8f-498f-89dc-fb089f42bacc",
+ "@id": "urn:e8191e7e-8505-4e9d-afc8-41e2324eb4dc",
"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:8774df07-e4e7-4f9e-b856-8d0b9dadadba"
+ "urn:53f02519-829b-4f61-9838-40048b816257"
]
},
{
- "@id": "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d",
+ "@id": "urn:8dc8374c-cbe1-47f8-9d6a-39ae8a5ebb34",
"Label": "cat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:07b4df38-c764-4ea2-90d2-4ec7525e4376"
+ "urn:df826b1c-74a5-4f67-be42-d15657ccada8"
]
},
{
- "@id": "urn:f75b7820-b35b-43ac-9529-7847898e65b0",
+ "@id": "urn:c6aa20f8-dfc4-434c-b06e-e6740edb0f2e",
"Label": "3dcopy",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:01695c88-880b-4165-a6c4-0832f9174f62"
+ "urn:5ec304ae-9211-417c-9b97-ef828474c68b"
]
},
{
- "@id": "urn:ecd84b96-96f0-4bc4-8120-3aa6ff2454cc",
+ "@id": "urn:cdeffd5b-2823-49f0-9667-028119716d19",
"Label": "3dcalc",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:8e1d5762-8fbd-4ff1-a41a-903dfe42bdbd",
- "urn:e2378519-04e3-4715-84b2-6bc7ea8690bf"
+ "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20"
]
},
{
- "@id": "urn:fcc1f2b7-e347-48be-9bfa-66d805405da8",
+ "@id": "urn:a878b257-a9ba-4bcb-bec8-cff004db2580",
"Label": "3dcopy",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4"
+ "urn:63697e02-287b-45a2-bb20-41e265601261"
]
},
{
- "@id": "urn:16dfbd17-9e1a-4db2-b261-ed07c3f0dc28",
+ "@id": "urn:0d96712d-754c-4811-b72f-475acab451eb",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:fcd0434b-5af5-4ca3-a091-42d2f7a8f886"
+ "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60"
]
},
{
- "@id": "urn:2f9bb8f0-6d78-4390-a502-3fcf6741b82c",
+ "@id": "urn:2b5a4047-ae13-4ad8-a91e-4bbedd00ee70",
"Label": "3dmerge",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:4132e44b-e44d-4b8f-b979-894d284c60f2",
- "urn:ba668017-e912-4946-b252-0bf10dffbfea"
+ "urn:ad783a8d-3eff-4062-aaaa-b0da2153285b",
+ "urn:c0c5482a-7a18-4535-99df-1f2f4b42155f"
]
},
{
- "@id": "urn:11a19e58-b18a-4068-9317-2e48372cc90a",
+ "@id": "urn:ba73f7d7-f70a-4503-aafa-a70b10d74b93",
"Label": "3dAutomask",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44"
+ "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
]
},
{
- "@id": "urn:afd5f1ae-2faf-4017-bf1b-0e6bf599fdf2",
+ "@id": "urn:300db58b-407a-44d5-a5bc-4ae178718157",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:949dab22-814b-4d66-942b-91c6f150c770",
+ "@id": "urn:5b0ca4be-398b-4a17-bcfd-4979613d6409",
"Label": "3dresample",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4",
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
+ "urn:63697e02-287b-45a2-bb20-41e265601261"
]
},
{
- "@id": "urn:90224fd2-1deb-4b86-8b71-b94bd3664cc2",
+ "@id": "urn:c5da5238-d255-4788-8c65-a97fbad74c2e",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:422bb061-d84a-4c7c-b975-081f8102361d"
+ "urn:c0b2dc25-6399-41b4-8c90-2115b9a9c877"
]
},
{
- "@id": "urn:abce3868-1f35-4d6d-ac4e-069f2712654a",
+ "@id": "urn:298d54e4-1c6b-48c3-94f7-7d82fa1b91b7",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:930ba2ac-0533-40e1-bcdd-f539a8bb6381",
- "urn:f9c4ecd6-9447-4417-88be-9ee9c8e00364"
+ "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454",
+ "urn:9cc3040c-923c-4223-bcdc-65e44e3724df"
]
},
{
- "@id": "urn:36c7c714-a31d-412a-84ab-3af060136b00",
+ "@id": "urn:afb793a2-e11b-40df-bbab-7c55f13dce6f",
"Label": "3ddot",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:930ba2ac-0533-40e1-bcdd-f539a8bb6381",
- "urn:f9c4ecd6-9447-4417-88be-9ee9c8e00364"
+ "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454",
+ "urn:9cc3040c-923c-4223-bcdc-65e44e3724df"
]
},
{
- "@id": "urn:9fb6f014-2e57-409d-a3c9-c4fca6e17362",
+ "@id": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
"Label": "3dresample",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:59c7d43f-8ff4-4168-b238-59b4a76e8be2",
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
+ "urn:c63f6bf6-7480-414e-a8fb-7a1c37996839"
]
},
{
- "@id": "urn:ff8f77a8-822e-474e-a600-d65d5ec87e8b",
+ "@id": "urn:9c4e2e74-846d-4682-a86d-4fa43b9361c7",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:f8bb27f6-9d25-4ab6-b221-05761b3e5145"
+ "urn:b052d775-addc-449b-a406-368acd0aaa97"
]
},
{
- "@id": "urn:ebfb1e00-7e6d-44ea-ac4d-9960f3dd8f56",
+ "@id": "urn:fd503d11-d2f7-4355-8724-cf332ba8f69b",
"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44"
+ "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
]
},
{
- "@id": "urn:85f41e69-6cd2-4fa0-9487-12aea9824cd2",
+ "@id": "urn:92e806a1-588a-400a-8267-1d331938bd79",
"Label": "3dcalc",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44",
- "urn:63005485-a633-492b-aab2-46783a515b0a",
- "urn:e2378519-04e3-4715-84b2-6bc7ea8690bf"
+ "urn:746a6f07-d57a-4b68-884b-13ab76184159",
+ "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20",
+ "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
]
},
{
- "@id": "urn:bd1b26cc-9601-4a1a-ae55-1e4eb56f2235",
+ "@id": "urn:24c48049-423b-4f4a-a68b-63c3d0593e99",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:324e098a-3bca-4dee-a253-bc65ca24c92a"
+ "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
]
},
{
- "@id": "urn:e2af053a-bac8-4264-9fc8-cffdb3b03757",
+ "@id": "urn:78b84e7b-706b-4025-b3d4-5ef478ebf581",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:324e098a-3bca-4dee-a253-bc65ca24c92a"
+ "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
]
},
{
- "@id": "urn:91a2005b-e8a3-446b-8124-414264c29ba2",
+ "@id": "urn:eabf2d58-12bc-4264-9a14-841b35d36c2e",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:324e098a-3bca-4dee-a253-bc65ca24c92a"
+ "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
]
},
{
- "@id": "urn:5d581780-9fea-4d4d-a765-d8d540dff86b",
+ "@id": "urn:dd7c30e9-086f-4453-b4e0-cfd2dd378337",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:0d04acc3-8cda-49f9-abe0-aeafcfd63461"
+ "urn:51fd66c2-887c-4586-9153-c4330b011c21"
]
},
{
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+ "@id": "urn:86fd4be2-654d-4f6d-8dcf-1c8eaf851151",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:8d47a160-4848-4b69-9041-d15d202a8069"
+ "urn:c92f09a2-3673-461a-b213-7e6e77ae9127"
]
},
{
- "@id": "urn:13031df9-3189-40e2-9cc2-4a682da74984",
+ "@id": "urn:f8cbfb50-209b-45f0-af1c-cb1e8654524f",
"Label": "3dTcat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:0d04acc3-8cda-49f9-abe0-aeafcfd63461"
+ "urn:51fd66c2-887c-4586-9153-c4330b011c21"
]
},
{
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"Label": "3dTstat",
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+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:0d39f685-e244-438e-97a9-db23ff3af802"
+ "urn:40b50dc9-2f0a-4a54-8f74-308039d60ecd"
]
},
{
- "@id": "urn:6b4ae610-f0ab-4c5c-95cb-7dae61918885",
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"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:2a408795-ebd3-4029-a8b9-3405eba4bdca"
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]
},
{
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"Label": "3dcalc",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
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"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
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- "urn:3cc19a04-79cd-4981-913b-a18b88d06449",
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
+ "urn:80fcdacd-a0b4-41a5-a625-30221b6d3350",
+ "urn:92d99567-2e04-4755-84bf-14cd9ef1de78"
]
},
{
- "@id": "urn:08f6f5f3-bd9b-44be-9d64-7caad9f19d62",
+ "@id": "urn:c073483a-c70c-494e-bc37-5a2327064f06",
"Label": "3dTnorm",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:26040560-8893-4c08-835e-2ae7ae40e431"
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]
},
{
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"Label": "3dmaskave",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:33552b33-dc97-4793-8385-2a87de22c0a4",
+ "@id": "urn:80f381a3-fcaa-49fb-885e-4debddb8a786",
"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:92adf46f-3cd0-4de7-8939-f18c8392f523"
+ "urn:2a93e9d8-8d47-40af-8bcf-eaf983b9add1"
]
},
{
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"Label": "3dcalc",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
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- "urn:8a911323-f909-40de-950d-d0cd49e1e599"
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]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:035c3970-5a13-491b-a04b-584ca86e8397"
+ "urn:25fc6c6e-026b-4ab5-b54f-ab765a104838"
]
},
{
- "@id": "urn:0935d3f6-d3b7-44a9-877c-9e3cc384b111",
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"Label": "1dcat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8"
+ "urn:604a1e3b-15de-497b-a525-ca9bd99f2a09"
]
},
{
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"Label": "1dcat",
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"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:d0b03493-daf8-4372-bd90-a7d591ad03a9"
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]
},
{
- "@id": "urn:ddb15529-6e64-418a-a74b-7a3d384dc0ab",
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"Label": "3dTstat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:045781d1-9e75-4834-9b30-4978b76070da"
+ "urn:a92420ab-a033-4844-a6f7-39500db2e482"
]
},
{
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"Label": "1dcat",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:045781d1-9e75-4834-9b30-4978b76070da"
+ "urn:a92420ab-a033-4844-a6f7-39500db2e482"
]
},
{
- "@id": "urn:dd40f1be-ca12-46a1-a52d-5d1f764d8b19",
+ "@id": "urn:314e11c6-9e73-48fd-80b8-5255796a06d1",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
]
},
{
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"Label": "3dFWHMx",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
]
},
{
- "@id": "urn:1f0c4c33-4ba6-430e-a3db-3bf7f03cdf13",
+ "@id": "urn:b1798fa5-41c3-4c32-af33-ba038526e4b9",
"Label": "3dClustSim",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:fdd6e038-1a52-480c-a86b-a07d58f356ee"
+ "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
]
},
{
- "@id": "urn:6ebcc108-fd65-49bb-8a39-6353b906a79c",
+ "@id": "urn:f1ad28d0-6c5d-4619-ac2a-c7f4bee41ea6",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:fe6ace26-ff04-4f79-91bd-71b9d2b0cdea"
+ "urn:fb2855e1-e166-43d1-82c1-370fde58b2ce"
]
},
{
- "@id": "urn:0fe907b9-525c-451d-b98b-6e4696857b52",
+ "@id": "urn:cc3659dd-8933-41f9-b132-b2a64e91ffaf",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
+ "AssociatedWith": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
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+ "@id": "urn:b83677f5-b62b-4acd-96b5-716f9da67ac6",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:82fea590-f798-46fe-a78f-7601887e0245",
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{
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+ "@id": "urn:d09ce11e-697a-4e13-bee2-7628d33893fd",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:116e0cb2-5547-433d-9b0a-cd59c277c6b8"
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},
{
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+ "@id": "urn:69fcfb15-c77c-40c4-a487-3ad726504cfb",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_f_test/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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+ "@id": "urn:d448379e-f728-47d2-9567-f7ba106cd541",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_f_test/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
- "@id": "urn:5c92426e-803d-4eb0-81de-03f890ca7386",
+ "@id": "urn:0bc910a4-11f0-409b-a806-fc0893a40976",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488"
+ "GeneratedBy": "urn:95c94be2-273b-4c7d-8a39-1ce112181183"
},
{
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+ "@id": "urn:3d997e80-8feb-4949-9ca6-5f2e3bd68fc6",
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"AtLocation": "sub-01_T1w.nii.gz",
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@@ -631,13 +631,13 @@
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{
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"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:42f5e934-e5d2-4707-ad09-4dd6a6b280fc"
+ "GeneratedBy": "urn:ab4d3e7f-fd6c-4189-a5dd-b726f1e3eaab"
},
{
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+ "@id": "urn:916a0919-3412-4ed1-b4b5-ea6838d333b7",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
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},
{
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:c405fbed-a681-458f-863a-a4a803fc0543"
+ "GeneratedBy": "urn:3e718433-e2b5-434d-a596-249413698da1"
},
{
- "@id": "urn:00aeec77-58fc-409c-a902-c1a79d93c8a9",
+ "@id": "urn:f8a81771-0ea9-47d0-8c3e-b3482efcb7a4",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
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{
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"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:fcf8088f-b2b9-4a81-a7e0-09c6db3b4aed",
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{
- "@id": "urn:d5506b4c-ab38-46d9-b17a-0e03a202eac8",
+ "@id": "urn:1e927d75-77b7-4b4e-baef-e3ee46d7b843",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
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@@ -676,25 +676,25 @@
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{
- "@id": "urn:ca08e7e4-ce9d-43ff-994b-c2be02f6a9f7",
+ "@id": "urn:739ed39d-7cda-4f20-a616-6cfacd7eb0ba",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:ebb97d70-b892-4949-9449-97c5864b16ae",
+ "GeneratedBy": "urn:e36979a0-f0bf-44cd-aadc-8b80d1ca6d10",
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+ "@id": "urn:bb40fcd5-09a3-4b42-93b4-ed8ed7ee95dd",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:3f94e5a2-855a-48ed-bcc8-11f9506e1f6f",
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{
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+ "@id": "urn:6b2dccb0-069c-4d61-91cb-9885fcb4a556",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
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{
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+ "@id": "urn:06372779-6792-4e37-84d1-cd68357b7aed",
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"AtLocation": "pb01.$subj.r01.tshift+orig",
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@@ -710,16 +710,16 @@
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{
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@@ -727,7 +727,7 @@
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@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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@@ -760,34 +760,34 @@
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@@ -795,16 +795,16 @@
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -846,16 +846,16 @@
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@@ -863,16 +863,16 @@
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@@ -880,7 +880,7 @@
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@@ -888,34 +888,34 @@
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@@ -923,7 +923,7 @@
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@@ -931,7 +931,7 @@
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@@ -939,25 +939,25 @@
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@@ -965,16 +965,16 @@
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@@ -982,16 +982,16 @@
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@@ -999,7 +999,7 @@
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@@ -1007,7 +1007,7 @@
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@@ -1015,16 +1015,16 @@
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@@ -1032,25 +1032,25 @@
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@@ -1058,34 +1058,34 @@
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@@ -1093,25 +1093,25 @@
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+ "@id": "urn:c92f09a2-3673-461a-b213-7e6e77ae9127",
"Label": "X.xmat.1D",
"AtLocation": "X.xmat.1D",
- "GeneratedBy": "urn:5d581780-9fea-4d4d-a765-d8d540dff86b",
+ "GeneratedBy": "urn:dd7c30e9-086f-4453-b4e0-cfd2dd378337",
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}
},
{
- "@id": "urn:c874b5fd-25bf-4784-8200-a2ea41b25922",
+ "@id": "urn:444b3aef-bed6-43e5-820a-7d79e2d179c9",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:13031df9-3189-40e2-9cc2-4a682da74984",
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"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:0d39f685-e244-438e-97a9-db23ff3af802",
+ "@id": "urn:40b50dc9-2f0a-4a54-8f74-308039d60ecd",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1119,16 @@
}
},
{
- "@id": "urn:5ae22539-5ee8-41d6-ac9b-8fc06f93b886",
+ "@id": "urn:44d37560-44a4-474b-a529-7de437cb6c75",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:41578a4c-7519-46df-9ddf-eda14e20a647",
+ "GeneratedBy": "urn:cda9ebcc-abd5-4d2a-b0dc-3b2680aa1967",
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}
},
{
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+ "@id": "urn:4ce7cdba-5a0b-4246-8ee3-840b44f92bf6",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1136,16 @@
}
},
{
- "@id": "urn:574d3e7d-e246-4b11-965f-aa666574b423",
+ "@id": "urn:e96a44c6-cc86-4fbd-80b1-ea93ccb3d990",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:6b4ae610-f0ab-4c5c-95cb-7dae61918885",
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},
{
- "@id": "urn:3cc19a04-79cd-4981-913b-a18b88d06449",
+ "@id": "urn:80fcdacd-a0b4-41a5-a625-30221b6d3350",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1153,7 @@
}
},
{
- "@id": "urn:22a3f6b3-48f6-4e6b-9396-de9d36478fb9",
+ "@id": "urn:92d99567-2e04-4755-84bf-14cd9ef1de78",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1161,16 @@
}
},
{
- "@id": "urn:12a4011c-5111-4324-a57c-19de78c71969",
+ "@id": "urn:b8c7e4ee-449e-490e-bb35-95baf776b6c0",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:3a5ec85b-4649-4e66-ae61-3226ead3490b",
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{
- "@id": "urn:26040560-8893-4c08-835e-2ae7ae40e431",
+ "@id": "urn:9b4436bc-3b0f-4b8f-ba17-18aac004a520",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1178,25 @@
}
},
{
- "@id": "urn:60e316e3-5de9-4cf0-a078-e0e086a169c5",
+ "@id": "urn:0a7647fc-2cdc-4fa3-b082-e96971482634",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:08f6f5f3-bd9b-44be-9d64-7caad9f19d62",
+ "GeneratedBy": "urn:c073483a-c70c-494e-bc37-5a2327064f06",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:8a911323-f909-40de-950d-d0cd49e1e599",
+ "@id": "urn:1da351b2-5bea-4433-a57f-1ed0437d697f",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:cf948276-59de-4443-883a-77d3fc5747a0",
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"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:92adf46f-3cd0-4de7-8939-f18c8392f523",
+ "@id": "urn:2a93e9d8-8d47-40af-8bcf-eaf983b9add1",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:88d6bd28-7a69-4044-b46a-836e2f61ccd3",
+ "@id": "urn:fa5a7811-b41a-413e-9cb5-a8ed8170aa68",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:33552b33-dc97-4793-8385-2a87de22c0a4",
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"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
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{
- "@id": "urn:5a177f0b-f843-4725-9475-1b1e4ddf5e18",
+ "@id": "urn:f8678749-7602-488a-9d3a-8f2490d6f419",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:1be6efab-9929-4b1e-8bbc-c165cd38270f",
+ "@id": "urn:b1d3f413-1a3f-4a66-8cee-b24bfdb8d5ea",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:4f45a00b-727c-40b2-a2c5-5cae947a56a8",
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"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:035c3970-5a13-491b-a04b-584ca86e8397",
+ "@id": "urn:25fc6c6e-026b-4ab5-b54f-ab765a104838",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:b1ed202d-bf85-425f-adac-b68fb17b5af0",
+ "@id": "urn:bfc5f78d-f8d3-4eee-8fd5-8835562215ba",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:b4680683-ecd5-4088-8bc2-63c2d6c6a59b",
+ "GeneratedBy": "urn:075b19d7-cccb-49e7-a9c8-4a0abc906eab",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
+ "@id": "urn:604a1e3b-15de-497b-a525-ca9bd99f2a09",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:153b277a-635d-42c0-a884-4bbfa0c6dd1b",
+ "@id": "urn:7ab095d7-8d81-4df7-aa9f-2167bce867fc",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:0935d3f6-d3b7-44a9-877c-9e3cc384b111",
+ "GeneratedBy": "urn:d48a8eec-56b1-4aa8-af22-922fc27586e6",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:d0b03493-daf8-4372-bd90-a7d591ad03a9",
+ "@id": "urn:4b941985-5a56-41fe-bdf5-274158f7437c",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:b86ebb2d-75c1-4ea3-a50c-aab763d3bc41",
+ "@id": "urn:5f12525b-764a-4493-b764-0c8b7057963b",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:a9fca6d2-d86c-450d-97a9-50415da048a5",
+ "GeneratedBy": "urn:c504956f-4b7b-4992-abbd-46b5fc4f8a21",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:045781d1-9e75-4834-9b30-4978b76070da",
+ "@id": "urn:a92420ab-a033-4844-a6f7-39500db2e482",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:a4c09a62-cb31-4c2b-ba17-d95d8005b33d",
+ "@id": "urn:ae3b0d12-52f4-48a2-88d4-0678d5f09e99",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:ddb15529-6e64-418a-a74b-7a3d384dc0ab",
+ "GeneratedBy": "urn:d749afb2-7262-4434-9504-06cb313cac64",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:91ed2886-1c20-431d-9c0f-8f3720ffea22",
+ "@id": "urn:ce793436-f751-49ce-83f6-51ec93dd4b41",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:3de44cfa-745b-4bfe-8115-0095c9f923ea",
+ "GeneratedBy": "urn:a04f7934-f7bc-4170-b2eb-5c6c732b5848",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:3f07d54e-e55d-4e7e-bc51-9c2e441a58b3",
+ "@id": "urn:4ae332d7-a922-405f-badd-a8bf6db8669f",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:dd40f1be-ca12-46a1-a52d-5d1f764d8b19",
+ "GeneratedBy": "urn:314e11c6-9e73-48fd-80b8-5255796a06d1",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:50736079-de9a-432b-a2db-79a26b418d57",
+ "@id": "urn:35b68be2-b883-4bde-9698-c01bc4e682f7",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:815e4ca6-6373-4dd2-9391-c5ceca637440",
+ "GeneratedBy": "urn:a6811528-b35b-46f8-8c64-c27db6cc51f3",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:969531e6-8e1f-4881-b5cb-ce83fe7ff1ac",
+ "@id": "urn:8547393d-de20-4286-9185-a5e3e8872ec0",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:1f0c4c33-4ba6-430e-a3db-3bf7f03cdf13",
+ "GeneratedBy": "urn:b1798fa5-41c3-4c32-af33-ba038526e4b9",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:fe6ace26-ff04-4f79-91bd-71b9d2b0cdea",
+ "@id": "urn:fb2855e1-e166-43d1-82c1-370fde58b2ce",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:689be361-2322-444c-81b5-551d7b16ab70",
+ "@id": "urn:0e8df35d-318a-47ab-aad9-59de5d48e26e",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:0fe907b9-525c-451d-b98b-6e4696857b52",
+ "GeneratedBy": "urn:cc3659dd-8933-41f9-b132-b2a64e91ffaf",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_con_f_proc.png b/examples/from_parsers/afni/afni_con_f_proc.png
index 0e9cae44f..b95002a44 100644
Binary files a/examples/from_parsers/afni/afni_con_f_proc.png and b/examples/from_parsers/afni/afni_con_f_proc.png differ
diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.jsonld b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
new file mode 100644
index 000000000..f5b7b06c4
--- /dev/null
+++ b/examples/from_parsers/afni/afni_con_f_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:669e1fc0-0ce7-4613-8e8b-08db4a63db9b",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_f_test/tone_counting_onset_times.txt ./afni_f_test/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:e5081baa-1acc-4ca1-b4e0-b504d7fed955",
+ "urn:ff6a8b57-ac8c-4df4-b617-4b3a0b2bc2b9",
+ "urn:3604a5a0-8d0a-446e-aaa0-a81b7138d093"
+ ]
+ },
+ {
+ "@id": "urn:5a9fabb2-3b10-40fa-8806-332d6cd96b61",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:3aa1e7d1-1fae-4173-89a7-0f4c340c28a2"
+ ]
+ },
+ {
+ "@id": "urn:68e5f037-ae24-4110-bf68-0f33967fcdb1",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8",
+ "urn:0e2391fb-c48d-4922-b20e-de1d93161959"
+ ]
+ },
+ {
+ "@id": "urn:23dc9eac-7e0a-4fb9-8c41-fd286cb8e6d4",
+ "Label": "tshift",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8"
+ ]
+ },
+ {
+ "@id": "urn:e284cc01-ac8b-4ecd-815d-0ca2f933f53d",
+ "Label": "align",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:d5e3f198-a9c4-4128-a3bc-7636be079ef3",
+ "urn:fb3bb527-ace9-4fc0-aa87-c2013e3eec38"
+ ]
+ },
+ {
+ "@id": "urn:f4df6cb7-c701-436a-9430-d2721a0a52a6",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:790edad4-6308-4c2b-9d08-5cf9b9a4a3e9",
+ "urn:d6edc215-1f9b-4996-8ac6-215c125316b0",
+ "urn:ab38c57b-f9d1-418f-b7da-f63d7457eea2"
+ ]
+ },
+ {
+ "@id": "urn:55245bd5-e2b9-4e3d-89f6-898175db3b62",
+ "Label": "volreg",
+ "AssociatedWith": "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
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+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
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+ "@id": "urn:e04b5ef2-2a17-4125-a6e2-6e59daa4fbfd",
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+ "AtLocation": "ClustSim",
+ "GeneratedBy": "urn:ad85f4d2-bc86-4eb0-b051-e88d0ec7f05c",
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+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
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+ "@id": "urn:2eb17bf4-6037-4b2b-8ee3-1b2c53770e8f",
+ "Label": "pb00.$subj.r*.tcat",
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+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
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+ "@id": "urn:41696253-13a1-4d14-a93f-f16cb8b3a7f9",
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+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_con_f_proc_block.png b/examples/from_parsers/afni/afni_con_f_proc_block.png
new file mode 100644
index 000000000..12e08973c
Binary files /dev/null and b/examples/from_parsers/afni/afni_con_f_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_default_proc.jsonld b/examples/from_parsers/afni/afni_default_proc.jsonld
index 82d161c53..bb1d5a019 100644
--- a/examples/from_parsers/afni/afni_default_proc.jsonld
+++ b/examples/from_parsers/afni/afni_default_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "@id": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:d458c54d-3dc8-4d05-8d6f-66f9f1a1f8ec",
+ "@id": "urn:28599e73-0c4c-4b01-94c8-564b4868263c",
"Label": "Make directory",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:8c858fbe-04ee-48dc-bab5-c1ae2ef9159c",
+ "@id": "urn:2eb28fb2-64cb-4f97-9585-a2a087bce5bf",
"Label": "Make directory",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:249dda2c-c59c-44e3-9a54-ec97b2d2c422",
+ "@id": "urn:63516713-fa00-46ee-a200-9dc82d0638f8",
"Label": "cp",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:4eec28c2-77b1-4e2a-b5ad-a4bf544143f9",
- "urn:df27cd3b-d715-4b02-b53b-a3b58ad15509"
+ "urn:1de21354-cb92-4e3e-a1b6-c21a2419f96f",
+ "urn:2869e5e8-c26d-476a-a9d5-74b7d6fd82d5"
]
},
{
- "@id": "urn:ef4d92a2-528c-4884-9e55-9b6f0f020e18",
+ "@id": "urn:3b740c47-c0b4-4191-8984-7dceb3d26b76",
"Label": "3dcopy",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:cb1c0160-0e2f-4a93-b70f-8f61530cdb27"
+ "urn:3e76f4d2-3306-41b7-8185-10c2a3996597"
]
},
{
- "@id": "urn:5fee107f-6a26-4850-849e-b57806b77df2",
+ "@id": "urn:d9607bb0-f064-4582-839b-f4e8c4476f7d",
"Label": "3dTcat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:03b235ce-bedb-404b-8ea4-83225a07fb37"
+ "urn:2c47c9a9-46b1-4440-a9fe-0c7e20eaa6e2"
]
},
{
- "@id": "urn:46e28345-fd6e-4493-8d14-61325dd2787f",
+ "@id": "urn:21fa3ee1-c7b0-4e1b-b2ad-1073d918da77",
"Label": "3dToutcount",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2"
+ "urn:244fd1a8-65d6-4b1b-b5e7-9442ce7edb1c"
]
},
{
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"Label": "cat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
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"Parameters": {},
"Used": [
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+ "urn:c7f2560b-59db-404e-9a2d-90b38ef07d05"
]
},
{
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"Label": "3dTshift",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
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"Parameters": {},
"Used": [
- "urn:0bb5d0b3-84fd-4dd6-86ca-6e39ee7c9ca2"
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]
},
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"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
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- "urn:af4526e8-a45d-47d0-9556-d2eccbaa0079"
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]
},
{
- "@id": "urn:0a6241b6-2152-4e5b-8113-cc6c69d9197b",
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"Label": "@auto_tlrc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
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- "urn:5420810d-a31a-49fd-acd7-8b299036cc1f"
+ "urn:15baa6b9-1d8a-46b3-bb31-b3c8ca05a87c",
+ "urn:f9d32dd5-4528-43c6-a237-1117da783451"
]
},
{
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+ "@id": "urn:788757af-9a31-406d-90d4-025832d851dd",
"Label": "cat_matvec",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:701df0dc-45e0-40bd-9782-a2e4d6b55efa"
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]
},
{
- "@id": "urn:ab91b3fd-d259-4e35-917b-15e7f7eb5390",
+ "@id": "urn:53f315a4-7a6b-4db3-bba3-38bc5949a9bb",
"Label": "3dvolreg",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:652558c1-a31d-4c8a-a9c3-822ea694f3d3"
+ "urn:2cad718c-d474-4b16-8ab8-10c7ba4cf0f8"
]
},
{
- "@id": "urn:f4ad58dc-3808-48a2-ab28-b91512eceeb8",
+ "@id": "urn:74503532-ae23-44ab-96e4-591e1832334c",
"Label": "3dcalc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:652558c1-a31d-4c8a-a9c3-822ea694f3d3"
+ "urn:2cad718c-d474-4b16-8ab8-10c7ba4cf0f8"
]
},
{
- "@id": "urn:b1cc91c7-f921-41c1-8be7-392416eeeb13",
+ "@id": "urn:d7134c48-220f-433f-b3b7-c18b5b63915d",
"Label": "cat_matvec",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:701df0dc-45e0-40bd-9782-a2e4d6b55efa"
+ "urn:c48be6e0-b508-4345-9c13-eb14cd44db9a"
]
},
{
- "@id": "urn:a2736bdd-b58b-4fd5-b985-64805c68ad20",
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"Label": "3dAllineate",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
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"Used": [
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- "urn:99e36abe-ae11-4401-99aa-a5ddc3092b09",
- "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0"
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]
},
{
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"Label": "3dAllineate",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
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- "urn:9fb1321c-e5fc-4d51-bbaf-b8c047d3ac80",
- "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0"
+ "urn:3558e558-c972-4123-9472-a48c6f390fb5",
+ "urn:73c8e3b1-d155-4190-ac0c-a7d60aab2841",
+ "urn:8a527b2d-12c9-45da-a415-905258b466a6"
]
},
{
- "@id": "urn:fec2d381-36fb-4e79-af50-fb87c41fb116",
+ "@id": "urn:e83f84e5-d148-4623-98a6-51db60ece79a",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:ad6afb1f-16c3-42d2-b5c1-ed7709d5baf8"
+ "urn:7453b882-53de-488b-b771-4e68323e3bed"
]
},
{
- "@id": "urn:2d6bc1b8-06a4-44f4-a749-6e56f1afb928",
+ "@id": "urn:aeefcc15-f430-486c-b626-64f77030f168",
"Label": "cat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:9df834a4-e7db-4a93-b135-78a21e8af4cf"
+ "urn:6c82a5b7-295e-4bf5-8ec9-8a86e1157907"
]
},
{
- "@id": "urn:9f0418c9-37e3-442e-9c7e-546a9ca91950",
+ "@id": "urn:e373bebe-5f90-472c-9c49-28fad5288cea",
"Label": "3dcopy",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:a03334c1-a3eb-4f6e-8950-27ed8c34fe59"
+ "urn:5e7aa0cf-14af-4515-98b5-bd86b8aabd16"
]
},
{
- "@id": "urn:bb9d4908-d26a-4fc3-a20b-7397089067ff",
+ "@id": "urn:5a35202d-8bdf-43f7-86af-0b7a0180b55a",
"Label": "3dcalc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:03f18f63-6da0-4cef-bc7c-af56235662fa",
- "urn:f22d3031-ad76-4284-a165-40cc1f7e75b2"
+ "urn:35bf05e6-7c83-4b09-be5d-a4347de635ad",
+ "urn:bbd72fc4-3902-4871-9552-bf7438111b8a"
]
},
{
- "@id": "urn:22967322-3dec-480a-a8aa-40245b9baa07",
+ "@id": "urn:a1c61c00-791a-4ea7-8b70-db69ded7d388",
"Label": "3dcopy",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0"
+ "urn:8a527b2d-12c9-45da-a415-905258b466a6"
]
},
{
- "@id": "urn:e8e9e392-b899-461a-8588-64440b803a57",
+ "@id": "urn:dbacb1d3-bc39-4290-b0f6-35ecd9dbef6b",
"Label": "3dAllineate",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:b552aaae-f3a6-43f9-a28e-2adaa38edc2c"
+ "urn:9955b7ff-84e8-4bb5-af94-b072f23ec249"
]
},
{
- "@id": "urn:f3da51a8-5835-48b7-b300-aa60d22b491a",
+ "@id": "urn:28f7601c-1797-410a-95cb-6ff6721c0fda",
"Label": "3dmerge",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:8ad2f8c8-b192-4c41-9949-ae52df0c39f4",
- "urn:ab283958-f080-464f-ae38-49bb0a5105e6"
+ "urn:75ec118a-dd30-4341-9849-6145a99eb6a3",
+ "urn:ac9ef81e-4361-4ae5-a5e6-6a4dedb6f55a"
]
},
{
- "@id": "urn:7138ee41-a1a7-4e90-8634-1fbd9e69bec4",
+ "@id": "urn:426cdc9a-3cb6-4c52-933f-a4883a051d40",
"Label": "3dAutomask",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8bde6cef-d597-4805-a798-f881ef0ce6da"
+ "urn:a3826de2-cc97-4c8d-9fe7-0dfc17615740"
]
},
{
- "@id": "urn:302ebdbf-d0d6-4b88-ab41-87f4f06e3912",
+ "@id": "urn:9e8e49ef-ce01-4f89-a883-bfdfc3e48d86",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:ac846955-fde3-40f9-b985-4b30238f1f1f",
+ "@id": "urn:91ee27ee-63a7-4b92-8f1e-a6bc5af873cd",
"Label": "3dresample",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94",
- "urn:fa33f60b-37bd-4d5b-b7a2-d803058269e0"
+ "urn:8a527b2d-12c9-45da-a415-905258b466a6",
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae"
]
},
{
- "@id": "urn:b4b9ae0b-4c3c-4412-acd1-762a876097d8",
+ "@id": "urn:aa415b9b-bf93-417b-8277-a5c49bd95a27",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:b869493c-9952-4578-8ce7-e15a2f6e1c23"
+ "urn:fc26cdab-5a85-4c01-ab9a-7cbebf471a3e"
]
},
{
- "@id": "urn:d83ee1fb-1d02-4962-8e9f-a92ff6acfbce",
+ "@id": "urn:36a79a14-45cd-45c0-8d6d-ce8b33c7de70",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1f8cef70-8e9f-4bb3-8c27-3bd187ade4d8",
- "urn:a85ccd3b-21d1-4d8c-b1d7-f8a029ba1691"
+ "urn:264a0ee7-47b6-4f2c-9bf1-933c6d9ad711",
+ "urn:49f8bfd0-d9cf-49ab-a537-461a68af5ebd"
]
},
{
- "@id": "urn:3f9dfd23-a816-4462-acac-8ed10abe6952",
+ "@id": "urn:bbde888e-4902-42c0-994b-a180d5edff4b",
"Label": "3ddot",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1f8cef70-8e9f-4bb3-8c27-3bd187ade4d8",
- "urn:a85ccd3b-21d1-4d8c-b1d7-f8a029ba1691"
+ "urn:264a0ee7-47b6-4f2c-9bf1-933c6d9ad711",
+ "urn:49f8bfd0-d9cf-49ab-a537-461a68af5ebd"
]
},
{
- "@id": "urn:9c48e073-f43b-4b4e-97d5-2fa117a6f722",
+ "@id": "urn:bb97fb22-0b0c-4c0a-b43e-9f3f90687556",
"Label": "3dresample",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94",
- "urn:5248fb52-7e25-4dcf-90d6-feb14056d454"
+ "urn:3b75dfdd-46fe-4619-a0d1-046d70b4d127",
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae"
]
},
{
- "@id": "urn:3fa05d1c-5c80-467d-9cae-e31f03718eeb",
+ "@id": "urn:af37ed47-62d0-4033-aaf3-b1a9bff13185",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:a50be786-02a1-4d07-98a7-c4b1b5d571c2"
+ "urn:ed039280-27f5-4133-b5da-56c4aa37acde"
]
},
{
- "@id": "urn:423b51c1-468f-4ff0-bc27-b2433543427f",
+ "@id": "urn:55cac575-b451-483d-89fd-26175de93e13",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:8bde6cef-d597-4805-a798-f881ef0ce6da"
+ "urn:a3826de2-cc97-4c8d-9fe7-0dfc17615740"
]
},
{
- "@id": "urn:bd0e92e9-9fa3-4e67-a0b9-08f61205ffb0",
+ "@id": "urn:437944b7-da8d-4fe2-9606-45329b04b990",
"Label": "3dcalc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:8bde6cef-d597-4805-a798-f881ef0ce6da",
- "urn:abf3d860-d14b-4a7c-932d-87e0d89d9e18",
- "urn:f22d3031-ad76-4284-a165-40cc1f7e75b2"
+ "urn:35bf05e6-7c83-4b09-be5d-a4347de635ad",
+ "urn:a3826de2-cc97-4c8d-9fe7-0dfc17615740",
+ "urn:af89af9c-125e-4b55-a644-10be24d34fb7"
]
},
{
- "@id": "urn:15a17ec9-afcd-4aa6-822c-563cf725d34d",
+ "@id": "urn:84f56de4-3465-4cf5-9217-cdfaa5a8257e",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:8e51b296-a8ad-4c3e-bfc3-297ae5ebdc88"
+ "urn:fa4a5008-018c-454b-9399-c24a2febe47b"
]
},
{
- "@id": "urn:534ae9e5-a369-405d-9cec-98b2f507db07",
+ "@id": "urn:62de0566-6cb1-4a25-bee0-6b7ed491b2af",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:8e51b296-a8ad-4c3e-bfc3-297ae5ebdc88"
+ "urn:fa4a5008-018c-454b-9399-c24a2febe47b"
]
},
{
- "@id": "urn:4850cca1-5789-48af-9d8b-1388f2a13215",
+ "@id": "urn:b4e36be6-aa1d-4ef3-a1ed-6ae35a8a0fdc",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:8e51b296-a8ad-4c3e-bfc3-297ae5ebdc88"
+ "urn:fa4a5008-018c-454b-9399-c24a2febe47b"
]
},
{
- "@id": "urn:e7244890-3561-4eaa-a5b7-bab4753e00ba",
+ "@id": "urn:12bb6358-d0b4-4fa6-b56a-57abca5f5173",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:eeaa7e7a-8cc7-4bd3-9632-8c53f23db6ea"
+ "urn:a0d9e6c4-68dd-48b7-a051-c3a2b8801090"
]
},
{
- "@id": "urn:1e958106-7c75-4c73-bb51-14d1b1ea95e1",
+ "@id": "urn:cf8b5c81-a106-484c-8287-f132f119ab5b",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:7092bcca-8a5c-4618-bc2f-d5ece8e076b5"
+ "urn:4de6638c-23f0-4324-bc91-5f022edec878"
]
},
{
- "@id": "urn:62463505-c485-4705-85f3-47da349c549c",
+ "@id": "urn:518cbb99-6802-4c2b-bdb1-a9271dc218c1",
"Label": "3dTcat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:eeaa7e7a-8cc7-4bd3-9632-8c53f23db6ea"
+ "urn:a0d9e6c4-68dd-48b7-a051-c3a2b8801090"
]
},
{
- "@id": "urn:70850153-4e6b-43fd-99b1-318d93e70b80",
+ "@id": "urn:f5cd9e8f-859f-4fc7-8132-9508cb8d7144",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:45fea0a2-13f6-4b49-bc0d-e67393412164"
+ "urn:348581c2-45e2-43bb-91e7-f0fec0b7fa58"
]
},
{
- "@id": "urn:6d1cd561-140c-46bc-b4f0-91480b25aad3",
+ "@id": "urn:12a489a2-e5c4-41fd-972b-12e91f20f6af",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:e1ce9fe6-0fdc-4973-bdb9-eb0e5bcbea6e"
+ "urn:900d0f5b-e68c-4fa6-9d84-c5c4209a2067"
]
},
{
- "@id": "urn:a32b44cb-e1b8-40d6-9c78-3aef16006ef5",
+ "@id": "urn:37154f93-c242-4db5-ac64-d883928bdcd3",
"Label": "3dcalc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94",
- "urn:2e269bf3-ecc6-4bfd-b04c-ddb690e70fdb",
- "urn:62a6be87-3a93-4a9b-9d61-b7e2d2227a93"
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae",
+ "urn:bf4ed4ca-115c-4320-bbfa-cf160080113d",
+ "urn:ed650386-5a53-4329-b53b-a0fd3776085b"
]
},
{
- "@id": "urn:72a0b816-a755-4ffc-907d-3aa43568e48f",
+ "@id": "urn:447b3e40-4c33-4a46-8121-5c9a3af866aa",
"Label": "3dTnorm",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:2e7bdac9-e43c-43cc-86e4-37ee58774229"
+ "urn:0c1f173a-a1e8-43ad-942f-d3231383ed70"
]
},
{
- "@id": "urn:aa7cc227-1492-4b80-a441-76db5060599b",
+ "@id": "urn:c00eeda2-be42-487f-b6e2-28515f578f3e",
"Label": "3dmaskave",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957",
+ "@id": "urn:b2754ee1-2e63-4e5b-a8e3-eb27e268ea7a",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:6a60a386-74a3-475a-a222-594448a74486"
+ "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
]
},
{
- "@id": "urn:9c9b4cb0-4148-4ac9-abec-285cd3234228",
+ "@id": "urn:ba717568-1edd-48b5-886a-54b1c13531dc",
"Label": "3dcalc",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
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- "urn:cd005f13-432d-442b-97fb-05f487b8d394"
+ "urn:1e0b939a-7f03-4ce5-94d3-ec2db95d67b5",
+ "urn:957b2a43-07df-4b2e-942d-783862b74031"
]
},
{
- "@id": "urn:757f4edc-d6f0-4c10-b93f-a62dbdff6c54",
+ "@id": "urn:958a9af3-d67a-49c5-be0f-f910d982040b",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:20adc457-4cb5-47e7-b992-ee701f634086"
+ "urn:7d15df61-0c90-47a2-b901-a49fb72542ad"
]
},
{
- "@id": "urn:ea89480e-c072-4df9-a9d5-d7ef51adb5ce",
+ "@id": "urn:2bfd1d18-9f2e-4320-aaef-09ce4964eab6",
"Label": "1dcat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:73216f9b-6c6c-4495-898c-b6e33ab2a9f4"
+ "urn:b90bda86-d4c6-4834-8a69-d115a75f5584"
]
},
{
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+ "@id": "urn:8bcccb64-6ecc-4f07-b27e-abb1ee23eb41",
"Label": "1dcat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:4eedac58-1578-4f7f-a158-576db499125e"
+ "urn:0690a611-adcc-4f06-aa92-734143220e88"
]
},
{
- "@id": "urn:b30575e5-b909-41d7-81b2-1c3b1f00624d",
+ "@id": "urn:9d0bc8f1-0e14-4d65-bbe5-70599bfa3f9b",
"Label": "3dTstat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:9e5668f5-2b7b-477c-883e-08a7cf7064c7"
+ "urn:9ee22513-1fd7-4480-bc21-82a8cc9d6ab3"
]
},
{
- "@id": "urn:e6e2b2a3-2877-473a-ac88-37bc4f7b79e6",
+ "@id": "urn:97719e5d-4229-4ff2-8310-05340e8ce878",
"Label": "1dcat",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:9e5668f5-2b7b-477c-883e-08a7cf7064c7"
+ "urn:9ee22513-1fd7-4480-bc21-82a8cc9d6ab3"
]
},
{
- "@id": "urn:cc3c31ab-c304-46e8-a45d-d21331ec0eba",
+ "@id": "urn:29952120-8a6e-40ba-bf71-baf362704948",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94"
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae"
]
},
{
- "@id": "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30",
+ "@id": "urn:934df8a7-1b3b-4fda-9cbd-36546f3149ed",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94"
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae"
]
},
{
- "@id": "urn:de3b0abf-5f0c-4836-84f6-bc9644c12c1f",
+ "@id": "urn:c774d4f0-4ad3-44d8-b9c5-7775c0dc9776",
"Label": "3dClustSim",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:0251ee81-099a-4ebc-98ce-451c65834a94"
+ "urn:98ce23d2-9cc2-4df9-a29a-82d7aa48e6ae"
]
},
{
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+ "@id": "urn:f0e62ba6-d164-4941-9425-560f6785c115",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:de1871d8-045a-467f-9dc9-e90f0985bb89"
+ "urn:40800cc0-4c6d-4a57-8d70-9e65b1bb50ca"
]
},
{
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+ "@id": "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:203b180e-1762-40ec-80d2-0e9ec0447898",
+ "AssociatedWith": "urn:91ce6272-68f4-4e66-ac0d-834d3a0c1096",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
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+ "@id": "urn:5e67d271-f37f-4cc9-9225-f11dbaeaf6dc",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:d458c54d-3dc8-4d05-8d6f-66f9f1a1f8ec",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:8c858fbe-04ee-48dc-bab5-c1ae2ef9159c"
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{
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+ "@id": "urn:1de21354-cb92-4e3e-a1b6-c21a2419f96f",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_p0001/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
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+ "@id": "urn:42dfcf03-5b5e-43ba-ae86-d88910e34559",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:249dda2c-c59c-44e3-9a54-ec97b2d2c422"
+ "GeneratedBy": "urn:63516713-fa00-46ee-a200-9dc82d0638f8"
},
{
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+ "@id": "urn:3e76f4d2-3306-41b7-8185-10c2a3996597",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
},
{
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"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:ef4d92a2-528c-4884-9e55-9b6f0f020e18"
+ "GeneratedBy": "urn:3b740c47-c0b4-4191-8984-7dceb3d26b76"
},
{
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+ "@id": "urn:2c47c9a9-46b1-4440-a9fe-0c7e20eaa6e2",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
}
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{
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"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:5fee107f-6a26-4850-849e-b57806b77df2"
+ "GeneratedBy": "urn:d9607bb0-f064-4582-839b-f4e8c4476f7d"
},
{
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+ "@id": "urn:244fd1a8-65d6-4b1b-b5e7-9442ce7edb1c",
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"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
}
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{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:46e28345-fd6e-4493-8d14-61325dd2787f",
+ "GeneratedBy": "urn:21fa3ee1-c7b0-4e1b-b2ad-1073d918da77",
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}
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{
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+ "@id": "urn:c7f2560b-59db-404e-9a2d-90b38ef07d05",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
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{
- "@id": "urn:e73ff039-8349-4916-94b3-209aa86d7a3f",
+ "@id": "urn:7944c31b-48a2-4aac-b27a-5187a7b04bd7",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:9138c461-25d9-4077-b2c2-acf0e0cef1fd",
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}
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{
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+ "@id": "urn:1ac09ee3-7059-4f0d-945c-2cb8e55b30e9",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:9f27626b-b95b-4840-a3d2-3c61d7d614f9",
+ "GeneratedBy": "urn:61794c4c-4573-4786-986e-fd6230a40307",
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}
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{
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+ "@id": "urn:62eb0889-4f7f-4b45-afa7-be2f445b4d65",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
}
},
{
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+ "@id": "urn:b3d702bf-d8fc-4bf9-9296-665a627c8d73",
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"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +710,16 @@
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{
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"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:8ef8df32-6435-4171-a299-d223d76c6c6e",
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{
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+ "@id": "urn:f9d32dd5-4528-43c6-a237-1117da783451",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +727,7 @@
}
},
{
- "@id": "urn:3a301cd9-25da-471b-8223-bad090c7347d",
+ "@id": "urn:15baa6b9-1d8a-46b3-bb31-b3c8ca05a87c",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
}
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{
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"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
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@@ -743,16 +743,16 @@
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{
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+ "@id": "urn:9955b7ff-84e8-4bb5-af94-b072f23ec249",
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"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:fa5adf0f-a40a-43dc-b563-398664d6a64e",
+ "GeneratedBy": "urn:788757af-9a31-406d-90d4-025832d851dd",
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@@ -760,34 +760,34 @@
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"AtLocation": "rm.epi.all1",
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@@ -1119,16 +1119,16 @@
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@@ -1136,16 +1136,16 @@
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- "@id": "urn:2e269bf3-ecc6-4bfd-b04c-ddb690e70fdb",
+ "@id": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1161,16 @@
}
},
{
- "@id": "urn:8168ad2f-138b-4b62-99c7-756dbb9cc014",
+ "@id": "urn:76e24d10-75b5-4d38-a1ea-1dfea30ed114",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:a32b44cb-e1b8-40d6-9c78-3aef16006ef5",
+ "GeneratedBy": "urn:37154f93-c242-4db5-ac64-d883928bdcd3",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:2e7bdac9-e43c-43cc-86e4-37ee58774229",
+ "@id": "urn:0c1f173a-a1e8-43ad-942f-d3231383ed70",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1178,25 @@
}
},
{
- "@id": "urn:4f97bf82-b77c-4170-b662-5007fe79ff6b",
+ "@id": "urn:487a1090-9911-41a3-b636-bba8ef69a034",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:72a0b816-a755-4ffc-907d-3aa43568e48f",
+ "GeneratedBy": "urn:447b3e40-4c33-4a46-8121-5c9a3af866aa",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:cd005f13-432d-442b-97fb-05f487b8d394",
+ "@id": "urn:957b2a43-07df-4b2e-942d-783862b74031",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:aa7cc227-1492-4b80-a441-76db5060599b",
+ "GeneratedBy": "urn:c00eeda2-be42-487f-b6e2-28515f578f3e",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:6a60a386-74a3-475a-a222-594448a74486",
+ "@id": "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:a5e9a442-6e07-4e62-aead-07f42bd0f50c",
+ "@id": "urn:f55c118c-56ab-4383-a123-3704c2418a98",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:1a7bf0ee-20cf-41e0-9479-2831210c5957",
+ "GeneratedBy": "urn:b2754ee1-2e63-4e5b-a8e3-eb27e268ea7a",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:3a074d65-3870-4836-8b82-142937eadec0",
+ "@id": "urn:1e0b939a-7f03-4ce5-94d3-ec2db95d67b5",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:bfce5176-4c49-4689-a492-b874f6fb9187",
+ "@id": "urn:e987b7b3-5351-425a-80bd-1c18f436aa05",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:9c9b4cb0-4148-4ac9-abec-285cd3234228",
+ "GeneratedBy": "urn:ba717568-1edd-48b5-886a-54b1c13531dc",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:20adc457-4cb5-47e7-b992-ee701f634086",
+ "@id": "urn:7d15df61-0c90-47a2-b901-a49fb72542ad",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:3639999c-eed2-4529-b8da-8e2e9ae92a0b",
+ "@id": "urn:886a634a-92ae-4b6a-a202-50de6c793825",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:757f4edc-d6f0-4c10-b93f-a62dbdff6c54",
+ "GeneratedBy": "urn:958a9af3-d67a-49c5-be0f-f910d982040b",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:73216f9b-6c6c-4495-898c-b6e33ab2a9f4",
+ "@id": "urn:b90bda86-d4c6-4834-8a69-d115a75f5584",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:ba9ecd0d-21dc-47fa-b7af-24e896b6acbd",
+ "@id": "urn:65b22365-2211-4d46-bfc4-975be5c60659",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:ea89480e-c072-4df9-a9d5-d7ef51adb5ce",
+ "GeneratedBy": "urn:2bfd1d18-9f2e-4320-aaef-09ce4964eab6",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:4eedac58-1578-4f7f-a158-576db499125e",
+ "@id": "urn:0690a611-adcc-4f06-aa92-734143220e88",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:3c19bb11-7590-494e-abd7-3bacb3868ae1",
+ "@id": "urn:6f21e13d-7fd5-41e1-bb1b-8fe9651d57b1",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:79cdd853-fa0c-45bb-b58a-4fa937a6c46c",
+ "GeneratedBy": "urn:8bcccb64-6ecc-4f07-b27e-abb1ee23eb41",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:9e5668f5-2b7b-477c-883e-08a7cf7064c7",
+ "@id": "urn:9ee22513-1fd7-4480-bc21-82a8cc9d6ab3",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:bd82cd22-8ef8-4d4b-b705-233e1e6f43d3",
+ "@id": "urn:ef409fbf-d2a1-4f68-a1ea-d7f905983286",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:b30575e5-b909-41d7-81b2-1c3b1f00624d",
+ "GeneratedBy": "urn:9d0bc8f1-0e14-4d65-bbe5-70599bfa3f9b",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:d11afa04-c763-4db2-99d2-2deb38f3189d",
+ "@id": "urn:9b687564-6599-4fc2-a127-ba19d5e56934",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:e6e2b2a3-2877-473a-ac88-37bc4f7b79e6",
+ "GeneratedBy": "urn:97719e5d-4229-4ff2-8310-05340e8ce878",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:4a128eec-b732-498f-9681-9f876d4f414a",
+ "@id": "urn:0ca14c7d-bdca-4c21-8942-3567d6212845",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:cc3c31ab-c304-46e8-a45d-d21331ec0eba",
+ "GeneratedBy": "urn:29952120-8a6e-40ba-bf71-baf362704948",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:a39b454f-e907-4aa9-8514-34bce78645df",
+ "@id": "urn:3f293e77-c0ee-4d38-8aad-1c5aa4760477",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:8da457f6-6aae-4cbb-8ed8-dd30f4cf4c30",
+ "GeneratedBy": "urn:934df8a7-1b3b-4fda-9cbd-36546f3149ed",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:4a159e34-28e3-4caf-acb3-9d8efe32ce7b",
+ "@id": "urn:ad20686e-7a8c-4964-a10e-799a1c8761c9",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:de3b0abf-5f0c-4836-84f6-bc9644c12c1f",
+ "GeneratedBy": "urn:c774d4f0-4ad3-44d8-b9c5-7775c0dc9776",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:de1871d8-045a-467f-9dc9-e90f0985bb89",
+ "@id": "urn:40800cc0-4c6d-4a57-8d70-9e65b1bb50ca",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:3bb92e5b-81c0-493e-8fbe-ba84c36c346d",
+ "@id": "urn:7b98fe35-6185-46c1-b6ab-218cd580fb53",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:03064a8a-0e28-467d-bbe9-8e9cdba8bc5d",
+ "GeneratedBy": "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_default_proc.png b/examples/from_parsers/afni/afni_default_proc.png
index 0c90d14ce..996441d23 100644
Binary files a/examples/from_parsers/afni/afni_default_proc.png and b/examples/from_parsers/afni/afni_default_proc.png differ
diff --git a/examples/from_parsers/afni/afni_default_proc_block.jsonld b/examples/from_parsers/afni/afni_default_proc_block.jsonld
new file mode 100644
index 000000000..0a99bd926
--- /dev/null
+++ b/examples/from_parsers/afni/afni_default_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:ddfcf1f2-5254-4261-bbd2-ef03ed5bb814",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_p0001/tone_counting_onset_times.txt ./afni_voxelwise_p0001/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_voxelwise_p0001/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:0f49472a-f8ac-456d-b970-2eb57e51efac",
+ "urn:5b90ef67-d464-423c-9769-46fed7afde85",
+ "urn:366c0c52-f6d3-4235-bb8e-05e917613730"
+ ]
+ },
+ {
+ "@id": "urn:191530b0-9eb9-46d7-8143-7d371359a1fc",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_voxelwise_p0001/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:0ea248cd-0b5c-47e6-86ab-b81edcdad19f"
+ ]
+ },
+ {
+ "@id": "urn:660e76f5-e52e-4958-ab9a-ca2aa5d72ee0",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:fe9f2e68-5450-4466-b842-ccc9dd39f6f7",
+ "urn:61509192-5cb3-441a-8c1d-ad52d092302a"
+ ]
+ },
+ {
+ "@id": "urn:ed406cf4-84e0-44ce-b9e3-96c8715b055b",
+ "Label": "tshift",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:fe9f2e68-5450-4466-b842-ccc9dd39f6f7"
+ ]
+ },
+ {
+ "@id": "urn:3cdcb204-61c7-49b5-aaf4-65a14fa0947c",
+ "Label": "align",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:431edd12-cde6-4811-9006-d6fed017d3c5",
+ "urn:ee2408cc-c449-4e10-93d3-7c11e0a58e0f"
+ ]
+ },
+ {
+ "@id": "urn:9706816c-e2a0-4428-a917-403ac5fdf50a",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:c7594a11-495b-4a28-a309-548106b04b0e",
+ "urn:e70dd1e8-a92b-4729-967d-c0dbcba46a21",
+ "urn:9c0ba698-c0c5-4305-977c-d9e1c1862185"
+ ]
+ },
+ {
+ "@id": "urn:7564c2c2-a931-4c72-a838-570247b2b213",
+ "Label": "volreg",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "urn:9c0ba698-c0c5-4305-977c-d9e1c1862185",
+ "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "urn:7dedc9bb-8c86-4990-a6b8-648da3100168",
+ "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "urn:cdecbeaf-18f4-4a48-8375-8486e681054a",
+ "urn:171aa06b-6403-4488-adb4-7f3e89d9caf0",
+ "urn:3ca7ac59-c231-4f0c-87ae-b1e12cd7e06a",
+ "urn:b3ed8412-1e48-46e4-ad7c-4485f55efb2d",
+ "urn:e0ccf79c-c0c8-4648-9c87-5d2049923838",
+ "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "urn:6fa21350-0c53-4a84-a153-14a2afab1044"
+ ]
+ },
+ {
+ "@id": "urn:0a5cfb70-7c38-4790-b0e2-bf22f32161b2",
+ "Label": "blur",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:b6bd7923-5f95-4de9-b336-d38e1ef54915",
+ "urn:f8993cd1-0f00-4bd3-9c0b-b93c14095ac4"
+ ]
+ },
+ {
+ "@id": "urn:8b7c4f4c-d4dc-49ef-8017-965a52f3b076",
+ "Label": "mask",
+ "AssociatedWith": "urn:c11a6fcf-a07d-4398-a82e-a3869ba399d2",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:addaa522-7bef-42e3-a6ac-aef2fa1b260b",
+ "urn:7c06248d-d806-4e4e-944e-78d2a6556e52",
+ "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "urn:73a232e8-f95e-4e7e-9a5d-ed8d542acf01",
+ "urn:6cc2dc97-7d0f-4575-aae6-5ea89fc778b7",
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+ "sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
+ }
+ },
+ {
+ "@id": "urn:7c06248d-d806-4e4e-944e-78d2a6556e52",
+ "Label": "full_mask.$subj",
+ "AtLocation": "full_mask.$subj+tlrc",
+ "digest": {
+ "sha256": "5ccbeeeef88c323d4141cd242861d39ffb389015ad6e1d788a67a1851123fc36"
+ }
+ },
+ {
+ "@id": "urn:fa4621bc-c290-4d99-a4f0-507a34817870",
+ "Label": "blur.epits.1D",
+ "AtLocation": "blur.epits.1D",
+ "GeneratedBy": "urn:f48b9d90-4542-4e86-a17f-230fb813fba2",
+ "digest": {
+ "sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
+ }
+ },
+ {
+ "@id": "urn:771ae86f-2170-4828-b748-e4319401099b",
+ "Label": "blur.errts.1D",
+ "AtLocation": "blur.errts.1D",
+ "GeneratedBy": "urn:f48b9d90-4542-4e86-a17f-230fb813fba2",
+ "digest": {
+ "sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
+ }
+ },
+ {
+ "@id": "urn:5cedd5b4-458c-4276-81ff-476367f5d9a4",
+ "Label": "ClustSim",
+ "AtLocation": "ClustSim",
+ "GeneratedBy": "urn:f48b9d90-4542-4e86-a17f-230fb813fba2",
+ "digest": {
+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:9bb3b3c7-d9e7-4990-b618-54e62cdb8449",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:26c85652-df8e-4d98-8ff4-7a8429f8f216",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:550ce33c-c8c6-470f-ad14-5f94187fffa6",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_default_proc_block.png b/examples/from_parsers/afni/afni_default_proc_block.png
new file mode 100644
index 000000000..ed2a57490
Binary files /dev/null and b/examples/from_parsers/afni/afni_default_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_gam_proc.jsonld b/examples/from_parsers/afni/afni_gam_proc.jsonld
index 6486fa7ad..825fde46a 100644
--- a/examples/from_parsers/afni/afni_gam_proc.jsonld
+++ b/examples/from_parsers/afni/afni_gam_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "@id": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,558 +13,558 @@
],
"Activities": [
{
- "@id": "urn:80b7d24d-5996-4955-9422-ddaca1aa7ffb",
+ "@id": "urn:413e1783-c57d-416f-9594-1b82ef39aa74",
"Label": "Make directory",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:a507c349-230f-4c60-a6c5-16b82223b1f5",
+ "@id": "urn:b5a35ff9-0434-42f2-9b5c-ef7669c25f2b",
"Label": "Make directory",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
+ "@id": "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893",
"Label": "cp",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:6d62c1a8-bb15-4ef4-b4a0-2121a034580e"
+ "urn:1164d63b-cf24-42cc-9f8f-c0ffaee54e74"
]
},
{
- "@id": "urn:7bc6a471-cae3-4f94-a8f2-6547d30e4279",
+ "@id": "urn:619b94b1-3e0e-4b72-828a-317b7c6bebd4",
"Label": "3dcopy",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:8cad6b99-d47b-4d64-88d3-d5135024d8d9"
+ "urn:0e8e8869-93db-4b86-8b5e-08ad3dc1982b"
]
},
{
- "@id": "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
+ "@id": "urn:e2e2d08d-3f8e-4b33-878c-67d75e93a4fa",
"Label": "3dTcat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:83af2c97-1b9c-4d19-8899-bf6d1dbbcbc3"
+ "urn:88abf868-a869-49a3-8dc4-1b3553c7ce81"
]
},
{
- "@id": "urn:e266a5e3-6b72-4e1b-9f60-d17a1bbc757e",
+ "@id": "urn:5d2556b0-25c4-4fcb-8d9e-e104f53f9c3f",
"Label": "3dToutcount",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:a8ac4ccf-6bef-4542-be2d-22e88af9c591"
+ "urn:3ef5d45b-c17d-4f9d-8c55-18a52b42ee5d"
]
},
{
- "@id": "urn:e53e3355-9001-471d-a597-e07049ea64f4",
+ "@id": "urn:d0e85058-717f-4004-9acc-c67b1be914ef",
"Label": "cat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06"
+ "urn:11f9b53f-10ed-481a-bf7c-bb31594d0e05"
]
},
{
- "@id": "urn:b210f01c-8996-4929-9d35-22bfed279734",
+ "@id": "urn:ce28a243-2750-43c3-a199-3011b90864e0",
"Label": "3dTshift",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:a8ac4ccf-6bef-4542-be2d-22e88af9c591"
+ "urn:3ef5d45b-c17d-4f9d-8c55-18a52b42ee5d"
]
},
{
- "@id": "urn:88a41a1d-66fb-452e-b388-09adadae62aa",
+ "@id": "urn:8e03f71c-41e6-46f9-91e6-de2dca2b9098",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:0ee5119d-90af-4a7c-8534-b4aa68c43aa4",
- "urn:599e915d-3120-45bb-8437-acd959e9b2aa"
+ "urn:6738197e-a379-44b2-9f89-57fa3f02ece2",
+ "urn:e3fc347c-23da-42f1-9c1e-0adba15a1643"
]
},
{
- "@id": "urn:d0988a04-e775-488c-aeeb-43257f04f61e",
+ "@id": "urn:23b55492-978b-4682-9b1f-fdd6e001aa8a",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:4397acb5-156a-4edd-93d3-54f9f0c2470a",
- "urn:e3b3345e-497f-4aeb-9b94-f2a7ce135c46"
+ "urn:b7bcd7dc-d322-4027-85b2-9213ca9a7e33",
+ "urn:e335ba2c-7aa9-42f2-9337-9d3fba7ccb43"
]
},
{
- "@id": "urn:3d780a29-7deb-4d27-8073-e716addd31b3",
+ "@id": "urn:b0285abd-bd4b-4e1a-8ef5-e5bb34f5165e",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:84148661-5823-4be4-a8f9-f0182c8a4254"
+ "urn:8fdce449-94ec-4a59-87d3-99b3f061ed36"
]
},
{
- "@id": "urn:e8ac1dda-2b57-4867-a4c5-1d7b501e068c",
+ "@id": "urn:96fa5306-ed18-4062-b390-9a7f9e2e366c",
"Label": "3dvolreg",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6"
+ "urn:d0bc9c2c-90c1-4292-8c34-2a60ec1de777"
]
},
{
- "@id": "urn:156a55d1-9adf-478c-9a01-9fadc0ca23d3",
+ "@id": "urn:312d1c87-774d-4e65-8b24-bbec781ac0c9",
"Label": "3dcalc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6"
+ "urn:d0bc9c2c-90c1-4292-8c34-2a60ec1de777"
]
},
{
- "@id": "urn:0b1cdca2-c124-4120-b5ed-f834e76946a6",
+ "@id": "urn:a4e634ec-6477-4701-8d92-e47373ff5397",
"Label": "cat_matvec",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:84148661-5823-4be4-a8f9-f0182c8a4254"
+ "urn:8fdce449-94ec-4a59-87d3-99b3f061ed36"
]
},
{
- "@id": "urn:e93e5be0-902b-4553-aba7-c605805d1146",
+ "@id": "urn:c6f3ed83-a724-4e2d-a805-0edc6c819be5",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:225eb9ff-dd7e-475a-8f7a-f07148982bb2",
- "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6",
- "urn:6f0b04f1-78e2-477b-8c97-91ac8fcaece8"
+ "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a",
+ "urn:94126632-60e0-4fb2-b4a4-1455377f72ab",
+ "urn:d0bc9c2c-90c1-4292-8c34-2a60ec1de777"
]
},
{
- "@id": "urn:995f49ae-4942-4e6f-83d6-c538a506a7c1",
+ "@id": "urn:e284c753-a44e-4920-8262-671f46d18dce",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:225eb9ff-dd7e-475a-8f7a-f07148982bb2",
- "urn:6f0b04f1-78e2-477b-8c97-91ac8fcaece8",
- "urn:b9bff359-7ed3-42e2-b4c9-c0643d112ddb"
+ "urn:83aa09f4-6318-4e4c-b012-5c1e1d08d425",
+ "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a",
+ "urn:94126632-60e0-4fb2-b4a4-1455377f72ab"
]
},
{
- "@id": "urn:adc60b45-337e-4906-beba-71d2ddc16d4e",
+ "@id": "urn:1aaaecec-a19d-4eae-9167-db3d5a5330c0",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:3f3adb46-2c8c-4af3-9b74-3b228f01bc25"
+ "urn:1ecd2636-c594-447c-9201-8fd7a8f03d69"
]
},
{
- "@id": "urn:0c9384d2-5ea5-411b-9fe3-3d83ebaa506b",
+ "@id": "urn:b5179c0a-3212-4552-8459-4cb76435a9ed",
"Label": "cat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:be84928c-d8ae-4338-bcf4-1ccc2ac748a9"
+ "urn:d19be31a-0d10-4fd8-bbb9-ecb3b04bb630"
]
},
{
- "@id": "urn:0a29010b-055a-4c9f-a691-467dd9a6592e",
+ "@id": "urn:596b4850-0e60-4fef-b836-31859e5acfd6",
"Label": "3dcopy",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:86d21eba-6ad9-444c-80da-f578ccd1e710"
+ "urn:11763a8d-cb69-4341-906a-023ac7c89975"
]
},
{
- "@id": "urn:e088b1af-cf4d-46bd-9312-a5ea52069771",
+ "@id": "urn:e92c4f07-cfee-4817-8dc5-21121c8f647c",
"Label": "3dcalc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:36febdec-c791-4426-8358-dc364642e701",
- "urn:a01d75ac-c17f-4f91-9f22-81e6b3027a66"
+ "urn:b63a4d9e-da22-432f-9425-14e1858c050d",
+ "urn:e26b5930-6e2f-4ec0-9f21-35b13e785b70"
]
},
{
- "@id": "urn:26b6c813-093d-4fba-acee-cb681fa1af8b",
+ "@id": "urn:6f94ef41-9565-416d-95a2-f2227bfac3de",
"Label": "3dcopy",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:6f0b04f1-78e2-477b-8c97-91ac8fcaece8"
+ "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a"
]
},
{
- "@id": "urn:e461db18-e9c3-4b8d-b479-84c6dada49e4",
+ "@id": "urn:e783d302-cb95-45c7-9e72-4cd37fece97d",
"Label": "3dAllineate",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:6e27b1d2-96b8-42e6-965e-395029626f08"
+ "urn:fa8fea7b-fbf6-4d14-8056-1ab07aa17d8c"
]
},
{
- "@id": "urn:adaed242-86b4-4f40-b755-3f0868eba72f",
+ "@id": "urn:7a55f318-70f7-435c-a4c3-a4421da5ad45",
"Label": "3dmerge",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:595e9e51-3851-44c5-ad4b-dbe50c2cba15",
- "urn:ee7a4504-7361-41ed-af89-d735a28b1750"
+ "urn:3088279e-3972-4eba-a902-ec857b348321",
+ "urn:a09a0349-c9d0-4c79-8d0c-60f7a56c2f33"
]
},
{
- "@id": "urn:350b0995-92f9-4e2e-b74d-5a483b619a3d",
+ "@id": "urn:70831a21-9367-4969-b6d0-7a9333bd935d",
"Label": "3dAutomask",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:266145c2-6cc9-4d78-89f4-c69b41d1dbbd"
+ "urn:512d926c-8516-47af-88d1-07e903350c49"
]
},
{
- "@id": "urn:f6724a6c-34c4-473b-b973-7c2ea7f218cb",
+ "@id": "urn:00177879-fe69-465f-b6c1-f0a11477b574",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:04bfadb6-1719-4808-b871-60398db9c3a6",
+ "@id": "urn:4c09be1d-5cbc-4f59-b9ba-9d22cb6a478e",
"Label": "3dresample",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:6f0b04f1-78e2-477b-8c97-91ac8fcaece8",
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091",
+ "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a"
]
},
{
- "@id": "urn:7c4915b1-ff35-4a5e-a569-440e5a5fc1dc",
+ "@id": "urn:44d126c5-0e33-423a-9bc6-0eeb27830d9d",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:c72bb9e6-337f-46f7-8262-4d92ff254cb6"
+ "urn:2ce72d11-51b1-4fef-82d7-02e62be41cfe"
]
},
{
- "@id": "urn:0e62a21a-0210-4e71-97a0-90148b6b759d",
+ "@id": "urn:f1939880-f643-4bfb-95ae-feaba72a6d4d",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:1a942535-5618-4bdc-ba96-e15cfa8f5cef",
- "urn:29e4cde7-2a6d-4eea-b111-f5ef59fa37e5"
+ "urn:17ec0eb3-5e3e-4a09-a2f4-84ca5f8b4752",
+ "urn:87c95662-2ebd-444d-8fa0-4faa70836610"
]
},
{
- "@id": "urn:5062e111-a526-4e9d-b848-7c6ebacd404c",
+ "@id": "urn:88d4bf46-d31e-433c-a6f6-849d5b08a398",
"Label": "3ddot",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:1a942535-5618-4bdc-ba96-e15cfa8f5cef",
- "urn:29e4cde7-2a6d-4eea-b111-f5ef59fa37e5"
+ "urn:17ec0eb3-5e3e-4a09-a2f4-84ca5f8b4752",
+ "urn:87c95662-2ebd-444d-8fa0-4faa70836610"
]
},
{
- "@id": "urn:975122d0-dc5b-4136-9564-a952e4b59436",
+ "@id": "urn:88d87a80-e427-4392-b670-1602b8d45fae",
"Label": "3dresample",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:38e524db-cce5-4263-884b-660ca792543f",
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091",
+ "urn:4bfb75c7-997a-4f9f-b33a-af1843939f5b"
]
},
{
- "@id": "urn:eaf3b170-c710-4fec-b825-95943f0d52c5",
+ "@id": "urn:f58a95a5-b40a-4064-a0ff-8df612775349",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:f6e8f45d-f00b-4355-940f-4fffe2ce660a"
+ "urn:7b140f3d-6abf-41b8-ad5a-22144fa236c2"
]
},
{
- "@id": "urn:a2b8e2be-47b0-445d-be09-276a9f3c96c1",
+ "@id": "urn:fd68f623-a09b-4e5b-aa19-e745c7e03a62",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:266145c2-6cc9-4d78-89f4-c69b41d1dbbd"
+ "urn:512d926c-8516-47af-88d1-07e903350c49"
]
},
{
- "@id": "urn:f6cfe28a-e166-4752-92f0-f7162e671ba1",
+ "@id": "urn:e0a8e579-f99e-458f-821d-5acd22c4a3ba",
"Label": "3dcalc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:266145c2-6cc9-4d78-89f4-c69b41d1dbbd",
- "urn:52abab30-8200-46c1-a7d5-5cd13fa04669",
- "urn:a01d75ac-c17f-4f91-9f22-81e6b3027a66"
+ "urn:512d926c-8516-47af-88d1-07e903350c49",
+ "urn:adc96e19-68de-4e67-a8d8-ff10b9a6ccfd",
+ "urn:b63a4d9e-da22-432f-9425-14e1858c050d"
]
},
{
- "@id": "urn:482e756c-1735-4552-aa69-a61ebd059d85",
+ "@id": "urn:d68b18e4-1c77-4350-be64-28f08db7bb70",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:80ead96e-5334-44ca-a43c-763052f7e42d"
+ "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5"
]
},
{
- "@id": "urn:a9f3eaa0-878b-4b96-9cae-1f2f9bb7d00f",
+ "@id": "urn:be821ff6-4e80-48df-9e6b-29d67cfa2267",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:80ead96e-5334-44ca-a43c-763052f7e42d"
+ "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5"
]
},
{
- "@id": "urn:7bfd59ea-0347-411d-bf0e-18104d70adef",
+ "@id": "urn:8dd07c11-68a6-4653-a5a9-a5222aa7e1d4",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:80ead96e-5334-44ca-a43c-763052f7e42d"
+ "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5"
]
},
{
- "@id": "urn:3c1c1553-6286-4be5-810b-d7bb1aad3ec1",
+ "@id": "urn:9706f591-7f1d-4258-84f9-400fda2b48a4",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:11f44ec4-ef4a-4148-851c-9470e7743b03"
+ "urn:3dac42e9-44c5-49f6-8f9b-31610a861698"
]
},
{
- "@id": "urn:8c0997e2-70f3-4866-a94d-51aa75171c3d",
+ "@id": "urn:748e083f-795d-442f-b1cf-3021e2192314",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:3562deaa-5b0a-48b1-8eaa-afe1d78e7fc4"
+ "urn:3d7b689f-3ef8-40b2-b094-a6f0e0de5710"
]
},
{
- "@id": "urn:08fd597b-f4a7-45bd-979f-e58fef88f940",
+ "@id": "urn:f0e64142-2ee2-4373-860e-9148861a3561",
"Label": "3dTcat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:11f44ec4-ef4a-4148-851c-9470e7743b03"
+ "urn:3dac42e9-44c5-49f6-8f9b-31610a861698"
]
},
{
- "@id": "urn:7038bb21-462d-49e4-8648-b1f551beb4f9",
+ "@id": "urn:7b7743c9-a3c9-4e67-af87-66383d6394dd",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:5121e8ee-779f-4958-a088-9628349736cf"
+ "urn:6c4894c7-3798-4745-a690-665bfb6093a2"
]
},
{
- "@id": "urn:2249bbef-f91d-41b1-ae95-d63b67759bbc",
+ "@id": "urn:bc8fbab4-e820-4f90-9081-1ba940db91d9",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:a4d31d13-6da8-4850-9575-5de3a1280498"
+ "urn:548fb52c-9c65-4932-ae44-f69ae07b3515"
]
},
{
- "@id": "urn:9a4a7929-932f-46fe-a3fe-77c45a06d74b",
+ "@id": "urn:9d094df6-ff9a-47a9-a555-224927dc6da5",
"Label": "3dcalc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:0041442d-735f-4ffe-8ae4-29004a1b4dfb",
- "urn:10aafe1c-8130-438e-a532-2e58da437e99",
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091",
+ "urn:8dd10906-ab30-45b6-b7bd-b140ffc50ba3",
+ "urn:e173ae42-58d0-48a2-82fa-c62929623f78"
]
},
{
- "@id": "urn:7935d373-23a0-4ddf-9106-346d23889ad4",
+ "@id": "urn:795f45f8-355e-4ce1-b896-2ce42d61bd5e",
"Label": "3dTnorm",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:62f97f3b-0511-4475-ac31-0099f01800fa"
+ "urn:3f5a1d1a-02fb-460a-8723-09a384c1d748"
]
},
{
- "@id": "urn:cd1e1f54-9b8d-481a-ab46-dba06afac2a6",
+ "@id": "urn:33f946ac-0009-46c5-8bb6-fe16c933a355",
"Label": "3dmaskave",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:6bca44aa-e57a-4b10-bc56-9a2b0922c588",
+ "@id": "urn:442b6af3-ed0a-47c2-9193-f40d028a9ea5",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:273e3231-0307-4f6b-ad9f-71c617e36b55"
+ "urn:d61eb845-557d-4b68-82b6-39e8f4d07f8c"
]
},
{
- "@id": "urn:5bdc542e-3b26-4f1c-8d64-4b0b147b00a1",
+ "@id": "urn:6572dde2-1994-4eba-a376-62c3349f581f",
"Label": "3dcalc",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:704c3a83-6508-4dcc-a911-ca32105c0e68",
- "urn:b9a3f24e-6935-416e-a55d-0902e4eb5784"
+ "urn:c52a5935-d494-420a-9062-826a8dab2c0c",
+ "urn:f573b6ea-612d-45fd-a896-4b26a7d67667"
]
},
{
- "@id": "urn:eb18da33-1c19-4e8e-a0e5-78055b53b9e5",
+ "@id": "urn:a67cf8f7-40a4-470c-ac4f-e8403f6c09cc",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:cc327189-2989-42fc-94e7-b5d178a5013c"
+ "urn:3f6ac167-493c-4dbb-b116-b5e75a6ae6a9"
]
},
{
- "@id": "urn:a36ed554-5488-48fc-be06-70df64cc8ec0",
+ "@id": "urn:23473f19-2887-4f4e-88e3-ccfa739597f3",
"Label": "1dcat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D",
"Parameters": {},
"Used": [
- "urn:55d1580e-1e33-4f71-889f-ca3253de9185"
+ "urn:a83d0e5f-4f11-45c6-94ab-b6e5c69267d8"
]
},
{
- "@id": "urn:cd9dbba9-5de0-48e7-9f12-fa304ba16d44",
+ "@id": "urn:49dc6666-5f32-487a-a672-291763f85be8",
"Label": "3dTstat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:18751749-1537-427c-9605-143c97185e93"
+ "urn:d9158bd6-6e62-4c76-82ee-8e24d9637a32"
]
},
{
- "@id": "urn:1fa44076-4389-4924-ab08-7cddf5656426",
+ "@id": "urn:6318e784-8873-4577-a8ec-ef187f68f5cd",
"Label": "1dcat",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:18751749-1537-427c-9605-143c97185e93"
+ "urn:d9158bd6-6e62-4c76-82ee-8e24d9637a32"
]
},
{
- "@id": "urn:99c997b4-e99a-468e-9bb5-e3157f75c708",
+ "@id": "urn:3de1f21e-79b4-4fe7-8b75-d771ae5637c1",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091"
]
},
{
- "@id": "urn:21785f36-0629-4cc3-a83b-2de18aac9d52",
+ "@id": "urn:99b1db24-3ebe-4d24-9bd4-4e1f6018c449",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091"
]
},
{
- "@id": "urn:68db26d2-85c8-4e1c-82ef-57b20a491822",
+ "@id": "urn:801d9025-851e-4ae3-88cc-c846408d6be6",
"Label": "3dClustSim",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:b231ed1a-43de-4a7f-b1fc-46d2dc47a058"
+ "urn:21599809-901f-409d-beb8-f9892d2c9091"
]
},
{
- "@id": "urn:5efcfaa0-9adb-4029-913f-25636acc25d1",
+ "@id": "urn:ae285646-f8c3-4275-ac7c-7b41cab822f8",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:0ac3c052-6f41-4547-870f-93b91ef0a84c"
+ "urn:bc8e8f41-1fd3-4773-b782-847b5d9487df"
]
},
{
- "@id": "urn:eb92f9df-ef75-491e-928e-c8328bd4532d",
+ "@id": "urn:b39c4b22-aece-40b1-a3a5-971be243f2bc",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857",
+ "AssociatedWith": "urn:3a6084be-8807-4dd7-86f7-d691b36e7ef9",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -575,22 +575,22 @@
],
"Entities": [
{
- "@id": "urn:2c5bec6e-f8bb-4c29-9ba0-2c37fff9df0f",
+ "@id": "urn:fe451eab-ab28-4f5f-8e5f-98855e0ed4a8",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:80b7d24d-5996-4955-9422-ddaca1aa7ffb",
+ "GeneratedBy": "urn:413e1783-c57d-416f-9594-1b82ef39aa74",
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{
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+ "@id": "urn:12efd317-2a31-4854-b0c0-60c333623961",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:a507c349-230f-4c60-a6c5-16b82223b1f5"
+ "GeneratedBy": "urn:b5a35ff9-0434-42f2-9b5c-ef7669c25f2b"
},
{
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+ "@id": "urn:1164d63b-cf24-42cc-9f8f-c0ffaee54e74",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_gam/tone_counting_onset_times.txt",
"digest": {
@@ -598,13 +598,13 @@
}
},
{
- "@id": "urn:f81101f9-c210-4bcc-99f6-7041f1243173",
+ "@id": "urn:af38b1c5-cfab-4f4c-a109-1cebae93f287",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a"
+ "GeneratedBy": "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893"
},
{
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+ "@id": "urn:0e8e8869-93db-4b86-8b5e-08ad3dc1982b",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_gam/sub-01_T1w.nii.gz",
"digest": {
@@ -612,13 +612,13 @@
}
},
{
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+ "@id": "urn:e78802d6-1bb2-429f-bd2e-590f9ca87a83",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:7bc6a471-cae3-4f94-a8f2-6547d30e4279"
+ "GeneratedBy": "urn:619b94b1-3e0e-4b72-828a-317b7c6bebd4"
},
{
- "@id": "urn:83af2c97-1b9c-4d19-8899-bf6d1dbbcbc3",
+ "@id": "urn:88abf868-a869-49a3-8dc4-1b3553c7ce81",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -626,13 +626,13 @@
}
},
{
- "@id": "urn:e62f2f62-daec-431c-9d29-0637e470bbe4",
+ "@id": "urn:79564ced-7998-4380-8c8f-3269d12b864f",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582"
+ "GeneratedBy": "urn:e2e2d08d-3f8e-4b33-878c-67d75e93a4fa"
},
{
- "@id": "urn:a8ac4ccf-6bef-4542-be2d-22e88af9c591",
+ "@id": "urn:3ef5d45b-c17d-4f9d-8c55-18a52b42ee5d",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -640,16 +640,16 @@
}
},
{
- "@id": "urn:d2bb77c1-5c5e-4898-b1ff-ba2ed3a5ee79",
+ "@id": "urn:493995db-4752-45aa-a7fe-8c271ece8525",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:e266a5e3-6b72-4e1b-9f60-d17a1bbc757e",
+ "GeneratedBy": "urn:5d2556b0-25c4-4fcb-8d9e-e104f53f9c3f",
"digest": {
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}
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{
- "@id": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "@id": "urn:11f9b53f-10ed-481a-bf7c-bb31594d0e05",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -657,25 +657,25 @@
}
},
{
- "@id": "urn:7ab27c3b-15b3-4627-9472-87f3d9bfb6ad",
+ "@id": "urn:1da1246e-8f5c-4ddb-a27f-be71f0701162",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:e53e3355-9001-471d-a597-e07049ea64f4",
+ "GeneratedBy": "urn:d0e85058-717f-4004-9acc-c67b1be914ef",
"digest": {
"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
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{
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+ "@id": "urn:a6fece11-f37d-4d67-86a2-f2789092ab56",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:b210f01c-8996-4929-9d35-22bfed279734",
+ "GeneratedBy": "urn:ce28a243-2750-43c3-a199-3011b90864e0",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
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{
- "@id": "urn:0ee5119d-90af-4a7c-8534-b4aa68c43aa4",
+ "@id": "urn:e3fc347c-23da-42f1-9c1e-0adba15a1643",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -683,7 +683,7 @@
}
},
{
- "@id": "urn:599e915d-3120-45bb-8437-acd959e9b2aa",
+ "@id": "urn:6738197e-a379-44b2-9f89-57fa3f02ece2",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -691,16 +691,16 @@
}
},
{
- "@id": "urn:30e8139b-7269-475c-9d90-595aa758dad6",
+ "@id": "urn:05b977f9-3054-4c8c-bca4-36bab8c25375",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:88a41a1d-66fb-452e-b388-09adadae62aa",
+ "GeneratedBy": "urn:8e03f71c-41e6-46f9-91e6-de2dca2b9098",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
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{
- "@id": "urn:4397acb5-156a-4edd-93d3-54f9f0c2470a",
+ "@id": "urn:e335ba2c-7aa9-42f2-9337-9d3fba7ccb43",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -708,7 +708,7 @@
}
},
{
- "@id": "urn:e3b3345e-497f-4aeb-9b94-f2a7ce135c46",
+ "@id": "urn:b7bcd7dc-d322-4027-85b2-9213ca9a7e33",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -716,7 +716,7 @@
}
},
{
- "@id": "urn:84148661-5823-4be4-a8f9-f0182c8a4254",
+ "@id": "urn:8fdce449-94ec-4a59-87d3-99b3f061ed36",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -724,16 +724,16 @@
}
},
{
- "@id": "urn:6e27b1d2-96b8-42e6-965e-395029626f08",
+ "@id": "urn:fa8fea7b-fbf6-4d14-8056-1ab07aa17d8c",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:3d780a29-7deb-4d27-8073-e716addd31b3",
+ "GeneratedBy": "urn:b0285abd-bd4b-4e1a-8ef5-e5bb34f5165e",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
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{
- "@id": "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6",
+ "@id": "urn:d0bc9c2c-90c1-4292-8c34-2a60ec1de777",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -741,34 +741,34 @@
}
},
{
- "@id": "urn:4fa706ea-7266-466f-a385-6e846c870d1b",
+ "@id": "urn:7bfb70e4-dd28-457b-9115-c026d7b0e481",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:e8ac1dda-2b57-4867-a4c5-1d7b501e068c",
+ "GeneratedBy": "urn:96fa5306-ed18-4062-b390-9a7f9e2e366c",
"digest": {
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}
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{
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+ "@id": "urn:94db4235-003c-488b-b589-6f29a7bd444f",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:156a55d1-9adf-478c-9a01-9fadc0ca23d3",
+ "GeneratedBy": "urn:312d1c87-774d-4e65-8b24-bbec781ac0c9",
"digest": {
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}
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{
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+ "@id": "urn:94126632-60e0-4fb2-b4a4-1455377f72ab",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:0b1cdca2-c124-4120-b5ed-f834e76946a6",
+ "GeneratedBy": "urn:a4e634ec-6477-4701-8d92-e47373ff5397",
"digest": {
"sha256": "7c536b6f582a067c718f9e5ea2566cb535c73b43b4e15116c4c46045734d6eee"
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{
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+ "@id": "urn:8c3dac7c-7b0c-46e3-bd94-66387114869a",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -776,16 +776,16 @@
}
},
{
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+ "@id": "urn:3f57ec61-e1a1-43d0-8fb9-75d582643f56",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:e93e5be0-902b-4553-aba7-c605805d1146",
+ "GeneratedBy": "urn:c6f3ed83-a724-4e2d-a805-0edc6c819be5",
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}
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{
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+ "@id": "urn:83aa09f4-6318-4e4c-b012-5c1e1d08d425",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -793,16 +793,16 @@
}
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{
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+ "@id": "urn:8c8352e6-2511-46a9-8127-c252ae9ce1e7",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:995f49ae-4942-4e6f-83d6-c538a506a7c1",
+ "GeneratedBy": "urn:e284c753-a44e-4920-8262-671f46d18dce",
"digest": {
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}
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{
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+ "@id": "urn:1ecd2636-c594-447c-9201-8fd7a8f03d69",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -810,16 +810,16 @@
}
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{
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+ "@id": "urn:658a862e-4043-4eca-9aa3-fa687a36306f",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:adc60b45-337e-4906-beba-71d2ddc16d4e",
+ "GeneratedBy": "urn:1aaaecec-a19d-4eae-9167-db3d5a5330c0",
"digest": {
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}
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{
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+ "@id": "urn:d19be31a-0d10-4fd8-bbb9-ecb3b04bb630",
"Label": "dfile.r*.1D",
"AtLocation": "dfile.r*.1D",
"digest": {
@@ -827,16 +827,16 @@
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{
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+ "@id": "urn:772cb077-7825-45a0-8ded-70a44fd2dcf5",
"Label": "dfile_rall.1D",
"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:0c9384d2-5ea5-411b-9fe3-3d83ebaa506b",
+ "GeneratedBy": "urn:b5179c0a-3212-4552-8459-4cb76435a9ed",
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{
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+ "@id": "urn:11763a8d-cb69-4341-906a-023ac7c89975",
"Label": "rm.epi.min.r01",
"AtLocation": "rm.epi.min.r01+tlrc",
"digest": {
@@ -844,16 +844,16 @@
}
},
{
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+ "@id": "urn:0a275e5c-c0d9-4118-b74f-803b5bc6cce4",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:0a29010b-055a-4c9f-a691-467dd9a6592e",
+ "GeneratedBy": "urn:596b4850-0e60-4fef-b836-31859e5acfd6",
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{
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+ "@id": "urn:e26b5930-6e2f-4ec0-9f21-35b13e785b70",
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"digest": {
@@ -861,7 +861,7 @@
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{
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+ "@id": "urn:b63a4d9e-da22-432f-9425-14e1858c050d",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents+tlrc",
"digest": {
@@ -869,34 +869,34 @@
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@@ -1236,16 +1236,16 @@
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"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1253,52 +1253,52 @@
}
},
{
- "@id": "urn:2ada9729-6572-4dff-b711-2397a07617e3",
+ "@id": "urn:323f4cd3-efa6-4fa6-834a-5e176620c273",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:cd9dbba9-5de0-48e7-9f12-fa304ba16d44",
+ "GeneratedBy": "urn:49dc6666-5f32-487a-a672-291763f85be8",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:f19716f5-039f-45fe-a46d-a39bde4da5fe",
+ "@id": "urn:eae5a68d-7651-46bc-909d-5dfcdec7a79b",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:1fa44076-4389-4924-ab08-7cddf5656426",
+ "GeneratedBy": "urn:6318e784-8873-4577-a8ec-ef187f68f5cd",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:0a4ff98b-cab9-4436-8cca-245bbc203236",
+ "@id": "urn:94a0d682-a073-4bea-abb0-c40a416bae72",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:99c997b4-e99a-468e-9bb5-e3157f75c708",
+ "GeneratedBy": "urn:3de1f21e-79b4-4fe7-8b75-d771ae5637c1",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:e6f949ee-3bc5-4f71-bbe5-d8a73afff672",
+ "@id": "urn:224b5b68-7dcd-4d3a-94d6-269fb988b937",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:21785f36-0629-4cc3-a83b-2de18aac9d52",
+ "GeneratedBy": "urn:99b1db24-3ebe-4d24-9bd4-4e1f6018c449",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:dc7e9182-537e-4e7e-8b63-8ce1b3041ae9",
+ "@id": "urn:b25e9de1-546f-4524-b6c2-5c27c995a79a",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:68db26d2-85c8-4e1c-82ef-57b20a491822",
+ "GeneratedBy": "urn:801d9025-851e-4ae3-88cc-c846408d6be6",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:0ac3c052-6f41-4547-870f-93b91ef0a84c",
+ "@id": "urn:bc8e8f41-1fd3-4773-b782-847b5d9487df",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1306,10 +1306,10 @@
}
},
{
- "@id": "urn:b12172b5-b120-4960-9e98-588064fe5d3d",
+ "@id": "urn:b6add10e-cf76-4004-ba18-ed21ee112374",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:eb92f9df-ef75-491e-928e-c8328bd4532d",
+ "GeneratedBy": "urn:b39c4b22-aece-40b1-a3a5-971be243f2bc",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_gam_proc.png b/examples/from_parsers/afni/afni_gam_proc.png
index b5d9a832f..f23015a5b 100644
Binary files a/examples/from_parsers/afni/afni_gam_proc.png and b/examples/from_parsers/afni/afni_gam_proc.png differ
diff --git a/examples/from_parsers/afni/afni_gam_proc_block.jsonld b/examples/from_parsers/afni/afni_gam_proc_block.jsonld
new file mode 100644
index 000000000..7f00c9c83
--- /dev/null
+++ b/examples/from_parsers/afni/afni_gam_proc_block.jsonld
@@ -0,0 +1,973 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:517a16eb-aa7f-4d32-8cd0-19db3ce2d355",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_gam/tone_counting_onset_times.txt $output_dir/stimuli; 3dcopy ./afni_gam/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:23c781ca-5477-4809-a1d1-521c42d06e6b",
+ "urn:de11a3ef-48eb-49af-8f70-74c35c37293a"
+ ]
+ },
+ {
+ "@id": "urn:ec085929-3a73-462c-837f-7b8ada04bdf4",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_gam/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:094008b5-3212-4aec-955d-717f4da89d2b"
+ ]
+ },
+ {
+ "@id": "urn:18bd9c7d-706e-46b0-9ef8-d845970d2f31",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:9c136708-8d68-4f75-a608-dc20ffc91b24",
+ "urn:00950c27-cd02-4bcf-a2f6-971b963c5868"
+ ]
+ },
+ {
+ "@id": "urn:a00d33e9-976c-4da2-bfd5-c323f5de4e6d",
+ "Label": "tshift",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:9c136708-8d68-4f75-a608-dc20ffc91b24"
+ ]
+ },
+ {
+ "@id": "urn:f1e10c64-fe4a-4263-b044-ebe6c840ffbf",
+ "Label": "align",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:b4a10ef4-4baf-42f7-9e81-f01844258b08",
+ "urn:cbf092fe-95f6-4477-a6d8-4ba609793da0"
+ ]
+ },
+ {
+ "@id": "urn:58eb8130-38d3-46cc-8a21-e4b5ff740ae4",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:4a3c2dd0-cd1a-4c81-84bf-68a9a4bb0ade",
+ "urn:90269c60-8ebf-417a-956f-6f48ef242e83",
+ "urn:0262d432-75d4-4d96-be19-e7bf0a821d30"
+ ]
+ },
+ {
+ "@id": "urn:9a8c6a5d-e331-49ee-9cbf-7aae85f6c449",
+ "Label": "volreg",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:2d85001c-40b1-466a-a9b6-372c7325ab1f",
+ "urn:2d85001c-40b1-466a-a9b6-372c7325ab1f",
+ "urn:0262d432-75d4-4d96-be19-e7bf0a821d30",
+ "urn:2d85001c-40b1-466a-a9b6-372c7325ab1f",
+ "urn:82f1696b-c28a-4313-9689-1038773c2bd0",
+ "urn:82f1696b-c28a-4313-9689-1038773c2bd0",
+ "urn:9eca7ae7-6ffe-446a-8603-7137fd4e4ee9",
+ "urn:8596c632-de2b-47b7-b261-0bcc1b11efb4",
+ "urn:16bf4939-3694-4686-af30-f2acf3976d7b",
+ "urn:12d262d4-d471-4599-a49d-b4cc3e0afab2",
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+ "urn:d9e0442e-5d73-4c85-8e4d-66f08337e10b",
+ "urn:82f1696b-c28a-4313-9689-1038773c2bd0",
+ "urn:68e0ea2d-b170-4e4d-914f-6fafeb106edd"
+ ]
+ },
+ {
+ "@id": "urn:1050fa11-dffe-4880-bdee-9ad82afbd4dc",
+ "Label": "blur",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:66c6f4a5-e5db-46b2-b07c-e741461d17cd",
+ "urn:e292cc0c-ded7-4fa3-ab9e-51890896d4dc"
+ ]
+ },
+ {
+ "@id": "urn:d59b253f-3a7c-4189-a01e-63f44ed5706b",
+ "Label": "mask",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:47364376-8009-46b5-9c2c-50f39f9aa7b7",
+ "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "urn:82f1696b-c28a-4313-9689-1038773c2bd0",
+ "urn:a1b2679b-c5c0-441b-a89d-c14f0248f813",
+ "urn:18a3d038-b80d-44fc-9706-301753499bc1",
+ "urn:42d9c5ac-c680-4d9a-ad99-b824a3b0f394",
+ "urn:18a3d038-b80d-44fc-9706-301753499bc1",
+ "urn:42d9c5ac-c680-4d9a-ad99-b824a3b0f394",
+ "urn:44cd8e21-b13b-4286-b2af-f17a942c5a99",
+ "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "urn:107e60e5-e48c-440a-b943-4a2265ab0c43"
+ ]
+ },
+ {
+ "@id": "urn:1e1b8b6a-4f33-4ce5-b008-9056f9eade30",
+ "Label": "scale",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:47364376-8009-46b5-9c2c-50f39f9aa7b7",
+ "urn:47364376-8009-46b5-9c2c-50f39f9aa7b7",
+ "urn:521a1422-bf72-4868-a196-36ea32e32333",
+ "urn:d9e0442e-5d73-4c85-8e4d-66f08337e10b"
+ ]
+ },
+ {
+ "@id": "urn:5174fcd8-825d-46ed-a9f2-6b364163d866",
+ "Label": "regress",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 7 -stim_times 1 stimuli/tone_counting_onset_times.txt 'GAM' -stim_label 1 tone_counting_onset_times.txt -stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting_onset_times.txt.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
+ "Used": [
+ "urn:77134def-200f-4e91-bf5b-5beae8522368",
+ "urn:77134def-200f-4e91-bf5b-5beae8522368",
+ "urn:77134def-200f-4e91-bf5b-5beae8522368",
+ "urn:e260306a-0d19-4ee0-9fc1-08f7c3aa2ec3",
+ "urn:e260306a-0d19-4ee0-9fc1-08f7c3aa2ec3",
+ "urn:8552e2e6-e17e-4c59-a484-215e804f9bc9",
+ "urn:993a79b8-7882-4321-8efe-8cd8a183e117",
+ "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "urn:9c267539-9f5e-4c6a-820b-652610506db1",
+ "urn:fe43eb18-b0fc-4dfc-9d79-e154b0bf1b40",
+ "urn:f96391da-8ad6-4968-90fc-e3e5e9d1f810",
+ "urn:4a586b50-9b84-4d1c-ae6a-04112b3056b3",
+ "urn:f5ff2181-2e0f-41da-93d1-7d37e905c7d1",
+ "urn:ad457a1a-305f-48e0-944c-307688941533",
+ "urn:8ffaad12-2674-47c2-b699-94f587264526",
+ "urn:9631dcb3-1dd3-4164-9c1b-c5b05917345a",
+ "urn:9631dcb3-1dd3-4164-9c1b-c5b05917345a"
+ ]
+ },
+ {
+ "@id": "urn:b0783160-cc25-4f90-87b0-62ea91dd364e",
+ "Label": "blur estimation",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
+ "Used": [
+ "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "urn:816045b3-2730-4afa-9cce-255578e9966f",
+ "urn:816045b3-2730-4afa-9cce-255578e9966f"
+ ]
+ },
+ {
+ "@id": "urn:fffdce39-1022-4364-aa1b-182e4f764878",
+ "Label": "auto block: generate review scripts",
+ "AssociatedWith": "urn:14991fc3-e30f-47f0-9d6e-afb462969a4e",
+ "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
+ "Used": [
+ "urn:32cbe895-a1a0-47d4-a58b-7ec37bc724b9"
+ ]
+ }
+ ],
+ "Entities": [
+ {
+ "@id": "urn:23c781ca-5477-4809-a1d1-521c42d06e6b",
+ "Label": "tone_counting_onset_times.txt",
+ "AtLocation": "./afni_gam/tone_counting_onset_times.txt",
+ "digest": {
+ "sha256": "6e1ea835097a723ebd7334a524942c94bde686ce98714ccc096c9457c3ec4bd6"
+ }
+ },
+ {
+ "@id": "urn:de11a3ef-48eb-49af-8f70-74c35c37293a",
+ "Label": "sub-01_T1w.nii.gz",
+ "AtLocation": "./afni_gam/sub-01_T1w.nii.gz",
+ "digest": {
+ "sha256": "0385daac07d47e066fc31192871eea6c37f75fc8c2f32ccbdb0a6d74e787207d"
+ }
+ },
+ {
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diff --git a/examples/from_parsers/afni/afni_gam_proc_block.png b/examples/from_parsers/afni/afni_gam_proc_block.png
new file mode 100644
index 000000000..858496bdb
Binary files /dev/null and b/examples/from_parsers/afni/afni_gam_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
index 989d12afb..acbd0378d 100644
--- a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
+++ b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.jsonld
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+ "@id": "urn:9fc62455-73dd-4732-8555-2a83319f69e3",
"Label": "3dTshift",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:014fe3ba-316e-4ce6-96ab-9c588e9e3376"
+ "urn:a40f9ca3-df62-492c-982a-3add9b872a76"
]
},
{
- "@id": "urn:51fd66c2-887c-4586-9153-c4330b011c21",
+ "@id": "urn:4754665a-16eb-480f-bfcd-88b9d170d65a",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:86fd4be2-654d-4f6d-8dcf-1c8eaf851151",
- "urn:c92f09a2-3673-461a-b213-7e6e77ae9127"
+ "urn:29663157-072a-468b-9e47-921f47d9e875",
+ "urn:afaaa713-1d26-4313-a970-3feebd8700eb"
]
},
{
- "@id": "urn:f8cbfb50-209b-45f0-af1c-cb1e8654524f",
+ "@id": "urn:2b1a7ae1-af74-4c55-b949-3d417afdf260",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:444b3aef-bed6-43e5-820a-7d79e2d179c9",
- "urn:8975ee46-f44f-4c13-81e8-c5cd1a35d9fa"
+ "urn:4f3d0144-7485-4165-a2fe-005b88ebf5e6",
+ "urn:6aedf88b-6fe2-45d4-b5b7-28bf7c208071"
]
},
{
- "@id": "urn:cda9ebcc-abd5-4d2a-b0dc-3b2680aa1967",
+ "@id": "urn:41a204e9-1848-4df7-93a1-c30b986f3042",
"Label": "cat_matvec",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:40b50dc9-2f0a-4a54-8f74-308039d60ecd"
+ "urn:73011544-3c7b-40fc-a4e2-4875797a05ab"
]
},
{
- "@id": "urn:af761f7e-80af-4622-bb60-411065c9e5d1",
+ "@id": "urn:7d32a82f-24af-4bee-91b0-02ee1102c9f5",
"Label": "3dvolreg",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:4ce7cdba-5a0b-4246-8ee3-840b44f92bf6"
+ "urn:70ffec24-924a-4cd7-844c-044fb416aad9"
]
},
{
- "@id": "urn:e6aad8a6-9056-4e8e-b591-ba2a4094b8a0",
+ "@id": "urn:0552d4c0-6c50-45cc-bcbb-d0fff1a58c2e",
"Label": "3dcalc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:4ce7cdba-5a0b-4246-8ee3-840b44f92bf6"
+ "urn:70ffec24-924a-4cd7-844c-044fb416aad9"
]
},
{
- "@id": "urn:fd1716f5-9c7a-4f67-869a-1c5dd7aea8ca",
+ "@id": "urn:0af4a5a4-304f-4649-87b3-1dc04d628fed",
"Label": "cat_matvec",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:40b50dc9-2f0a-4a54-8f74-308039d60ecd"
+ "urn:73011544-3c7b-40fc-a4e2-4875797a05ab"
]
},
{
- "@id": "urn:9b4436bc-3b0f-4b8f-ba17-18aac004a520",
+ "@id": "urn:06728249-4ffc-4603-b140-7caa08e743c2",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:0a7647fc-2cdc-4fa3-b082-e96971482634",
- "urn:4ce7cdba-5a0b-4246-8ee3-840b44f92bf6",
- "urn:c073483a-c70c-494e-bc37-5a2327064f06"
+ "urn:190b6895-634d-4cd9-9869-84a4418e0b03",
+ "urn:70ffec24-924a-4cd7-844c-044fb416aad9",
+ "urn:81b4feac-9606-47d8-8017-e256fb9fb699"
]
},
{
- "@id": "urn:2a93e9d8-8d47-40af-8bcf-eaf983b9add1",
+ "@id": "urn:4012b491-3ae3-4848-8074-bfa332f439e7",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:0a7647fc-2cdc-4fa3-b082-e96971482634",
- "urn:c073483a-c70c-494e-bc37-5a2327064f06",
- "urn:c879c188-eaba-4d99-a76b-7031e921db86"
+ "urn:190b6895-634d-4cd9-9869-84a4418e0b03",
+ "urn:81b4feac-9606-47d8-8017-e256fb9fb699",
+ "urn:ae1ca939-9a9a-4d62-b535-cafd3fa44a68"
]
},
{
- "@id": "urn:b1d3f413-1a3f-4a66-8cee-b24bfdb8d5ea",
+ "@id": "urn:bdc3428f-9888-480f-abf0-64468fa52057",
"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:075b19d7-cccb-49e7-a9c8-4a0abc906eab"
+ "urn:2882c8ed-c1db-4ef4-8981-d39df13b5080"
]
},
{
- "@id": "urn:bfc5f78d-f8d3-4eee-8fd5-8835562215ba",
+ "@id": "urn:3eafcf21-6255-4ba7-bd80-78455dd0f901",
"Label": "cat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:d48a8eec-56b1-4aa8-af22-922fc27586e6"
+ "urn:8dbbbca1-8bc2-4b0e-a357-1e05f5c0fc1f"
]
},
{
- "@id": "urn:7ab095d7-8d81-4df7-aa9f-2167bce867fc",
+ "@id": "urn:0813e30b-9cdc-415d-b3cd-0645ea508097",
"Label": "3dcopy",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:c504956f-4b7b-4992-abbd-46b5fc4f8a21"
+ "urn:6deda758-ef02-498f-a4a6-535b3f4fb043"
]
},
{
- "@id": "urn:5f12525b-764a-4493-b764-0c8b7057963b",
+ "@id": "urn:21411b96-1a6e-4640-8ea1-69e64343c162",
"Label": "3dcalc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:a92420ab-a033-4844-a6f7-39500db2e482",
- "urn:d749afb2-7262-4434-9504-06cb313cac64"
+ "urn:7caddf4f-423b-4db3-b628-cbac240104b3",
+ "urn:edb1bdc5-b136-41ad-8df7-ac98335d54b7"
]
},
{
- "@id": "urn:a04f7934-f7bc-4170-b2eb-5c6c732b5848",
+ "@id": "urn:1b3ad86b-c8fb-4714-8d00-bafd6168d6ca",
"Label": "3dcopy",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:0a7647fc-2cdc-4fa3-b082-e96971482634"
+ "urn:81b4feac-9606-47d8-8017-e256fb9fb699"
]
},
{
- "@id": "urn:314e11c6-9e73-48fd-80b8-5255796a06d1",
+ "@id": "urn:cefc4a69-2580-432a-9712-462d38e98ed3",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:44d37560-44a4-474b-a529-7de437cb6c75"
+ "urn:7d32da7c-f063-4104-9d88-ae97dd8e5608"
]
},
{
- "@id": "urn:a6811528-b35b-46f8-8c64-c27db6cc51f3",
+ "@id": "urn:d1ea45e7-a812-4de4-9c30-1ec9a59e9d41",
"Label": "3dmerge",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:35b68be2-b883-4bde-9698-c01bc4e682f7",
- "urn:79083b6e-477d-460c-a565-c07d683b963f"
+ "urn:986f8c11-eedf-404b-bea2-fad45a7d6986",
+ "urn:b405b370-8eaa-48b0-92c3-fcbba8236113"
]
},
{
- "@id": "urn:b1798fa5-41c3-4c32-af33-ba038526e4b9",
+ "@id": "urn:77e850b5-6812-461e-93f0-580c0bd99f98",
"Label": "3dAutomask",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:ffb2acef-8473-4ab4-8b06-f476123def32"
+ "urn:529e73e1-7848-46e1-b58f-24e6441cdb1e"
]
},
{
- "@id": "urn:f1ad28d0-6c5d-4619-ac2a-c7f4bee41ea6",
+ "@id": "urn:a443387d-ae1c-47b0-be9f-f85b0fd90438",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:cc3659dd-8933-41f9-b132-b2a64e91ffaf",
+ "@id": "urn:118fb4ec-dde5-416b-aba9-4dad18c4c6ed",
"Label": "3dresample",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:0a7647fc-2cdc-4fa3-b082-e96971482634",
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e"
+ "urn:81b4feac-9606-47d8-8017-e256fb9fb699",
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
]
},
{
- "@id": "urn:89d4725b-2aa6-443d-a502-65b941ec8bdc",
+ "@id": "urn:0b7c6124-4e20-4583-ad3f-b7cacb34ed43",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:16b45600-eb00-4a51-a6be-8d47329b96a3"
+ "urn:e2e35562-610f-4238-bbea-f339229b4f33"
]
},
{
- "@id": "urn:f58e75d3-583d-4af3-8ec2-e280fef8a6c7",
+ "@id": "urn:dd4cd79c-c8c5-4f25-b7fd-0fe1731c5694",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:e5081baa-1acc-4ca1-b4e0-b504d7fed955",
- "urn:ff6a8b57-ac8c-4df4-b617-4b3a0b2bc2b9"
+ "urn:0519e719-8734-4119-b7e1-c2ae7ecb72ab",
+ "urn:457d391d-f8af-4766-94cd-9b534bda02f2"
]
},
{
- "@id": "urn:cd99b9e2-3b36-46e3-95ec-8cb54f617d02",
+ "@id": "urn:97e65b94-ae5f-4f1f-8829-877b3f883ff4",
"Label": "3ddot",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:e5081baa-1acc-4ca1-b4e0-b504d7fed955",
- "urn:ff6a8b57-ac8c-4df4-b617-4b3a0b2bc2b9"
+ "urn:0519e719-8734-4119-b7e1-c2ae7ecb72ab",
+ "urn:457d391d-f8af-4766-94cd-9b534bda02f2"
]
},
{
- "@id": "urn:e43a2d82-17b0-4519-90f0-4792c2240a1b",
+ "@id": "urn:5bb8508a-eda5-4365-81fb-999ffd24853e",
"Label": "3dresample",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/cmaumet/Softs/external/AFNI/macosx_10.7_Intel_64/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
- "urn:7aa0c7ac-09a1-460d-9ee8-49068220f007"
+ "urn:1f98c4b0-daf2-4e68-9c91-1148e6a5e140",
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
]
},
{
- "@id": "urn:25110572-7c22-4331-a8df-051904b8d272",
+ "@id": "urn:4830f327-2309-4954-8099-23d6077d7c00",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:e27a29e8-02ac-43cb-8f10-e82b13654dc8"
+ "urn:c4c118f0-ce74-41f3-910b-79f9f4d747eb"
]
},
{
- "@id": "urn:23978496-a117-4025-93da-ba42dba39567",
+ "@id": "urn:e61bbb8d-d5d3-4835-958e-c7de860c6474",
"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:ffb2acef-8473-4ab4-8b06-f476123def32"
+ "urn:529e73e1-7848-46e1-b58f-24e6441cdb1e"
]
},
{
- "@id": "urn:aa934436-fe38-49ec-a181-f803adf4cb19",
+ "@id": "urn:99fdddd9-cb59-44fc-a275-ee3393b74160",
"Label": "3dcalc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:a92420ab-a033-4844-a6f7-39500db2e482",
- "urn:bc49a77f-927c-4ccd-8959-e00cae2dbe65",
- "urn:ffb2acef-8473-4ab4-8b06-f476123def32"
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]
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{
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+ "@id": "urn:f95a770c-8509-4d92-9064-08ba635398ef",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
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"Parameters": {},
"Used": [
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]
},
{
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"Label": "1d_tool.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
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"Parameters": {},
"Used": [
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]
},
{
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"Label": "1d_tool.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
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"Parameters": {},
"Used": [
- "urn:604a1e3b-15de-497b-a525-ca9bd99f2a09"
+ "urn:7ceb1b7b-507f-432b-a8ee-af9cc600339d"
]
},
{
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"Label": "3dDeconvolve",
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"Parameters": {},
"Used": [
- "urn:049ce5bc-724a-4c47-9d72-b77a52f94361"
+ "urn:130b200a-a004-4ac6-917b-fae4be88252d"
]
},
{
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"Label": "1d_tool.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
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"Parameters": {},
"Used": [
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+ "urn:b7d21574-2f03-409f-b7d5-363bb4297b36"
]
},
{
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+ "@id": "urn:ae7558b3-c12b-4858-b7d2-b1fd79149b23",
"Label": "3dTcat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:049ce5bc-724a-4c47-9d72-b77a52f94361"
+ "urn:130b200a-a004-4ac6-917b-fae4be88252d"
]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:979f2869-ec3c-43b7-ba7b-aa31c0de43e3"
+ "urn:d1e1cda7-db65-4013-a6e5-eff822140f17"
]
},
{
- "@id": "urn:c74c08f1-a405-47fa-814a-e8b8f5cdad68",
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"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:7e54dc0e-4d26-4be5-8889-672418722fb9"
+ "urn:4e86443f-aeb9-467a-87cd-921d8561e79d"
]
},
{
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+ "@id": "urn:bd40b1fe-f58d-4f57-abba-63275e76d0c1",
"Label": "3dcalc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:2a874c72-652a-4395-a282-238a0e8df62d",
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e",
- "urn:d125919a-7459-4cba-a931-e0422691e66d"
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe",
+ "urn:c512daa6-81d5-4f4b-b599-ad2406137f3c",
+ "urn:ffbf1f1d-cc38-47b8-a1a2-c0242ca8e8f8"
]
},
{
- "@id": "urn:60870a37-f1be-49dc-9ed1-97145a1186c6",
+ "@id": "urn:9749c11a-671c-4c79-9951-10d84f2c77a6",
"Label": "3dTnorm",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:07e15c34-289b-4c89-93b3-2b34fda0c07b"
+ "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286"
]
},
{
- "@id": "urn:401fc3e8-c7c1-4822-a33a-b26e502b4cf8",
+ "@id": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
"Label": "3dmaskave",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:7931efc7-71d6-4b0d-a464-dfb77e182541",
+ "@id": "urn:1c42556b-6ea5-40c5-ba7f-d049ffbfac3c",
"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:5e6b8718-a8c8-46d8-bfcc-c68b0d22e2bf"
+ "urn:deec3fb9-4e28-4d7c-8a47-599403e4edcd"
]
},
{
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"Label": "3dcalc",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
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- "urn:30ce15aa-b1f3-470f-b216-c9bfba4b1af6"
+ "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d",
+ "urn:bd25383b-d975-4195-831d-bb521d441d8b"
]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:ee4396da-a398-435e-af36-5041459454af"
+ "urn:cf72bf6d-c398-4e69-9a8d-dbd8c530a31e"
]
},
{
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"Label": "1dcat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:f6d3d73c-cfee-40ec-820f-a6c60b7a3e37"
+ "urn:8adb28e5-349d-4f53-8b18-4ed3975fae39"
]
},
{
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"Label": "1dcat",
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"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:3d3fff2a-8dc3-4d57-9a75-02c39114856b"
+ "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b"
]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
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"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:8d264a79-1906-4b4e-a5a3-d3f6b3e0c794"
+ "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174"
]
},
{
- "@id": "urn:0bff3dca-19e8-4125-94c0-6a76d3eede2f",
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"Label": "1dcat",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:8d264a79-1906-4b4e-a5a3-d3f6b3e0c794"
+ "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174"
]
},
{
- "@id": "urn:fb72c5bd-574c-4069-aef4-9fc148874640",
+ "@id": "urn:1f3ccb95-5c68-4eda-a0e2-23aef8d5c592",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e"
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
]
},
{
- "@id": "urn:2fe045c8-4b3e-42e8-a6f6-dc8f76543448",
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"Label": "3dFWHMx",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e"
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
]
},
{
- "@id": "urn:aff94046-a755-4235-b8f9-02d51dd8354e",
+ "@id": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
"Label": "3dClustSim",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:5e24e0c2-394f-49db-9a68-e68d7d5c0b1e"
+ "urn:a5389e7d-d431-43bb-8d2c-c68cdfdd10fe"
]
},
{
- "@id": "urn:4172ba06-847c-4616-ab77-c3c41b1d787c",
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"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:3a3ccb87-c00b-4c97-9064-3a93b3d31cd2"
+ "urn:c09831f3-2daa-4d46-8cc2-8d3a6d13e061"
]
},
{
- "@id": "urn:d052dad6-137f-45af-8fb4-39e4b54fbd17",
+ "@id": "urn:a0828193-6c5d-4073-910f-4d6ef6b19f1a",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:b3713446-96d2-4b62-bbdd-2a210b8dcc5a",
+ "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:dda8878a-fa84-4fd5-af90-5c6cc49f53ed",
+ "@id": "urn:4a800646-417a-4105-bc31-99944567ceb1",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:c63f6bf6-7480-414e-a8fb-7a1c37996839",
+ "GeneratedBy": "urn:3f372617-f0ba-4f3a-86f0-ce2ea6ec39c1",
"digest": {
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}
},
{
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+ "@id": "urn:df7142dc-af29-46f8-b774-4cca4d909eb2",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:6e9e8852-ec0b-4feb-aae6-63f620e09c84"
+ "GeneratedBy": "urn:732242fd-a890-4e32-9297-9bfcbbeb508f"
},
{
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+ "@id": "urn:deeda8b2-3927-47d6-8375-d0341e4f6f2a",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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+ "@id": "urn:cecf4f4e-5ba8-4780-90ce-f798e6c648e7",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/afni_voxelwise_p0001/subject_results/group.DS0011/subj.sub_001/sub_001.results/stimuli/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
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+ "@id": "urn:a1fa7d4a-cde5-40db-9c54-e05b42a9ba21",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:b052d775-addc-449b-a406-368acd0aaa97"
+ "GeneratedBy": "urn:e8af30f7-c70b-43bf-a4d0-b50f658c6762"
},
{
- "@id": "urn:92e806a1-588a-400a-8267-1d331938bd79",
+ "@id": "urn:467c0714-a9fb-4797-aa59-c1698d242349",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "/Users/cmaumet/Projects/Data_sharing/dev/nidmresults-examples/raw/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
},
{
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@@ -1093,25 +1093,25 @@
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@@ -1289,52 +1289,52 @@
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@@ -1342,10 +1342,10 @@
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diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png
index 6e57c9dd4..ea3347083 100644
Binary files a/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.jsonld
new file mode 100644
index 000000000..3b3f6b88d
--- /dev/null
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diff --git a/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png
new file mode 100644
index 000000000..142084331
Binary files /dev/null and b/examples/from_parsers/afni/afni_hrf_gammadiff_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
index 292a7297e..9fc6bb1e3 100644
--- a/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
+++ b/examples/from_parsers/afni/afni_hrf_tent_proc.jsonld
@@ -4,7 +4,7 @@
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"Software": [
{
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@@ -13,398 +13,398 @@
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"Parameters": {},
"Used": [
- "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
+ "urn:6bf38f81-d157-48c7-809c-9d6fdbd4ea47"
]
},
{
- "@id": "urn:8f056e6d-ce22-46c1-8a64-9b84414f4382",
+ "@id": "urn:55fb5f69-aafd-48d6-a779-1beb8875af98",
"Label": "3dcalc",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
+ "urn:6bf38f81-d157-48c7-809c-9d6fdbd4ea47"
]
},
{
- "@id": "urn:57a1e7f9-e61f-40a5-aba2-3dc9559d3f09",
+ "@id": "urn:ea9ce4ff-53f7-45de-a21b-ccab8b353caf",
"Label": "cat_matvec",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:49db383a-f7ce-4b02-b18a-301f09f8ca2e"
+ "urn:b185efef-8306-47df-9b4e-4d359d1ed28a"
]
},
{
- "@id": "urn:a44737d5-bbe8-45aa-bbda-e4e39c4fc2e4",
+ "@id": "urn:1d0e7df0-934e-4348-b758-3e3f0fd2d999",
"Label": "3dAllineate",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:442666e8-e2d2-433a-95af-f6c9290f625d",
- "urn:ca75045e-e6e1-4f42-b342-11111042cfd4",
- "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
+ "urn:377e3ee2-d526-4e90-b489-8992ce228785",
+ "urn:6bf38f81-d157-48c7-809c-9d6fdbd4ea47",
+ "urn:f04d7a27-d1d5-4be0-b103-38bdcd5eb0e3"
]
},
{
- "@id": "urn:375dfc81-5906-4f37-869d-a5f3d511c1f1",
+ "@id": "urn:52163e9a-5b61-49c5-8a41-ffb9e4014483",
"Label": "3dAllineate",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:1f93c51d-0af7-428b-87d0-7e9cb9f08dc1",
- "urn:442666e8-e2d2-433a-95af-f6c9290f625d",
- "urn:ca75045e-e6e1-4f42-b342-11111042cfd4"
+ "urn:1790034e-03d6-44e2-9434-fa01a361bc8e",
+ "urn:377e3ee2-d526-4e90-b489-8992ce228785",
+ "urn:f04d7a27-d1d5-4be0-b103-38bdcd5eb0e3"
]
},
{
- "@id": "urn:0d20d783-5c33-47b9-acc0-d7c6c576fd63",
+ "@id": "urn:413711a9-eae9-4ace-9bb6-e4d09cea35d8",
"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:96db2e6e-5e2a-4e31-8f64-424d2b4025de"
+ "urn:55fc28fb-de6a-46a5-9b3a-8e8ddfddbff8"
]
},
{
- "@id": "urn:bbc5cfa9-fc2a-4a19-b7cd-6eff9a5300b2",
+ "@id": "urn:2a023c53-e9a3-423b-ae8f-67e446826eb8",
"Label": "cat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:57e1e447-c13d-4bd5-ac34-e7c12ee6ff0e"
+ "urn:c88080b6-995a-41c4-88ce-a7d6c176e52f"
]
},
{
- "@id": "urn:dd2943db-d18f-4c3b-b091-b2392fb26750",
+ "@id": "urn:a6417bc2-bf60-4cfc-87b3-969db1d6c23c",
"Label": "3dcopy",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:a88fe79f-9c31-48c7-a3fd-d9aa03416151"
+ "urn:f5c9f82a-b785-4bbf-87ef-489a139ab78b"
]
},
{
- "@id": "urn:9977a87f-a67e-46c5-9208-6d52284bb1ee",
+ "@id": "urn:d1b4cbde-57bb-48bc-b03c-333cbba29eca",
"Label": "3dcalc",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:02e6c51d-962c-4a4b-8b77-ca222c537f17",
- "urn:62757c28-bbaf-44ef-b41d-fba68148f8c4"
+ "urn:14031aea-2c77-49f0-bf28-aa68bf199afa",
+ "urn:601dd07b-c372-4753-ae81-340c406e60c7"
]
},
{
- "@id": "urn:13e01b1e-8691-4c67-8b2f-3f8a6a3dc9ec",
+ "@id": "urn:a5426e27-b44f-4ee5-9f79-99f13c820e2d",
"Label": "3dcopy",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:ca75045e-e6e1-4f42-b342-11111042cfd4"
+ "urn:f04d7a27-d1d5-4be0-b103-38bdcd5eb0e3"
]
},
{
- "@id": "urn:876868d9-b90c-4dbe-b1c0-e8081a6b5783",
+ "@id": "urn:4ab0a510-1e34-41b9-a913-9db8b8c40537",
"Label": "3dAllineate",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:ffd8b61e-9219-4196-8acf-5c7e304172a6"
+ "urn:84f0b77a-0276-4ce9-9370-78ab87dbbe31"
]
},
{
- "@id": "urn:2fa48d2a-f515-483c-a7fe-9da4123ea66a",
+ "@id": "urn:0b66eade-b9cf-457f-a7a8-520a4b9771de",
"Label": "3dmerge",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:b1dfae7b-a755-4880-bb1b-2943bb5dabe6",
- "urn:cf35254c-cfa1-47a4-b6fa-0bbfd48f1f2e"
+ "urn:212a98ba-e6e1-4edb-a72f-352f455c2f01",
+ "urn:675c5cc6-03dd-4a1d-a584-7d3637126fe7"
]
},
{
- "@id": "urn:edc4d342-e3a2-4a70-9590-c7cd4293922d",
+ "@id": "urn:e0cf6796-f3d4-4408-801a-580d81d2167d",
"Label": "3dAutomask",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857"
+ "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4"
]
},
{
- "@id": "urn:3181950d-f9a7-408e-945c-c9b5103e06a7",
+ "@id": "urn:3f7a5206-52c1-41b7-aa5a-aad9f9eccf59",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:58eadaf7-7a2c-435b-aa5b-9e9e982ec4fb",
+ "@id": "urn:e7b671f3-5938-4982-9518-9fc1f631d613",
"Label": "3dresample",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7",
- "urn:ca75045e-e6e1-4f42-b342-11111042cfd4"
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491",
+ "urn:f04d7a27-d1d5-4be0-b103-38bdcd5eb0e3"
]
},
{
- "@id": "urn:e3b4c9b6-c534-42ec-b134-a78421c8db3e",
+ "@id": "urn:abf52df2-1460-441a-9eb8-93b744118fce",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:4912dc91-d374-4b1e-b893-ce6cf0a9dc35"
+ "urn:8a8fc13d-f4c7-485c-a2f7-f49f774d29de"
]
},
{
- "@id": "urn:9244d50f-27f2-4a26-9f27-b728870aaefa",
+ "@id": "urn:1088143c-d7d4-4f9d-98ed-a958a30f0650",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:aa053e5f-cbc9-42d8-abb9-b90d70044136",
- "urn:e3c8e006-f1fa-4f68-9ded-84f0ac9e44cd"
+ "urn:096b2bb0-07a4-4e58-bb1b-fde0c7781fc9",
+ "urn:a51008db-25b7-4e5b-9dd4-3332e54c1340"
]
},
{
- "@id": "urn:5e66964f-ad8f-467e-b290-2956f00ef1a2",
+ "@id": "urn:50bdb27a-fefd-4bc4-b12f-e03609ea2f44",
"Label": "3ddot",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:aa053e5f-cbc9-42d8-abb9-b90d70044136",
- "urn:e3c8e006-f1fa-4f68-9ded-84f0ac9e44cd"
+ "urn:096b2bb0-07a4-4e58-bb1b-fde0c7781fc9",
+ "urn:a51008db-25b7-4e5b-9dd4-3332e54c1340"
]
},
{
- "@id": "urn:4aa4cd22-277d-4275-a53e-46b3d6ae63b5",
+ "@id": "urn:3d0dda92-91be-4978-95fe-28b76df35115",
"Label": "3dresample",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7",
- "urn:5c10fcbd-bf1a-4dec-8e9e-4731987020fa"
+ "urn:56a41cb2-9d52-42bc-bbba-a4eecabc8257",
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491"
]
},
{
- "@id": "urn:9d494e57-2f2f-4ae9-9cee-f3fbb0da1e60",
+ "@id": "urn:d2b04583-62a4-4acb-a5b7-533bf65853b2",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:64fe3794-20dd-46e0-90fc-56a8b309c17d"
+ "urn:727ab8db-ebd4-4d1e-9f24-9b2471be1cfa"
]
},
{
- "@id": "urn:4ed3ae31-2469-4eea-8d7d-094dbe725b35",
+ "@id": "urn:40085074-470f-40a7-8592-5cfde205f538",
"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857"
+ "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4"
]
},
{
- "@id": "urn:b4a0c70b-b21e-4841-9aa4-9162e50e00f8",
+ "@id": "urn:0eed29c2-767d-42bf-9aa3-d1747f773e3a",
"Label": "3dcalc",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:02e6c51d-962c-4a4b-8b77-ca222c537f17",
- "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857",
- "urn:93a80c83-735c-49fe-a04f-eceeb9e9716c"
+ "urn:601dd07b-c372-4753-ae81-340c406e60c7",
+ "urn:cf4823ef-3d1f-43bb-b014-d95d7677f3ab",
+ "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4"
]
},
{
- "@id": "urn:3c93a0f8-9da1-4d13-8f7b-06e36b99e86e",
+ "@id": "urn:9e5b02ef-3ed2-4f0f-96ec-59134e367424",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:f2562dbf-e257-4183-8d17-d2fe0c9b3b70"
+ "urn:d62cb163-faad-415d-b1a8-afb62b829694"
]
},
{
- "@id": "urn:1b82a18a-a7ff-46a9-afd5-53fbf7bfb66a",
+ "@id": "urn:7422254b-05f7-476f-9a0f-4e86f4333240",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:f2562dbf-e257-4183-8d17-d2fe0c9b3b70"
+ "urn:d62cb163-faad-415d-b1a8-afb62b829694"
]
},
{
- "@id": "urn:05d99bd1-1aa9-452a-9162-19459c4a4c71",
+ "@id": "urn:99743df4-ee90-462d-bbfe-52cce238b77d",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:f2562dbf-e257-4183-8d17-d2fe0c9b3b70"
+ "urn:d62cb163-faad-415d-b1a8-afb62b829694"
]
},
{
- "@id": "urn:7da2e5ed-45c6-4bef-bbe6-aefef427df2c",
+ "@id": "urn:1430ed23-73d6-42db-8269-2236d93df758",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'TENT(0,12,7)' -stim_label 1 tone_counting -stim_times 2 stimuli/tone_counting_probe_onsets.txt 'TENT(0,14,8)' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -iresp 1 iresp_tone_counting.$subj -iresp 2 iresp_probe.$subj -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:176f5667-ceaa-47a1-ba89-54e565469876"
+ "urn:3eefdc1a-c3e2-427b-be45-b122ff464a33"
]
},
{
- "@id": "urn:111fbef2-a325-48ad-b79a-d9df47e8b19f",
+ "@id": "urn:3135e215-2b94-4562-8b8e-a48f87f57f2d",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:c1887097-aa8e-4ded-9839-159c05a8ff2c"
+ "urn:489ee359-4af7-4f70-b93c-6fd638b112b3"
]
},
{
- "@id": "urn:f416139d-e9f8-4692-b181-11e4888553af",
+ "@id": "urn:b1ffe3d9-ecc1-40f5-b3c4-b2a6dd8a0b7c",
"Label": "timing_tool.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "timing_tool.py -multi_timing stimuli/tone_counting_onset_times.txt stimuli/tone_counting_probe_onsets.txt -tr 2.0 -warn_tr_stats |& tee out.TENT_warn.txt",
"Parameters": {
"-multi_timing": "stimuli/tone_counting_onset_times.txt",
@@ -412,164 +412,164 @@
"-warn_tr_stats": "|&"
},
"Used": [
- "urn:6ef54973-75ba-4848-936d-52b187bb822f"
+ "urn:bd3ca465-bdf8-4c4b-bb01-4fb8ab6d1942"
]
},
{
- "@id": "urn:4dc7b638-37ac-46f6-88e5-3e711bd3a4cc",
+ "@id": "urn:9afabe47-2e28-4f5c-a59d-d227240eda46",
"Label": "3dTcat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:176f5667-ceaa-47a1-ba89-54e565469876"
+ "urn:3eefdc1a-c3e2-427b-be45-b122ff464a33"
]
},
{
- "@id": "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
+ "@id": "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:1bd62035-1ac7-4b81-927d-358b4ce0cb7d"
+ "urn:50ddd606-41a0-4639-aacf-d98eb28946a2"
]
},
{
- "@id": "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8",
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"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:be1edb32-3e58-45fa-a6af-df2d560cc972"
+ "urn:e0bafa2c-0dbd-4301-8b22-a76846ba1df9"
]
},
{
- "@id": "urn:7f0c37a4-8362-411a-9cab-3f45e445a60d",
+ "@id": "urn:e88ac25a-1920-4693-b775-d9aa77d9e2b5",
"Label": "3dcalc",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7",
- "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
- "urn:b51a7314-e006-4e60-ba3c-388d5f9b5a35"
+ "urn:8a4a6702-69d9-4650-86a0-98d29459e20d",
+ "urn:bd192b25-b688-4062-a17d-1fda0f6bdc79",
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491"
]
},
{
- "@id": "urn:5c158d02-850a-4940-8969-7bcebd489cc2",
+ "@id": "urn:b025ef9a-00f4-4f4a-853f-2c2f83b9a149",
"Label": "3dTnorm",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:372e1c72-64f3-4c31-b37a-a3d62f6a7933"
+ "urn:04ccee0f-77ac-4156-be6e-20d59511d6d4"
]
},
{
- "@id": "urn:4752a95b-fa74-4f9d-90b6-54cd74bf4c5e",
+ "@id": "urn:640b9809-dad4-4832-9ce8-182ffd348e71",
"Label": "3dmaskave",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:57a6d013-8c5a-4f73-903c-31102e6983f5",
+ "@id": "urn:d8b82d32-0f19-46cb-9355-082f1a0568eb",
"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb"
+ "urn:bf7337de-6268-4c59-abef-5961f97933b6"
]
},
{
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+ "@id": "urn:2d19aac9-48f4-41ee-b21f-e77731c5a2ed",
"Label": "3dcalc",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
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- "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99"
+ "urn:3600cb48-ad73-46e5-8e0c-5eb61601e385",
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]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:4e8380f4-779e-4fb0-8055-3853d04e3c3e"
+ "urn:dfc7f499-0b68-4f62-9327-6d5997de2574"
]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:6a86f7e6-4e1a-444d-8f14-4617146d3d26"
+ "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857"
]
},
{
- "@id": "urn:5c80367c-60c3-4da6-9dbc-a232cb748064",
+ "@id": "urn:2c5bec6e-f8bb-4c29-9ba0-2c37fff9df0f",
"Label": "1dcat",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:6a86f7e6-4e1a-444d-8f14-4617146d3d26"
+ "urn:e02c5bed-a199-4b23-99cd-c75d11d5f857"
]
},
{
- "@id": "urn:b3813f7b-85fb-4fbe-9def-1f72fb51ca15",
+ "@id": "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7"
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491"
]
},
{
- "@id": "urn:234c02d8-5e39-4f8e-8dd2-5a7672838f05",
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"Label": "3dFWHMx",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7"
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491"
]
},
{
- "@id": "urn:2c6bd779-8a07-4308-993e-5c23beed49b7",
+ "@id": "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
"Label": "3dClustSim",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:1b6bc660-3002-4209-b970-2bf3816c16f7"
+ "urn:c9b570f8-3272-4cb8-91fc-a33ea9a79491"
]
},
{
- "@id": "urn:43812cb6-b4d0-4133-9c67-ee4cc4b43261",
+ "@id": "urn:e266a5e3-6b72-4e1b-9f60-d17a1bbc757e",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:751652bc-9d36-4f1b-b279-5d118517ab48"
+ "urn:a8ac4ccf-6bef-4542-be2d-22e88af9c591"
]
},
{
- "@id": "urn:924f9353-8183-4a4a-be9d-b9e23d735f3f",
+ "@id": "urn:d2bb77c1-5c5e-4898-b1ff-ba2ed3a5ee79",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:972ae7c7-2673-4696-9362-ed2210c16011",
+ "AssociatedWith": "urn:e3fc81c2-5aa4-478d-9b5e-94b86277f4eb",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -580,22 +580,22 @@
],
"Entities": [
{
- "@id": "urn:31493e8e-6002-4207-b099-de7f25d7df59",
+ "@id": "urn:9069fe27-aedd-4de1-b70a-6c1dd553f1a3",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:05ca7568-0ad0-495e-8456-fbc9ff878699",
+ "GeneratedBy": "urn:fb9b46cd-af5c-4e0d-a6a0-437314eb72ab",
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}
},
{
- "@id": "urn:edc04ecc-b0d2-4ef2-9882-a31284993675",
+ "@id": "urn:cd3b4ccd-e2c1-44f1-b372-4b7152273b09",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
+ "GeneratedBy": "urn:0369ec03-893d-47e1-92a6-e77ecd990622"
},
{
- "@id": "urn:e0181246-8e96-4072-b1d0-fa45343c01a2",
+ "@id": "urn:ce64db29-078f-46fe-9fc0-a1a6ab13c2d3",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_onset_times.txt",
"digest": {
@@ -603,7 +603,7 @@
}
},
{
- "@id": "urn:fa30e6eb-06b6-4084-8b84-2246196531dc",
+ "@id": "urn:58dfc685-09a9-4cd9-872c-6619d3616f30",
"Label": "tone_counting_probe_onsets.txt",
"AtLocation": "./afni_tent_basis_function/tone_counting_probe_onsets.txt",
"digest": {
@@ -611,13 +611,13 @@
}
},
{
- "@id": "urn:579301fe-cc07-4b7e-9f44-f990d3d76bf5",
+ "@id": "urn:573da5fb-2825-437b-b7e4-0de6289e15e3",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:d5b299e3-40d3-438b-86c6-f0cc41f05345"
+ "GeneratedBy": "urn:eb23f479-d3a4-4687-93f2-ff639fff3aaf"
},
{
- "@id": "urn:925c8d49-ab58-4373-8b9b-57ee08f09074",
+ "@id": "urn:5678dd33-1122-46a4-9af5-3e3f6c6d7875",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_T1w.nii.gz",
"digest": {
@@ -625,13 +625,13 @@
}
},
{
- "@id": "urn:7389473f-485d-491b-8432-a4d07111e05e",
+ "@id": "urn:0d5637ef-3522-47f3-8fbe-129a0ffa7c36",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:a50b87fb-4dad-4045-af1b-5fb7218f58f6"
+ "GeneratedBy": "urn:76ae161f-4380-481d-979a-2cef8e7cdd9e"
},
{
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+ "@id": "urn:2e52d984-c548-4ec2-acb6-6bb5a6dfbfd4",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -639,13 +639,13 @@
}
},
{
- "@id": "urn:859744a1-aec1-40a3-ad00-8006fdd1b111",
+ "@id": "urn:4fed7ac4-779c-4b17-8c30-5c636dc89acd",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:00be7c67-3470-4109-aac0-ce3457fe672f"
+ "GeneratedBy": "urn:f0f425b4-421f-41e7-8e26-b4a1b41f5c5e"
},
{
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+ "@id": "urn:36d562e7-c693-4a28-bdd0-17e2c4b39660",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -653,16 +653,16 @@
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{
- "@id": "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2",
+ "@id": "urn:9cd152ef-df9c-4f65-8ab3-4cf1246b8ed1",
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:6244338e-5df1-4496-829a-7ee82e6af2cf",
+ "GeneratedBy": "urn:d32c3631-eb16-4b7c-8ed4-5f4e26b86b85",
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}
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{
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+ "@id": "urn:70c07c46-ffd5-4ef3-819e-2ee6f5265dd5",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -670,25 +670,25 @@
}
},
{
- "@id": "urn:a8c06dac-29ad-4202-b47d-c3852118ca61",
+ "@id": "urn:2628c9dd-445d-4d40-a564-4cf6c295da04",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:df7bed39-e2be-4ad5-a90e-79193079851a",
+ "GeneratedBy": "urn:593fce14-4a1b-4d64-bfaa-b0f7fd3ce024",
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+ "@id": "urn:14941916-403b-4ccc-b73e-6d0d634b013a",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:7b9b59ac-2c07-45fc-9bd2-6f3602b9c7d6",
+ "GeneratedBy": "urn:7e94df31-aad8-46fa-bf0a-8485fc32c054",
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@@ -696,7 +696,7 @@
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@@ -704,16 +704,16 @@
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@@ -721,7 +721,7 @@
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@@ -729,7 +729,7 @@
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@@ -737,16 +737,16 @@
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@@ -754,34 +754,34 @@
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@@ -789,16 +789,16 @@
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@@ -806,16 +806,16 @@
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@@ -823,16 +823,16 @@
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@@ -840,16 +840,16 @@
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@@ -857,16 +857,16 @@
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@@ -874,7 +874,7 @@
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@@ -882,34 +882,34 @@
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@@ -917,7 +917,7 @@
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@@ -925,7 +925,7 @@
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@@ -933,25 +933,25 @@
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@@ -959,16 +959,16 @@
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@@ -976,16 +976,16 @@
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@@ -993,7 +993,7 @@
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@@ -1001,7 +1001,7 @@
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@@ -1009,16 +1009,16 @@
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@@ -1026,25 +1026,25 @@
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@@ -1052,34 +1052,34 @@
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{
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@@ -1087,16 +1087,16 @@
}
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{
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{
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"AtLocation": "stimuli/tone_counting_probe_onsets.txt",
"digest": {
@@ -1104,25 +1104,25 @@
}
},
{
- "@id": "urn:62724743-d128-48d9-b0a9-b8bb0f6800ac",
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{
- "@id": "urn:0ed6b3ac-dce1-4927-93ac-a8a05131d6c8",
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- "GeneratedBy": "urn:4dc7b638-37ac-46f6-88e5-3e711bd3a4cc",
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{
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"Label": "all_runs.$subj",
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"digest": {
@@ -1130,16 +1130,16 @@
}
},
{
- "@id": "urn:473dc7c2-1028-4a00-9592-5b20a96d2401",
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{
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@@ -1147,16 +1147,16 @@
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{
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"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:e76c13e2-2635-44ea-9631-0f1dd0ed99d8",
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{
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"AtLocation": "rm.signal.all+tlrc",
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@@ -1164,7 +1164,7 @@
}
},
{
- "@id": "urn:b51a7314-e006-4e60-ba3c-388d5f9b5a35",
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@@ -1172,16 +1172,16 @@
}
},
{
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"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:7f0c37a4-8362-411a-9cab-3f45e445a60d",
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{
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"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1189,25 +1189,25 @@
}
},
{
- "@id": "urn:5ec203ef-e9b5-4e08-97a5-1a212b51a7c7",
+ "@id": "urn:5e7a05e8-f457-47a2-8924-d55827fda455",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:5c158d02-850a-4940-8969-7bcebd489cc2",
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{
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+ "@id": "urn:3600cb48-ad73-46e5-8e0c-5eb61601e385",
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"AtLocation": "gmean.errts.unit.1D",
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{
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"AtLocation": "out.gcor.1D",
"digest": {
@@ -1215,16 +1215,16 @@
}
},
{
- "@id": "urn:5fb0915d-c741-4a5b-802d-8b14cff8a199",
+ "@id": "urn:05b80375-0a64-4cc0-9761-7134588d04e9",
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{
- "@id": "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99",
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@@ -1232,16 +1232,16 @@
}
},
{
- "@id": "urn:6a224b53-f44c-4f61-b812-ea70fd0752b1",
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"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:eb34f522-1fa9-4daa-acde-8c9c860d2868",
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{
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"digest": {
@@ -1249,16 +1249,16 @@
}
},
{
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"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
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{
- "@id": "urn:6a86f7e6-4e1a-444d-8f14-4617146d3d26",
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"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1266,52 +1266,52 @@
}
},
{
- "@id": "urn:22d5d091-3520-4934-84b2-b3c4408924f3",
+ "@id": "urn:80b7d24d-5996-4955-9422-ddaca1aa7ffb",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7",
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}
},
{
- "@id": "urn:08d14d34-64e4-4de6-93bf-2be4a4840fca",
+ "@id": "urn:eea66627-8a14-4670-8dfc-e23e1a6df51a",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:5c80367c-60c3-4da6-9dbc-a232cb748064",
+ "GeneratedBy": "urn:2c5bec6e-f8bb-4c29-9ba0-2c37fff9df0f",
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}
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{
- "@id": "urn:4c4b965b-fede-4d18-bc71-3e9f05e713ac",
+ "@id": "urn:f81101f9-c210-4bcc-99f6-7041f1243173",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:b3813f7b-85fb-4fbe-9def-1f72fb51ca15",
+ "GeneratedBy": "urn:aad6fc92-8eef-49f4-9fa8-d8c2f463412a",
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},
{
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+ "@id": "urn:fbbdd34f-6ac6-4d64-bb9b-51e927222174",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:234c02d8-5e39-4f8e-8dd2-5a7672838f05",
+ "GeneratedBy": "urn:7bc6a471-cae3-4f94-a8f2-6547d30e4279",
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}
},
{
- "@id": "urn:cbe4b414-9e92-4601-a8c2-67f453efbf50",
+ "@id": "urn:e62f2f62-daec-431c-9d29-0637e470bbe4",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:2c6bd779-8a07-4308-993e-5c23beed49b7",
+ "GeneratedBy": "urn:17a72a6f-17b3-484f-bd82-73ac77bb2582",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:751652bc-9d36-4f1b-b279-5d118517ab48",
+ "@id": "urn:a8ac4ccf-6bef-4542-be2d-22e88af9c591",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1319,10 +1319,10 @@
}
},
{
- "@id": "urn:c9548786-b53b-42ef-9721-6f3db66bcb69",
+ "@id": "urn:e53e3355-9001-471d-a597-e07049ea64f4",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:924f9353-8183-4a4a-be9d-b9e23d735f3f",
+ "GeneratedBy": "urn:d2bb77c1-5c5e-4898-b1ff-ba2ed3a5ee79",
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diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc.png b/examples/from_parsers/afni/afni_hrf_tent_proc.png
index 8986baf2a..3a6a20e78 100644
Binary files a/examples/from_parsers/afni/afni_hrf_tent_proc.png and b/examples/from_parsers/afni/afni_hrf_tent_proc.png differ
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
new file mode 100644
index 000000000..f3e05cc36
--- /dev/null
+++ b/examples/from_parsers/afni/afni_hrf_tent_proc_block.jsonld
@@ -0,0 +1,982 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:130f1168-701b-4ae0-a70d-f5fd03e3e729",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_tent_basis_function/tone_counting_onset_times.txt ./afni_tent_basis_function/tone_counting_probe_onsets.txt $output_dir/stimuli; 3dcopy ./afni_tent_basis_function/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:0ee5119d-90af-4a7c-8534-b4aa68c43aa4",
+ "urn:599e915d-3120-45bb-8437-acd959e9b2aa",
+ "urn:4397acb5-156a-4edd-93d3-54f9f0c2470a"
+ ]
+ },
+ {
+ "@id": "urn:c04a8817-03a1-42de-bceb-57bfcf5274c3",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_tent_basis_function/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:84148661-5823-4be4-a8f9-f0182c8a4254"
+ ]
+ },
+ {
+ "@id": "urn:2b1ff054-4323-4a81-a8b2-ab40230aae81",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6",
+ "urn:f2f041c8-c006-426f-a90b-11e41d5b55c1"
+ ]
+ },
+ {
+ "@id": "urn:5c99fbfa-175c-45d4-81cc-ba9545d0077a",
+ "Label": "tshift",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:58e14c3c-a6ae-4ea7-b8e3-405904f13da6"
+ ]
+ },
+ {
+ "@id": "urn:734090d0-c29c-41e6-b2f3-9ebcef2a771c",
+ "Label": "align",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:63dc7fcd-c329-451f-b756-ffb7402f2c0f",
+ "urn:6f0b04f1-78e2-477b-8c97-91ac8fcaece8"
+ ]
+ },
+ {
+ "@id": "urn:4e6ee55a-2606-43d5-8318-fe5853c29fc2",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:2d5e64f3-453a-4325-8af6-c3fa3066aff9",
+ "urn:995f49ae-4942-4e6f-83d6-c538a506a7c1",
+ "urn:218cfda2-6551-46ae-b33b-98a6bcb9c3c2"
+ ]
+ },
+ {
+ "@id": "urn:8c983441-d454-42c9-a6c2-0ac8fd4e7844",
+ "Label": "volreg",
+ "AssociatedWith": "urn:5a5791ee-c6d4-4622-aef5-6f0645ea1f06",
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+ "urn:96bd688a-b104-434a-8d80-3a7761587dd4",
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+ },
+ {
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+ "sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
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+ },
+ {
+ "@id": "urn:55d1580e-1e33-4f71-889f-ca3253de9185",
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+ "AtLocation": "rm.noise.all",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
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+ "sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
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+ {
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+ "AtLocation": "TSNR.$subj",
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+ "AtLocation": "rm.errts.unit",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
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+ "sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
+ }
+ },
+ {
+ "@id": "urn:e6f949ee-3bc5-4f71-bbe5-d8a73afff672",
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+ "AtLocation": "-",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
+ "digest": {
+ "sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
+ }
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+ {
+ "@id": "urn:5efcfaa0-9adb-4029-913f-25636acc25d1",
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+ "AtLocation": "rm.DP",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
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+ "sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
+ }
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+ {
+ "@id": "urn:b12172b5-b120-4960-9e98-588064fe5d3d",
+ "Label": "corr_brain",
+ "AtLocation": "corr_brain",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
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+ "sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
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+ "@id": "urn:6bfc4ae6-5c3a-4973-a4f8-1a23e1780ca3",
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+ "sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
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+ "AtLocation": "X.stim.xmat.1D",
+ "GeneratedBy": "urn:8f9d2d72-9169-489e-a681-528405d545fb",
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+ "sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
+ }
+ },
+ {
+ "@id": "urn:9274c0b4-0087-4c70-9ddf-f04828990ad0",
+ "Label": "full_mask.$subj",
+ "AtLocation": "full_mask.$subj+tlrc",
+ "digest": {
+ "sha256": "5ccbeeeef88c323d4141cd242861d39ffb389015ad6e1d788a67a1851123fc36"
+ }
+ },
+ {
+ "@id": "urn:146e65ce-01ff-4b1b-93a6-8d9697dc5f58",
+ "Label": "blur.epits.1D",
+ "AtLocation": "blur.epits.1D",
+ "GeneratedBy": "urn:f5f40dd2-8ee4-4318-861b-9070b035cd17",
+ "digest": {
+ "sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
+ }
+ },
+ {
+ "@id": "urn:c137464a-c04b-4db9-8189-34c3690525ad",
+ "Label": "blur.errts.1D",
+ "AtLocation": "blur.errts.1D",
+ "GeneratedBy": "urn:f5f40dd2-8ee4-4318-861b-9070b035cd17",
+ "digest": {
+ "sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
+ }
+ },
+ {
+ "@id": "urn:7e44b770-8d71-419f-acc7-53ddd529ea51",
+ "Label": "ClustSim",
+ "AtLocation": "ClustSim",
+ "GeneratedBy": "urn:f5f40dd2-8ee4-4318-861b-9070b035cd17",
+ "digest": {
+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:c6a9dd36-7589-4de6-8fa2-2fdcd43dfe88",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:6687424b-809a-4438-be40-6a6c62056b73",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:5942de21-999c-4019-8e04-6978dbabc03c",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_hrf_tent_proc_block.png b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png
new file mode 100644
index 000000000..4d1e531b1
Binary files /dev/null and b/examples/from_parsers/afni/afni_hrf_tent_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_other_template_proc.jsonld b/examples/from_parsers/afni/afni_other_template_proc.jsonld
index f0db44da9..bf6831a52 100644
--- a/examples/from_parsers/afni/afni_other_template_proc.jsonld
+++ b/examples/from_parsers/afni/afni_other_template_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "@id": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:034865b2-36f6-45ff-9ca0-89dd56ddd22d",
+ "@id": "urn:015dc35c-8205-4f8b-8c13-a2f68723ce0e",
"Label": "Make directory",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:6442d6c7-861e-47b6-a7ec-869397d3fd3c",
+ "@id": "urn:820883ac-814d-49c1-95b6-2129629530ef",
"Label": "Make directory",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:01916163-39ab-406b-a4ad-fe365cf6bf5e",
+ "@id": "urn:829059e7-40d3-402e-acd7-52ce046b7263",
"Label": "cp",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:057be9c0-35ac-49f8-a62a-d3917a8736cf",
- "urn:6d537e2c-415f-4500-beec-7ff9617cd3c9"
+ "urn:81bdbe32-8fd2-4c86-ad90-d75314e52071",
+ "urn:c59e7f5b-8800-43da-9512-3cf33aa2d64f"
]
},
{
- "@id": "urn:f8ad3805-7098-4b47-bba8-e210230c5e80",
+ "@id": "urn:132f3df2-fdac-4638-b3f8-9cd0419c22c1",
"Label": "3dcopy",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:b7aa1492-f271-4938-ba63-83b2832e399d"
+ "urn:b43412a0-0f56-4d67-8a7e-634c25544801"
]
},
{
- "@id": "urn:a5fc0d33-b76e-4555-a307-ff6b719128b6",
+ "@id": "urn:9c045eed-e0d8-4752-9f38-b03c8961ba54",
"Label": "3dTcat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:67953245-9625-4958-9ed6-f255c3196cd3"
+ "urn:10c6cdeb-975a-41c9-9aaf-33d0116e2f1a"
]
},
{
- "@id": "urn:40782800-0f18-44eb-927b-9a18f874c562",
+ "@id": "urn:8c1d797a-e34c-4dd4-824a-c86c07724873",
"Label": "3dToutcount",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:1f498cde-c4ee-44f0-9366-98075fbf4117"
+ "urn:b41be70e-3eba-42fd-92e5-4df0444a18d4"
]
},
{
- "@id": "urn:e14ccb8f-542f-4043-aa5b-2ad720a90fa5",
+ "@id": "urn:ac3714cf-12be-4dc0-9fcb-85e5d0bbd814",
"Label": "cat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:ac927f49-4167-4dc0-b0da-d215e9262d89"
+ "urn:a5544002-4cbd-4868-b71c-6e0c24c19d43"
]
},
{
- "@id": "urn:f1e74580-01fc-4bcb-8267-dfeca3c1fcab",
+ "@id": "urn:f3ad61b2-b139-4bad-a97d-9573066dfecf",
"Label": "3dTshift",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:1f498cde-c4ee-44f0-9366-98075fbf4117"
+ "urn:b41be70e-3eba-42fd-92e5-4df0444a18d4"
]
},
{
- "@id": "urn:9f95d75b-2960-4442-b622-cfa279765332",
+ "@id": "urn:28dda7e2-20ef-4432-8591-f8a7685dfa2c",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:05d94c20-ed16-47dd-855c-7eeb5b6b8da2",
- "urn:f18b385c-ae9d-432e-a000-11b8fcc937f0"
+ "urn:72873482-a03b-4df2-a3cf-7cbffadb3ca7",
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]
},
{
- "@id": "urn:94eca642-e7a4-4516-bb04-d3ec7205f2f0",
+ "@id": "urn:7f373576-0167-4294-9e8a-e15cfad9516b",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:34a6ccc1-c1a9-4abc-9c95-3c421aed66d5",
- "urn:525db306-486b-4f71-9290-dbb1682ab1f7"
+ "urn:8728fc5c-5b88-4df7-8a17-9a0db37977b2",
+ "urn:a022eaa3-cbe6-449f-ad71-de6f40c3385b"
]
},
{
- "@id": "urn:055168ca-a31a-46a5-9856-c4d65f4ff571",
+ "@id": "urn:114e3532-8f75-43c4-8325-0411b3f2d898",
"Label": "cat_matvec",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:5ac2aa06-d1d0-4302-9070-1a4f8ee7298d"
+ "urn:d4caa5e8-8399-4a90-8650-f7ddb831f026"
]
},
{
- "@id": "urn:23b3a8fd-1d9d-4840-b592-ff7a5854e10b",
+ "@id": "urn:519fc1f0-12e8-4d55-8221-a9a1782415ef",
"Label": "3dvolreg",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:7fd9b3c1-a451-4a03-8201-3e8beeab3afe"
+ "urn:9981c55e-0d2a-4cac-8dac-2cbbc84e1fef"
]
},
{
- "@id": "urn:af12b69b-fe39-4e11-90eb-ebe03f5f448a",
+ "@id": "urn:ec3229a5-b849-4c4b-b171-3c3e320464b3",
"Label": "3dcalc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:7fd9b3c1-a451-4a03-8201-3e8beeab3afe"
+ "urn:9981c55e-0d2a-4cac-8dac-2cbbc84e1fef"
]
},
{
- "@id": "urn:e777f8b9-880c-4a71-ad01-43f3f0abbeee",
+ "@id": "urn:692f3e44-6c57-4be4-bf7f-74b19df5f43a",
"Label": "cat_matvec",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:5ac2aa06-d1d0-4302-9070-1a4f8ee7298d"
+ "urn:d4caa5e8-8399-4a90-8650-f7ddb831f026"
]
},
{
- "@id": "urn:c73caae5-64c6-4d21-8599-9e670b9bfb9b",
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"Label": "3dAllineate",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
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"Used": [
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- "urn:9e25a10e-d3da-4de0-b8c9-87b55ec50cb5",
- "urn:bc3e53a0-c4c7-497a-9f5f-a6a01ce571da"
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+ "urn:9981c55e-0d2a-4cac-8dac-2cbbc84e1fef",
+ "urn:eedd8373-eafa-4cf2-bc65-202f4d903685"
]
},
{
- "@id": "urn:46e4ccb6-9f24-41af-a5f0-3d0c94cad925",
+ "@id": "urn:3f92f1e1-053e-48b9-98b9-7e3b9031e479",
"Label": "3dAllineate",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
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"Used": [
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- "urn:bc3e53a0-c4c7-497a-9f5f-a6a01ce571da",
- "urn:f869b0e7-5c2d-4f08-9bc5-026509af7d14"
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+ "urn:120c218e-37ec-43c4-bf0b-6e126b10530e",
+ "urn:eedd8373-eafa-4cf2-bc65-202f4d903685"
]
},
{
- "@id": "urn:68954e54-5941-4ec9-ac55-7d2e944fbb74",
+ "@id": "urn:f52c1e63-64da-4756-9061-4b73f40950b5",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:565d6945-cf43-4637-91dd-959ef59fd94f"
+ "urn:764c0eea-2131-4923-bc27-c745a22d1bd9"
]
},
{
- "@id": "urn:beae7e86-fb11-4df3-84b4-4666debc7e5f",
+ "@id": "urn:d0817bad-4522-48f7-9e50-31e3489d82ae",
"Label": "cat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:a593e27f-7e1a-44ef-85cc-4712ba305740"
+ "urn:44317bf6-99a8-4fa3-a1d4-6c5b970ddeda"
]
},
{
- "@id": "urn:2b244cf4-5e67-41c2-bf50-4eab48c53424",
+ "@id": "urn:52d1ab38-a102-45af-8923-fd9dd2a3cbb8",
"Label": "3dcopy",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:848d10fa-989f-4a16-9db9-e9f346013291"
+ "urn:b3739448-eeb9-483a-becc-989cce766a2d"
]
},
{
- "@id": "urn:0aaa9b00-90b6-4f7c-bef2-5e46efd3abe5",
+ "@id": "urn:4342af1c-2b81-4c02-b669-ccdebeaafff8",
"Label": "3dcalc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:dbc11716-e865-4e0f-9e6b-70c3603b6f2c",
- "urn:f330816b-b82a-4d29-83cd-78e2d6e6a680"
+ "urn:8357220e-6ce0-4b76-a86e-9e52f8105a66",
+ "urn:efe55a24-f1b1-4b61-8343-0087b38ed521"
]
},
{
- "@id": "urn:6552d457-a0a9-4e38-8b97-5b3f3c6e4d0e",
+ "@id": "urn:6e82ab5e-2cae-4566-b691-f4eb52ac5a93",
"Label": "3dcopy",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:bc3e53a0-c4c7-497a-9f5f-a6a01ce571da"
+ "urn:eedd8373-eafa-4cf2-bc65-202f4d903685"
]
},
{
- "@id": "urn:87b39aea-7485-4ccb-be46-cf814c21fc7b",
+ "@id": "urn:fb0a4cf2-0b8a-445d-b252-7e765e1ba496",
"Label": "3dAllineate",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:555bcac3-727b-420f-be4c-d8e506e33ce6"
+ "urn:354f9b5f-7299-4cb0-ac4f-d336008774f5"
]
},
{
- "@id": "urn:f0ecf845-76ce-4699-8ae5-ba0bb2ad4118",
+ "@id": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
"Label": "3dmerge",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:a2e9a27e-e4fc-454e-a015-e4591a0003df",
- "urn:ac9e2bcd-cb54-40e8-a68c-9962174801f5"
+ "urn:ca9a4718-ff12-4c49-bc9b-c8e5d0c67304",
+ "urn:ee05cd16-9e60-45d8-9454-736cb892f197"
]
},
{
- "@id": "urn:e3e660d5-d5a7-48fc-98fe-18d4e59a04e0",
+ "@id": "urn:406533ba-f5f6-475d-b834-784305e689ce",
"Label": "3dAutomask",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:a68b66ec-2367-4d43-8664-e02dd673998a"
+ "urn:da0a1900-b8f3-4fff-85b1-b9f700cefdff"
]
},
{
- "@id": "urn:c62bd1a0-c919-4b92-8fce-570a872cf405",
+ "@id": "urn:2ec46422-3d77-4635-82fc-107101bfe479",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:14fea31e-6012-42ea-b435-728cb9bb44ae",
+ "@id": "urn:2cf39d2b-1f46-4df9-9f1f-0ee01340ad6d",
"Label": "3dresample",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916",
- "urn:bc3e53a0-c4c7-497a-9f5f-a6a01ce571da"
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad",
+ "urn:eedd8373-eafa-4cf2-bc65-202f4d903685"
]
},
{
- "@id": "urn:d15ed113-62ce-4ed3-8307-f7c9aa747f99",
+ "@id": "urn:213ba206-6549-42b3-90f5-5dbaa5443c31",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:095384b1-8649-42be-85d8-93f6790e8498"
+ "urn:0105302f-6dee-4f56-b390-8f4c7b70f68b"
]
},
{
- "@id": "urn:614e1d98-68ea-4037-959c-218caac702b4",
+ "@id": "urn:73ac48b8-1ba7-42d9-b8a3-86ad316270d6",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:36bd51f7-6a7b-4972-9e3f-128f1e3bc200",
- "urn:e4093739-43a7-4659-8500-2162b6e06ac1"
+ "urn:482a00bc-4f3f-4866-adff-1ca4914f0f9c",
+ "urn:82368305-14a5-444d-9f57-a96589e51937"
]
},
{
- "@id": "urn:bba20b2d-4d4a-4190-8d90-d76d8a736f06",
+ "@id": "urn:afd3d158-c888-4146-81cc-da7a53e3cd8c",
"Label": "3ddot",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:36bd51f7-6a7b-4972-9e3f-128f1e3bc200",
- "urn:e4093739-43a7-4659-8500-2162b6e06ac1"
+ "urn:482a00bc-4f3f-4866-adff-1ca4914f0f9c",
+ "urn:82368305-14a5-444d-9f57-a96589e51937"
]
},
{
- "@id": "urn:cd0c6bf0-a4e1-4661-91d7-3ac3a921f611",
+ "@id": "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
"Label": "3dresample",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc",
"Parameters": {},
"Used": [
- "urn:073168b5-b593-4406-9b08-d95f08b1cd1e",
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916"
+ "urn:0840ffaf-344d-4b50-b9b5-1a4dd76fe080",
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad"
]
},
{
- "@id": "urn:cd2192eb-05ca-4a36-b7f3-02f2de727f03",
+ "@id": "urn:fa9c14f8-dc0e-4bf6-a4c1-efa702904c63",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:01dc9cfe-e1e5-4460-b7cc-8bffb7c50a91"
+ "urn:a2ee4c90-f39a-4adc-accc-81bfff2a3fd8"
]
},
{
- "@id": "urn:a7f17246-55db-4911-bfc2-1c25c8cbd171",
+ "@id": "urn:42579cc8-6d6b-44d4-bbb5-b30f3f880bfc",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:a68b66ec-2367-4d43-8664-e02dd673998a"
+ "urn:da0a1900-b8f3-4fff-85b1-b9f700cefdff"
]
},
{
- "@id": "urn:6fbdb553-8156-4158-aa41-c34fe4536a6f",
+ "@id": "urn:db70a010-5f90-48af-8c31-6be63a2c5d14",
"Label": "3dcalc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:5f9b6c63-f114-4763-a153-e4ba8a4c510e",
- "urn:a68b66ec-2367-4d43-8664-e02dd673998a",
- "urn:f330816b-b82a-4d29-83cd-78e2d6e6a680"
+ "urn:d3bbe5ef-0da2-4c47-bf61-d804b9ebc44b",
+ "urn:da0a1900-b8f3-4fff-85b1-b9f700cefdff",
+ "urn:efe55a24-f1b1-4b61-8343-0087b38ed521"
]
},
{
- "@id": "urn:fe55b2a7-0de1-499d-a868-a5dc04c73443",
+ "@id": "urn:2f1d7d43-4b07-48b9-8496-eebbf76893b0",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:7b9e73d4-ce1b-4f85-90c1-720b737aecf6"
+ "urn:539f3203-1cf0-4089-8fa6-4ad57307a697"
]
},
{
- "@id": "urn:957b0079-9662-4836-b6d5-563dd2d7b239",
+ "@id": "urn:9e154a04-adf5-4892-9856-fd8ce771786a",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:7b9e73d4-ce1b-4f85-90c1-720b737aecf6"
+ "urn:539f3203-1cf0-4089-8fa6-4ad57307a697"
]
},
{
- "@id": "urn:1c858060-3800-44dc-bcab-8a540f7d215c",
+ "@id": "urn:5145d4af-4d72-4daa-9067-cb76d89eed9c",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:7b9e73d4-ce1b-4f85-90c1-720b737aecf6"
+ "urn:539f3203-1cf0-4089-8fa6-4ad57307a697"
]
},
{
- "@id": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
+ "@id": "urn:78f3984b-919a-4bcb-8f8d-2868961736c1",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83"
+ "urn:f3e2b286-a6e2-427e-b5fe-bc4389dea257"
]
},
{
- "@id": "urn:15bea182-294d-4fe1-9350-ae103cb0dddb",
+ "@id": "urn:cf0b023c-b6b6-4cc3-b7eb-3708194092e5",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:a40b63b6-38da-40a5-96fa-d18592e31414"
+ "urn:a6ea5103-3e65-49ed-8c46-e7dd0671cb33"
]
},
{
- "@id": "urn:7328a639-5800-430e-9d20-d0c7d77f0daa",
+ "@id": "urn:3d1775e1-e6d1-44d4-9cc6-e7b2558fbaec",
"Label": "3dTcat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83"
+ "urn:f3e2b286-a6e2-427e-b5fe-bc4389dea257"
]
},
{
- "@id": "urn:30867f07-efcd-414b-bdbf-1878b3578d18",
+ "@id": "urn:a6f01e18-f324-4587-938f-b524db505088",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:448c001b-fbf0-4915-b959-b7b87a921c7c"
+ "urn:9002f1b5-4239-44e4-8932-7d943f25e6e9"
]
},
{
- "@id": "urn:fe6b1502-266f-4d26-84fb-040ce6fc2a3d",
+ "@id": "urn:2c0f03e8-19de-4de6-8318-65d031bacb43",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:65628bdc-1cf9-43c5-99eb-74f20c8e7278"
+ "urn:fb916597-66ca-4bbc-b771-b741c3716c95"
]
},
{
- "@id": "urn:e9ae82db-e47b-4e45-954e-a7e7d27708c1",
+ "@id": "urn:fcee0b5c-13c9-4567-8f44-629ba9e7a513",
"Label": "3dcalc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:1756ff39-a0cf-41b2-a7c8-d940ea52eaab",
- "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916"
+ "urn:3844eec4-0749-4130-aed2-99ca8096e764",
+ "urn:6061039d-c936-4440-aab6-07af6a1345ea",
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad"
]
},
{
- "@id": "urn:496fc0fe-61c9-4f9f-9f38-fda4fc784cd0",
+ "@id": "urn:70a2e9c1-f699-4996-92ea-cc6e5e822379",
"Label": "3dTnorm",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:b6285a9f-3c3b-4835-8421-b287dd391f8a"
+ "urn:4ea18168-83ac-411f-90fa-b3fcdee833a6"
]
},
{
- "@id": "urn:57e2f46d-dd77-4e80-91e3-0ca1293cc9eb",
+ "@id": "urn:9455faad-b8cd-462a-a17d-795342424c45",
"Label": "3dmaskave",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18",
+ "@id": "urn:77118d6c-abae-4566-a58f-c5813e9b102c",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:7d63f25f-d6b3-4cdc-8adb-96dd6839ae99"
+ "urn:935b4ec8-79a3-4e1f-994e-29c2f7242a36"
]
},
{
- "@id": "urn:adf3450f-9bdb-4b4c-8f53-8d0a2f0dfd37",
+ "@id": "urn:86c6e3c7-7ffe-4555-8dc3-3b571ddee012",
"Label": "3dcalc",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
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- "urn:98687417-079d-459f-ab4a-89047b25a9ea"
+ "urn:c5c4d138-bb2c-48b5-a3c2-79041dd19565",
+ "urn:e69f21ae-6759-4681-95b6-c8ad39e7de22"
]
},
{
- "@id": "urn:a8fe7655-9fee-499e-892a-e6bdb67b388b",
+ "@id": "urn:f4544d21-aeac-43af-8bee-dce242d6ad99",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:e050691d-f536-4747-9ebe-064e710a975e"
+ "urn:e0e86ef2-0070-4e6a-a7ef-2048348dca4a"
]
},
{
- "@id": "urn:1f300416-cb44-4146-9f15-9c00172b67c2",
+ "@id": "urn:dfcbdf85-06e9-4175-ad85-a65841a04ff1",
"Label": "1dcat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:a1376e07-2ae9-42a9-8615-463d27aac63d"
+ "urn:fdf9bf5c-f5b2-418f-809d-c9ae3fb7c49a"
]
},
{
- "@id": "urn:ee1dc8c2-1f47-49cd-be91-a9401a7b67e3",
+ "@id": "urn:06dd1a96-a05a-4144-b35a-53463465f137",
"Label": "1dcat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:b65d59ee-f13f-453c-8a53-7f81bbb2b531"
+ "urn:d9d80477-49d0-45ec-9721-6439160eab83"
]
},
{
- "@id": "urn:93e140f6-011a-4a88-a0e2-45d4dcabf556",
+ "@id": "urn:5dd29509-b5b3-44e5-a292-7d62809c22b2",
"Label": "3dTstat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:106c67ad-3cda-4b75-9642-0d563c02bba6"
+ "urn:30436b61-6099-453e-a5a4-2cabd5f7c9af"
]
},
{
- "@id": "urn:2b724579-87a4-402f-aeb6-403c1971174d",
+ "@id": "urn:d6457024-b31d-4316-a44c-204f5f2b561b",
"Label": "1dcat",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:106c67ad-3cda-4b75-9642-0d563c02bba6"
+ "urn:30436b61-6099-453e-a5a4-2cabd5f7c9af"
]
},
{
- "@id": "urn:0c95da24-bf76-40de-be8e-720ca4a8bc09",
+ "@id": "urn:e0e55412-d874-484b-9271-f297fc987ca8",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916"
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad"
]
},
{
- "@id": "urn:3990b2ab-c24a-4737-a70a-2d9e95fae845",
+ "@id": "urn:5a83e6ba-4f1c-459f-8b9f-60f61e9444e5",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916"
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad"
]
},
{
- "@id": "urn:e65f2878-6f13-488c-ac81-1600790903d6",
+ "@id": "urn:3e2049c4-7134-443a-bcaa-32771d013ee9",
"Label": "3dClustSim",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:8306f482-d9ff-4eb9-b0b1-67182a7af916"
+ "urn:e5c7fec3-13ac-43b2-b147-e6c89efc06ad"
]
},
{
- "@id": "urn:9c2c6c31-e6f6-4773-a202-95c36cda8dc2",
+ "@id": "urn:9436c7f5-ce44-4311-8385-1d54351a4e9f",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:7bc3df53-d61f-4ead-96d2-ec4e5c114672"
+ "urn:30833595-df15-473c-9fbc-b51b46f6220f"
]
},
{
- "@id": "urn:59c6504b-32b9-4a78-88ba-e3e3e4518c34",
+ "@id": "urn:05e2ae8c-a0d2-4c68-bdf1-06b76f859ccd",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:eeb49e8b-7789-4684-b1c9-777ee690492a",
+ "AssociatedWith": "urn:bf539143-ed61-483a-9a54-b5409615e050",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f",
+ "@id": "urn:5f88ea35-c580-447b-9fcd-a365ca8b1160",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:034865b2-36f6-45ff-9ca0-89dd56ddd22d",
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+ "@id": "urn:bf13f751-1153-4368-91c1-d903622f7d4d",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:6442d6c7-861e-47b6-a7ec-869397d3fd3c"
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},
{
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+ "@id": "urn:c59e7f5b-8800-43da-9512-3cf33aa2d64f",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_other_template/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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+ "@id": "urn:81bdbe32-8fd2-4c86-ad90-d75314e52071",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_other_template/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:01916163-39ab-406b-a4ad-fe365cf6bf5e"
+ "GeneratedBy": "urn:829059e7-40d3-402e-acd7-52ce046b7263"
},
{
- "@id": "urn:b7aa1492-f271-4938-ba63-83b2832e399d",
+ "@id": "urn:b43412a0-0f56-4d67-8a7e-634c25544801",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "./afni_other_template/sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
},
{
- "@id": "urn:7cbb179d-b703-4f73-8e1f-296962f7bdf8",
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"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:f8ad3805-7098-4b47-bba8-e210230c5e80"
+ "GeneratedBy": "urn:132f3df2-fdac-4638-b3f8-9cd0419c22c1"
},
{
- "@id": "urn:67953245-9625-4958-9ed6-f255c3196cd3",
+ "@id": "urn:10c6cdeb-975a-41c9-9aaf-33d0116e2f1a",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
}
},
{
- "@id": "urn:1f493787-989c-4c06-97df-d5dde83c5dcf",
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"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:a5fc0d33-b76e-4555-a307-ff6b719128b6"
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{
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+ "@id": "urn:b41be70e-3eba-42fd-92e5-4df0444a18d4",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
}
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{
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+ "@id": "urn:7a4a12d7-5a06-4bdf-8fd7-293ac5d81594",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:40782800-0f18-44eb-927b-9a18f874c562",
+ "GeneratedBy": "urn:8c1d797a-e34c-4dd4-824a-c86c07724873",
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{
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+ "@id": "urn:a5544002-4cbd-4868-b71c-6e0c24c19d43",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
}
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{
- "@id": "urn:82533282-c050-4033-8227-7a8e5d1dcc98",
+ "@id": "urn:998766df-e6b7-4f78-9b68-f4ee34f913b1",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:e14ccb8f-542f-4043-aa5b-2ad720a90fa5",
+ "GeneratedBy": "urn:ac3714cf-12be-4dc0-9fcb-85e5d0bbd814",
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+ "@id": "urn:cd71ca90-9d31-4ea5-8682-c1ffa03bd643",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:f1e74580-01fc-4bcb-8267-dfeca3c1fcab",
+ "GeneratedBy": "urn:f3ad61b2-b139-4bad-a97d-9573066dfecf",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
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{
- "@id": "urn:05d94c20-ed16-47dd-855c-7eeb5b6b8da2",
+ "@id": "urn:e2ea16a5-484e-40af-a288-0b67e8bad57d",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
}
},
{
- "@id": "urn:f18b385c-ae9d-432e-a000-11b8fcc937f0",
+ "@id": "urn:72873482-a03b-4df2-a3cf-7cbffadb3ca7",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +710,16 @@
}
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{
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+ "@id": "urn:5a798d51-b0f0-4d2e-81da-8f835a289d93",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:9f95d75b-2960-4442-b622-cfa279765332",
+ "GeneratedBy": "urn:28dda7e2-20ef-4432-8591-f8a7685dfa2c",
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}
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{
- "@id": "urn:525db306-486b-4f71-9290-dbb1682ab1f7",
+ "@id": "urn:8728fc5c-5b88-4df7-8a17-9a0db37977b2",
"Label": "TT_icbm452",
"AtLocation": "TT_icbm452+tlrc",
"digest": {
@@ -727,7 +727,7 @@
}
},
{
- "@id": "urn:34a6ccc1-c1a9-4abc-9c95-3c421aed66d5",
+ "@id": "urn:a022eaa3-cbe6-449f-ad71-de6f40c3385b",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
}
},
{
- "@id": "urn:5ac2aa06-d1d0-4302-9070-1a4f8ee7298d",
+ "@id": "urn:d4caa5e8-8399-4a90-8650-f7ddb831f026",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +743,16 @@
}
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{
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+ "@id": "urn:354f9b5f-7299-4cb0-ac4f-d336008774f5",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:055168ca-a31a-46a5-9856-c4d65f4ff571",
+ "GeneratedBy": "urn:114e3532-8f75-43c4-8325-0411b3f2d898",
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{
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+ "@id": "urn:9981c55e-0d2a-4cac-8dac-2cbbc84e1fef",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +760,34 @@
}
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{
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"AtLocation": "mat.r$run.vr.aff12.1D",
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+ "@id": "urn:b7832027-315a-4c02-a724-80f5aec4ff08",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:af12b69b-fe39-4e11-90eb-ebe03f5f448a",
+ "GeneratedBy": "urn:ec3229a5-b849-4c4b-b171-3c3e320464b3",
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+ "@id": "urn:120c218e-37ec-43c4-bf0b-6e126b10530e",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:e777f8b9-880c-4a71-ad01-43f3f0abbeee",
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"digest": {
@@ -795,16 +795,16 @@
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{
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"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:c73caae5-64c6-4d21-8599-9e670b9bfb9b",
+ "GeneratedBy": "urn:dfa1c116-dd9b-4a89-b521-148073f45dd4",
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@@ -812,16 +812,16 @@
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@@ -1093,25 +1093,25 @@
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@@ -1161,16 +1161,16 @@
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@@ -1178,25 +1178,25 @@
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"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:57e2f46d-dd77-4e80-91e3-0ca1293cc9eb",
+ "GeneratedBy": "urn:9455faad-b8cd-462a-a17d-795342424c45",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:7d63f25f-d6b3-4cdc-8adb-96dd6839ae99",
+ "@id": "urn:935b4ec8-79a3-4e1f-994e-29c2f7242a36",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:b2fca499-d8d3-420e-8e29-639297190429",
+ "@id": "urn:39034638-6c66-4cb9-9372-fde68eb5b1a0",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18",
+ "GeneratedBy": "urn:77118d6c-abae-4566-a58f-c5813e9b102c",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:0a236937-57ed-4fa9-8a42-42c9f451dcab",
+ "@id": "urn:c5c4d138-bb2c-48b5-a3c2-79041dd19565",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:7fc2e81a-11c5-4b76-920d-9f1edce0cf30",
+ "@id": "urn:fef2a43c-eaae-4ebc-b7ef-589205bef810",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:adf3450f-9bdb-4b4c-8f53-8d0a2f0dfd37",
+ "GeneratedBy": "urn:86c6e3c7-7ffe-4555-8dc3-3b571ddee012",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:e050691d-f536-4747-9ebe-064e710a975e",
+ "@id": "urn:e0e86ef2-0070-4e6a-a7ef-2048348dca4a",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:d12ea473-b377-4973-9a8e-a4370097b02e",
+ "@id": "urn:2511e06b-b1e2-40db-8fb8-b4b80d6be4f9",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:a8fe7655-9fee-499e-892a-e6bdb67b388b",
+ "GeneratedBy": "urn:f4544d21-aeac-43af-8bee-dce242d6ad99",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:a1376e07-2ae9-42a9-8615-463d27aac63d",
+ "@id": "urn:fdf9bf5c-f5b2-418f-809d-c9ae3fb7c49a",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb",
+ "@id": "urn:243917d6-f1de-4d9b-9a28-5b18b08c2b7d",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:1f300416-cb44-4146-9f15-9c00172b67c2",
+ "GeneratedBy": "urn:dfcbdf85-06e9-4175-ad85-a65841a04ff1",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:b65d59ee-f13f-453c-8a53-7f81bbb2b531",
+ "@id": "urn:d9d80477-49d0-45ec-9721-6439160eab83",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:35b33c51-06cd-4fc3-9a42-dc5335988375",
+ "@id": "urn:a8a46b77-99a6-42bf-837a-9a8c1c51f833",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:ee1dc8c2-1f47-49cd-be91-a9401a7b67e3",
+ "GeneratedBy": "urn:06dd1a96-a05a-4144-b35a-53463465f137",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:106c67ad-3cda-4b75-9642-0d563c02bba6",
+ "@id": "urn:30436b61-6099-453e-a5a4-2cabd5f7c9af",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:ae4b287d-dd72-480d-8334-3c0539a4d541",
+ "@id": "urn:dc20e262-17a0-4086-a588-6fd64f621ed6",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:93e140f6-011a-4a88-a0e2-45d4dcabf556",
+ "GeneratedBy": "urn:5dd29509-b5b3-44e5-a292-7d62809c22b2",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:ce5318f7-cbe7-499e-bbb5-4ad119b79e07",
+ "@id": "urn:93f66e36-dea1-4356-88fe-da648830d7e3",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:2b724579-87a4-402f-aeb6-403c1971174d",
+ "GeneratedBy": "urn:d6457024-b31d-4316-a44c-204f5f2b561b",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:b69ed67d-30d0-4ac4-b43a-90f19d8aeb04",
+ "@id": "urn:f6487662-966c-4737-93d3-db7ce991e7ec",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:0c95da24-bf76-40de-be8e-720ca4a8bc09",
+ "GeneratedBy": "urn:e0e55412-d874-484b-9271-f297fc987ca8",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:c4f4cc11-80af-41f1-af25-079c326a068c",
+ "@id": "urn:75ea91ca-4795-435d-8ac0-1e19fd2ff4c0",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:3990b2ab-c24a-4737-a70a-2d9e95fae845",
+ "GeneratedBy": "urn:5a83e6ba-4f1c-459f-8b9f-60f61e9444e5",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:2abffd1a-63a7-49a5-a031-c8a4bcbc73e0",
+ "@id": "urn:2dd4bdd9-81a3-4671-ae2b-3303e79bd597",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:e65f2878-6f13-488c-ac81-1600790903d6",
+ "GeneratedBy": "urn:3e2049c4-7134-443a-bcaa-32771d013ee9",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:7bc3df53-d61f-4ead-96d2-ec4e5c114672",
+ "@id": "urn:30833595-df15-473c-9fbc-b51b46f6220f",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:635786d0-a31c-4c2c-8cff-86fb4e69561f",
+ "@id": "urn:ce6d0fcd-9703-44df-9e5e-d126eaee7f4c",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:59c6504b-32b9-4a78-88ba-e3e3e4518c34",
+ "GeneratedBy": "urn:05e2ae8c-a0d2-4c68-bdf1-06b76f859ccd",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_other_template_proc.png b/examples/from_parsers/afni/afni_other_template_proc.png
index fff87d267..954de11da 100644
Binary files a/examples/from_parsers/afni/afni_other_template_proc.png and b/examples/from_parsers/afni/afni_other_template_proc.png differ
diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.jsonld b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
new file mode 100644
index 000000000..fcc5c0377
--- /dev/null
+++ b/examples/from_parsers/afni/afni_other_template_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:c298904f-7dd0-43d6-850f-e024a40b1cf2",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_other_template/tone_counting_onset_times.txt ./afni_other_template/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy ./afni_other_template/sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:52dc58df-35c5-4d53-999e-2377d2e2eddd",
+ "urn:fb9f4b8d-e79b-4082-952e-839608db3b81",
+ "urn:79ddf8b9-1b42-46e8-ae11-c94065e05fa1"
+ ]
+ },
+ {
+ "@id": "urn:b5ef5827-8b9c-420a-ba5d-ff074a4816e4",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat ./afni_other_template/sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:51621115-ddfd-4b47-a945-1f41a2d2d1ae"
+ ]
+ },
+ {
+ "@id": "urn:2c2a2a5f-12d9-443d-8307-038476e05738",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:785ab00d-b2b2-4d41-9517-5340e9a6b666",
+ "urn:b9abc1ea-bd24-4d11-9265-b47515b60018"
+ ]
+ },
+ {
+ "@id": "urn:1094048a-35c9-4b7e-a180-70ace816a1b5",
+ "Label": "tshift",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:785ab00d-b2b2-4d41-9517-5340e9a6b666"
+ ]
+ },
+ {
+ "@id": "urn:b3d8eda4-b9f9-403e-a4c2-21b5fb08c82e",
+ "Label": "align",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:876c515d-0b2c-4896-a395-f5208dbee953",
+ "urn:ad185281-72cb-4c30-9556-4af3978bbe83"
+ ]
+ },
+ {
+ "@id": "urn:c32b3dea-3bb5-460f-836b-f0d37c0c92f4",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "@auto_tlrc -base TT_icbm452+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:5a20644f-8235-42e5-b56f-e86bb7753ecd",
+ "urn:c4a84cc8-b43e-4379-8adc-83c8d4b5727e",
+ "urn:37121a7c-b567-4f85-a500-bb3562563a9d"
+ ]
+ },
+ {
+ "@id": "urn:dfe214b8-a7ec-45f5-90bd-927c66e253c2",
+ "Label": "volreg",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "urn:37121a7c-b567-4f85-a500-bb3562563a9d",
+ "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
+ "urn:170a2642-1f39-449a-b52c-43a3f96332f4",
+ "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
+ "urn:e263f16e-cedc-4489-bc9a-a3b69f9a926e",
+ "urn:0b2b92bb-d5a0-481b-b286-f5524c5174c7",
+ "urn:c7b8d196-180d-4429-99a9-be28c989cfc1",
+ "urn:0b1a99ce-3115-4f96-b2c8-98f09202047a",
+ "urn:18029782-11f3-474d-a4b0-03ab12abe0b6",
+ "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
+ "urn:5b603fd4-6998-4e64-b80b-e8c5d0c4544a"
+ ]
+ },
+ {
+ "@id": "urn:bcca5728-ee7a-4910-b04e-4afe1f0100d4",
+ "Label": "blur",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:5b07097b-74e7-4377-be56-e02e611bc43f",
+ "urn:67c675a6-233a-4f89-9391-a7e140980dfb"
+ ]
+ },
+ {
+ "@id": "urn:1e06fa49-f568-4a8d-95b1-1b00344d42c2",
+ "Label": "mask",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_icbm452+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:4274fe0d-59d1-4526-b361-8143401dfa7e",
+ "urn:559ab88d-a226-41c0-aee7-6b3c5cfbe790",
+ "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
+ "urn:b979651c-e069-41c3-9435-6a7efa49c0f1",
+ "urn:0d886edf-85d6-4249-a71d-d809e5498e82",
+ "urn:37a9d9ad-1722-4d7b-a9fd-2cd6c084801b",
+ "urn:0d886edf-85d6-4249-a71d-d809e5498e82",
+ "urn:37a9d9ad-1722-4d7b-a9fd-2cd6c084801b",
+ "urn:559ab88d-a226-41c0-aee7-6b3c5cfbe790",
+ "urn:5bb841a2-ccbb-4a7a-8b72-a203131c444e",
+ "urn:e10fd682-f04d-4409-acd1-93a8ee367508"
+ ]
+ },
+ {
+ "@id": "urn:a3f2f8a1-7fef-44a9-9328-c23a6932e226",
+ "Label": "scale",
+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:4274fe0d-59d1-4526-b361-8143401dfa7e",
+ "urn:0b1a99ce-3115-4f96-b2c8-98f09202047a",
+ "urn:189beb08-e9a2-4516-9240-a715584e0031",
+ "urn:4274fe0d-59d1-4526-b361-8143401dfa7e"
+ ]
+ },
+ {
+ "@id": "urn:dbb3dfce-3c0a-4c43-89f6-c10b5c5dacb7",
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+ "AssociatedWith": "urn:035f1ae5-a898-46bd-a450-430331b8b987",
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+ "GeneratedBy": "urn:1e97af62-8e80-4922-b801-9fbfd1c08e95",
+ "digest": {
+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:1e8511ba-b59a-4a5f-b495-420e96ddf884",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:0613b8de-2123-4f1e-9661-006a4bb01370",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:dd59d2c2-9e43-4dac-b1d2-71a3db038952",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_other_template_proc_block.png b/examples/from_parsers/afni/afni_other_template_proc_block.png
new file mode 100644
index 000000000..8129764e9
Binary files /dev/null and b/examples/from_parsers/afni/afni_other_template_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
index e1a113da0..50036bd3b 100644
--- a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "@id": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:bfa4a7f1-6a8c-46fc-82d2-6b2698f7d075",
+ "@id": "urn:9409d309-6e12-4b1c-94b2-7bee390b752e",
"Label": "Make directory",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620",
+ "@id": "urn:19ab30f4-d471-4bcc-9a78-eec044705c90",
"Label": "Make directory",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:623eb35c-21fa-4b31-8073-dfdba666871f",
+ "@id": "urn:2d9ff369-4529-4847-81b1-9444562e5d64",
"Label": "cp",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:b144c679-bde6-4e53-9a44-652deac50c93",
- "urn:e4344175-20ec-4b1d-b49f-7542d37e6caa"
+ "urn:33c75be3-aa4e-406c-baeb-c6b0c73dd6e4",
+ "urn:e6787718-533c-4ee0-9c8b-804f603f9942"
]
},
{
- "@id": "urn:e9dcd1ce-f9a5-4c85-8831-8e2118f3e436",
+ "@id": "urn:9a05342f-5bd5-43c7-ad4c-c0335f9a38fb",
"Label": "3dcopy",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:52cfe718-8d39-42bd-9e65-221b5e1969e8"
+ "urn:fefe30f0-2f4a-4307-9cad-d79ba9e76530"
]
},
{
- "@id": "urn:57c70746-bc5d-4d0f-ac6b-cf37f0e790d1",
+ "@id": "urn:96a73f71-358d-457f-8892-670c9b5e4c54",
"Label": "3dTcat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:0c66e2d5-902c-44fa-b9ac-fed0bf0f581f"
+ "urn:9723d944-903b-4c04-8a8f-b4d78556e8b4"
]
},
{
- "@id": "urn:1dc5978a-3a2c-41fe-93da-da44031facdc",
+ "@id": "urn:f018e574-c168-4881-888c-9219e4b677b5",
"Label": "3dToutcount",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:591e78c6-f12c-49e6-b053-b365d9daf3b8"
+ "urn:7b77f6cf-4ed2-464a-90d4-623dd12ada75"
]
},
{
- "@id": "urn:771015e0-2dcd-4c90-b82f-1910bff41ca0",
+ "@id": "urn:1b781f3e-d5fd-400c-89de-ff3f0fa207a7",
"Label": "cat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:0ae1180e-9758-449b-96a6-998f6c382716"
+ "urn:57568e78-c209-4703-8379-c145283e032f"
]
},
{
- "@id": "urn:c11c7f24-d9c0-48d8-9db1-fe7b3d9f617f",
+ "@id": "urn:c6a468b6-cc4a-43b3-ac27-31554da9d2fc",
"Label": "3dTshift",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:591e78c6-f12c-49e6-b053-b365d9daf3b8"
+ "urn:7b77f6cf-4ed2-464a-90d4-623dd12ada75"
]
},
{
- "@id": "urn:7d6b4ad3-03f6-4196-a307-35cc3bd624d6",
+ "@id": "urn:c0a5b861-e47c-4344-9a73-9d2816eaea9c",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:05e8ba57-1f57-44a5-bad6-794adef06065",
- "urn:d124a1ec-ede9-4c55-9f3b-5534ba2d4bf1"
+ "urn:0bbb1294-8273-4059-89d9-af92f4a71b99",
+ "urn:cb843ce6-4f3d-488c-8ca2-98c312821d59"
]
},
{
- "@id": "urn:5a483cd7-a169-420c-b682-fe81b2fb4411",
+ "@id": "urn:6d71a816-eb5c-40c8-abd0-ba55ee51be5c",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:4d9e730a-a6b0-4067-8b79-32276517f8bc",
- "urn:987e241d-ef25-4cbc-a063-20943d5391b1"
+ "urn:17e338e3-78a3-420f-ab4b-f48e30cbd207",
+ "urn:4c92e3a4-6cf2-4fa0-9fa6-91e0dcda8b8d"
]
},
{
- "@id": "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
+ "@id": "urn:0f4d707a-72e8-42d9-bfe8-0c2db37553b3",
"Label": "cat_matvec",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:8e09f9b8-62f0-43fa-9be3-9d37b3e3ffb0"
+ "urn:24d65676-5458-4491-b14d-afc59bdc3e7c"
]
},
{
- "@id": "urn:8a10bc3b-8f5a-48c0-86e4-74a908ff2dff",
+ "@id": "urn:fc13645c-7312-4383-ae53-acf45451ee3b",
"Label": "3dvolreg",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:f419f0a0-b006-4fad-abe7-2d18c1268838"
+ "urn:f4d3c9da-afba-4300-bdb6-8b2eddc90883"
]
},
{
- "@id": "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
+ "@id": "urn:a39399d3-0741-43a7-9dfb-b26d5ad05a16",
"Label": "3dcalc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:f419f0a0-b006-4fad-abe7-2d18c1268838"
+ "urn:f4d3c9da-afba-4300-bdb6-8b2eddc90883"
]
},
{
- "@id": "urn:f8d879cd-b835-4036-a683-af5dccf73a8e",
+ "@id": "urn:f22c9f55-f2c2-4817-92f3-730166d502e6",
"Label": "cat_matvec",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:8e09f9b8-62f0-43fa-9be3-9d37b3e3ffb0"
+ "urn:24d65676-5458-4491-b14d-afc59bdc3e7c"
]
},
{
- "@id": "urn:816a65be-5552-4100-89ab-2eb490723213",
+ "@id": "urn:f19ccc20-154f-4cee-9abd-ec0a43848b3d",
"Label": "3dAllineate",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:6dff238f-00fc-4ce2-9c25-489dbde3e9e7",
- "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407",
- "urn:f419f0a0-b006-4fad-abe7-2d18c1268838"
+ "urn:43044f87-e488-43eb-8305-0ff802654d36",
+ "urn:f4d3c9da-afba-4300-bdb6-8b2eddc90883",
+ "urn:f58b2410-1003-4339-820b-f8d53e229a17"
]
},
{
- "@id": "urn:3ac15d53-254f-4af7-9550-dbf93b032f0a",
+ "@id": "urn:0b111a92-c24b-463f-b287-d4090823ed0c",
"Label": "3dAllineate",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:6dff238f-00fc-4ce2-9c25-489dbde3e9e7",
- "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407",
- "urn:fa158950-3648-4ab8-a9b3-b11a2c48ac17"
+ "urn:43044f87-e488-43eb-8305-0ff802654d36",
+ "urn:b7bd3c57-1d8d-4cd8-9a1c-67c8b0962dfc",
+ "urn:f58b2410-1003-4339-820b-f8d53e229a17"
]
},
{
- "@id": "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "@id": "urn:09963577-4d12-4c45-b9d1-d37b89b1772f",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f"
+ "urn:91318679-1f06-4646-bf2f-168ab6ba91ed"
]
},
{
- "@id": "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "@id": "urn:e4ffa6c2-3aaa-4e9c-86ef-f100b66c8858",
"Label": "cat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3"
+ "urn:1d22dfd7-820c-47f1-a56f-71c83fc51b1a"
]
},
{
- "@id": "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "@id": "urn:9efbf360-3367-48bb-84f5-b1c6d36200fc",
"Label": "3dcopy",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae"
+ "urn:09394dac-4d4d-4232-b1eb-73e58f8eb813"
]
},
{
- "@id": "urn:b97857bc-8e1c-448e-82f9-d862603dac3a",
+ "@id": "urn:b07e9f43-bab7-4505-bb00-8d93a7da789f",
"Label": "3dcalc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
- "urn:5bad2a8e-da77-4dab-8f6a-3821b93f7584"
+ "urn:1fb8b55b-7e5a-4562-a76a-8de3078be908",
+ "urn:4d096062-937a-423a-b156-281a3a0a9777"
]
},
{
- "@id": "urn:aae37e92-7f20-4842-85f6-e8dea5c49544",
+ "@id": "urn:8cfe4c47-39a7-4a5f-b536-c73da420a8c7",
"Label": "3dcopy",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407"
+ "urn:43044f87-e488-43eb-8305-0ff802654d36"
]
},
{
- "@id": "urn:9b02e101-35be-41fb-81cb-4ebd4c4fb7ad",
+ "@id": "urn:33a215f5-9350-45b5-a102-e4271fdf8a02",
"Label": "3dAllineate",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:f7c6cade-4218-4595-9786-416f1729ab69"
+ "urn:91e6e90d-7fd9-4fe3-9c65-1029ada5d21f"
]
},
{
- "@id": "urn:3ab3463b-3e76-4459-b00c-557a44d4c9c9",
+ "@id": "urn:7bd74fec-fc5a-41bb-8129-3c537670646c",
"Label": "3dmerge",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:69a32e1f-1ad9-4ef3-bd2f-8f089d7c77a2",
- "urn:ba9a1f75-9c10-4b6d-a32e-c00a9bf2b14d"
+ "urn:90825931-1e37-4c79-845e-6ce2e98b2146",
+ "urn:99201411-5eee-469b-81c1-36c191c6b6e5"
]
},
{
- "@id": "urn:791a37dd-7139-4be3-8f65-6c9aeb2c26fc",
+ "@id": "urn:694c8087-4fe7-49de-ab21-f825fba8cd0c",
"Label": "3dAutomask",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:f4774edf-b61c-4c85-8419-6b40dc2dbefb"
+ "urn:1ffb7dad-6d9a-435f-b673-8b407b6969d3"
]
},
{
- "@id": "urn:76cbe384-e9c5-4aee-a9eb-7366d46724c1",
+ "@id": "urn:2ee58116-eebd-4488-8377-a427284d53ad",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:bf3a439e-808c-464e-9cd8-69074082b387",
+ "@id": "urn:9d5421c8-486d-42bc-b1d3-2fbb5ac86472",
"Label": "3dresample",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407",
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:43044f87-e488-43eb-8305-0ff802654d36",
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6"
]
},
{
- "@id": "urn:5c5699fb-c65a-4996-825d-ce14595563a1",
+ "@id": "urn:5403d109-bb63-40c4-9259-6bdc9aac185b",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:e81bd603-ebba-48a7-b6bd-4c1a05624465"
+ "urn:e72745d0-8643-4d35-ba85-e602bf262c70"
]
},
{
- "@id": "urn:ae87f8ec-8897-45c2-ad21-3a90f68cc8a3",
+ "@id": "urn:ad5b6124-ac68-4f65-9a83-9311a31d76d0",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:34719411-7497-4c69-b992-c6f535d92daf",
- "urn:954374eb-04ef-496a-9bdf-67dd9f2e356f"
+ "urn:4535058f-5e78-4d0f-8345-43b9cac46637",
+ "urn:edba3b28-6853-47ac-93a6-362a4e4cf4a4"
]
},
{
- "@id": "urn:62bdae8b-6b1c-4858-b2cf-d5c2ff2cb091",
+ "@id": "urn:3860facc-04c6-484f-bfdc-1c8f26e35046",
"Label": "3ddot",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:34719411-7497-4c69-b992-c6f535d92daf",
- "urn:954374eb-04ef-496a-9bdf-67dd9f2e356f"
+ "urn:4535058f-5e78-4d0f-8345-43b9cac46637",
+ "urn:edba3b28-6853-47ac-93a6-362a4e4cf4a4"
]
},
{
- "@id": "urn:6a92fc75-06fa-4645-ada0-51d2db7973ff",
+ "@id": "urn:2a39471a-4d01-4594-9f52-1bc9808a9542",
"Label": "3dresample",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:19061152-20cb-44a9-b105-37ea07b1c40c",
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6",
+ "urn:e91c878a-3a1c-4e2e-afb2-cea694f8cfab"
]
},
{
- "@id": "urn:cea362b5-c487-4ac4-83e4-18c7930ab27b",
+ "@id": "urn:18ce82e3-98b1-4bc1-8d21-6baecf8def51",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:3d0a295f-b783-4a04-94ac-2699c42f2e93"
+ "urn:7bba9bc4-f141-4036-bfe9-719e2f2f674d"
]
},
{
- "@id": "urn:d3466c6f-52aa-4ec1-9675-14ca8a0c829d",
+ "@id": "urn:7db798dd-6c0b-44c4-9157-25acc6391ff8",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:f4774edf-b61c-4c85-8419-6b40dc2dbefb"
+ "urn:1ffb7dad-6d9a-435f-b673-8b407b6969d3"
]
},
{
- "@id": "urn:d49417ba-b147-45e6-b7ff-817b9cb3b843",
+ "@id": "urn:73e1291d-b339-436f-b8c7-f9c93ceb0c63",
"Label": "3dcalc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:5bad2a8e-da77-4dab-8f6a-3821b93f7584",
- "urn:b948ef91-aa46-4140-b8b7-c6abf40b9022",
- "urn:f4774edf-b61c-4c85-8419-6b40dc2dbefb"
+ "urn:1ffb7dad-6d9a-435f-b673-8b407b6969d3",
+ "urn:4d096062-937a-423a-b156-281a3a0a9777",
+ "urn:75548ade-ead8-4b08-8c99-a4b85a134c18"
]
},
{
- "@id": "urn:f3acd084-9b36-409e-a912-a64754a2c496",
+ "@id": "urn:7fff857f-dabf-408d-af75-bf7637c2e7ca",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d"
+ "urn:5fe35b80-571f-4c9a-8515-bbf775026802"
]
},
{
- "@id": "urn:dc701791-8a77-4bd3-824a-7020c444d4ad",
+ "@id": "urn:c424e895-a3c1-481a-8fdc-27f12b374808",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d"
+ "urn:5fe35b80-571f-4c9a-8515-bbf775026802"
]
},
{
- "@id": "urn:6f970a8c-d670-4c0e-8b97-41839e3c3c90",
+ "@id": "urn:61c7bd3a-5bdf-448f-9deb-d13ead4dd708",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d"
+ "urn:5fe35b80-571f-4c9a-8515-bbf775026802"
]
},
{
- "@id": "urn:6f0bc278-4854-410a-8ce5-2c52d30c5e7b",
+ "@id": "urn:8f9c2f28-04d8-4c7f-803d-b3227c169a98",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:62ffd710-b951-4dcd-b02a-998f4f6c013a"
+ "urn:a745a2fb-4636-4f0f-829b-76e7ea216015"
]
},
{
- "@id": "urn:24abf5de-fe14-4a83-8d3c-5e3a723811fc",
+ "@id": "urn:ea0e14e3-1598-42d3-a812-3e2ba8bdbbdc",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:91b73b5b-9e5a-4fce-b26f-5ae449d84088"
+ "urn:987d4ecb-adbd-4da2-bee7-80c8e1c21133"
]
},
{
- "@id": "urn:26ec0d70-3f21-4bfe-be83-27f9b8eda5f9",
+ "@id": "urn:38551fef-e588-44a6-b934-93cb671a56f6",
"Label": "3dTcat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:62ffd710-b951-4dcd-b02a-998f4f6c013a"
+ "urn:a745a2fb-4636-4f0f-829b-76e7ea216015"
]
},
{
- "@id": "urn:2efbc0e7-5b73-40dc-aab5-ba4b75054202",
+ "@id": "urn:077d73ee-2b99-43bb-8424-92d76d6ace15",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:f9da1d1c-0b53-4cf6-8ce5-8d37378b9b39"
+ "urn:afe8afc2-9672-4930-8691-fb8cea8239b2"
]
},
{
- "@id": "urn:2f09814e-eede-4696-bec8-1ffdf054d5e3",
+ "@id": "urn:f8bf025a-bf6e-49f7-a38c-ca65385dd71d",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:9c40682e-36d5-484f-a9ff-c5cfe101b371"
+ "urn:c448dd97-8997-44c6-b2f6-886a6a116cbf"
]
},
{
- "@id": "urn:f03a6b50-e568-43a5-b8d2-7f9a7461a358",
+ "@id": "urn:3c91a86f-673d-40f3-b844-24466965e0c9",
"Label": "3dcalc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:9233b191-251a-4f59-890e-8d49c8a317bc",
- "urn:aec70b1e-a52a-4c34-afbe-58bab274e85c",
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6",
+ "urn:9254ee69-c36c-4f52-a2d5-9b6f37782f50",
+ "urn:d2ec1e1f-6b72-4cd0-8bdd-015b1729e259"
]
},
{
- "@id": "urn:12c84262-3f99-41ec-a2e4-182b6dd07816",
+ "@id": "urn:e5f10ca6-7c17-452e-8bb8-60d5ef7cbcbe",
"Label": "3dTnorm",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:579d4770-d941-467a-9f45-5d41330a8ad1"
+ "urn:dbde917c-9ba0-4d04-bd2d-fd2c34c2d061"
]
},
{
- "@id": "urn:35549801-9a17-47fb-97c5-a7626cf33543",
+ "@id": "urn:907eef82-bdc1-44ab-b082-0dfa2a28a026",
"Label": "3dmaskave",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:f07ae6c3-d6bc-42a7-861b-015c6da45356",
+ "@id": "urn:67e45d40-4521-44a7-9a69-4a557fce1120",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:868c4d90-2686-4717-8992-e2f78f71982f"
+ "urn:6d0e42e6-fee1-4138-92a2-dc17b126e960"
]
},
{
- "@id": "urn:4aeeec3d-c0c4-41b2-9b59-e75fc2b134e9",
+ "@id": "urn:20e019c2-47db-4582-bbbf-757165739cfb",
"Label": "3dcalc",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:4079b5d6-6d03-4f4f-8e0b-feafb5108030",
- "urn:4b6329f7-79ad-4a55-aa01-952b8b7513db"
+ "urn:349bfb32-1123-4a2f-8fe3-09f4f6f984ec",
+ "urn:5a5ed666-cf2f-4213-b4c3-9fb49c784d57"
]
},
{
- "@id": "urn:97a7a594-07de-445f-a94a-6a1132660219",
+ "@id": "urn:f0bdef22-eca3-4681-b767-71d5b60df1bc",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:5ab4d3ac-a283-4eb9-a6fe-522e161c6524"
+ "urn:1d2c7c93-358b-4b29-8071-c1dd84302329"
]
},
{
- "@id": "urn:c9d55f80-276d-4292-ac96-5869007a076f",
+ "@id": "urn:a3534236-e1a6-40b2-8f8f-b033d89a9d0d",
"Label": "1dcat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:58710505-ae1c-4e15-8b8d-49eb446c14c6"
+ "urn:4582228c-5c9e-4362-af4f-037553005fcb"
]
},
{
- "@id": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
+ "@id": "urn:bbc46cf1-2945-44ae-a29d-9453d9dc7d90",
"Label": "1dcat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:20835fc2-3de2-4f26-a384-721971a8011c"
+ "urn:b6aa3e9a-7625-4de7-a443-a1d0caffeedb"
]
},
{
- "@id": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "@id": "urn:12b01b25-f812-4a96-b44f-5de5c04b952a",
"Label": "3dTstat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce"
+ "urn:a8cb53b6-104c-4d2f-be09-f14150ec2a23"
]
},
{
- "@id": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "@id": "urn:8067fd08-5f7e-4f27-9136-ac7073d14839",
"Label": "1dcat",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce"
+ "urn:a8cb53b6-104c-4d2f-be09-f14150ec2a23"
]
},
{
- "@id": "urn:39f1ca8b-66d3-4d02-b1e6-5af2de7b426a",
+ "@id": "urn:3ce0d53d-6b9c-4ee6-9c0d-426ad9f2ce5d",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6"
]
},
{
- "@id": "urn:19fb39c5-b85c-4be4-8f4a-c8be81315b19",
+ "@id": "urn:cd429bbc-d81b-4918-ae96-ded7b7e18ce3",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6"
]
},
{
- "@id": "urn:60e714fe-8ee1-42e7-a6da-d0bd9dde8c93",
+ "@id": "urn:ba63182a-d2c9-4442-8ebf-8702b0055293",
"Label": "3dClustSim",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:bca2de57-cd10-45e9-ad12-fe4cdceb7863"
+ "urn:6c86b3b9-616a-44e3-b672-aa3119a86cb6"
]
},
{
- "@id": "urn:cbc9d9a1-d1a6-44f4-a551-6a3c652bccbc",
+ "@id": "urn:25eaecbc-9e22-47b3-bb25-bc1cd9c184a9",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:7875fa28-0d90-44a1-a518-b16af69727f1"
+ "urn:e6e749e0-26ba-4cdb-9160-a7fc1b49740e"
]
},
{
- "@id": "urn:608b662d-4757-4c39-94d5-44c28ff93938",
+ "@id": "urn:5ab6aa9e-0882-49b0-8c88-f1d550948dd0",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
+ "AssociatedWith": "urn:abeb18f9-753c-4bcd-899e-20cd21a9e6bc",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:5ecbb2f9-d628-4980-8bed-9166dcee801a",
+ "@id": "urn:a0e4adbb-6344-4a60-991e-336d5f663b71",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:bfa4a7f1-6a8c-46fc-82d2-6b2698f7d075",
+ "GeneratedBy": "urn:9409d309-6e12-4b1c-94b2-7bee390b752e",
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+ "@id": "urn:837c6c1f-5c41-4ce9-8bf6-5ee96151ec45",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620"
+ "GeneratedBy": "urn:19ab30f4-d471-4bcc-9a78-eec044705c90"
},
{
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+ "@id": "urn:e6787718-533c-4ee0-9c8b-804f603f9942",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_clusterwise_fwe/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
- "@id": "urn:b144c679-bde6-4e53-9a44-652deac50c93",
+ "@id": "urn:33c75be3-aa4e-406c-baeb-c6b0c73dd6e4",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_clusterwise_fwe/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
- "@id": "urn:5620cc29-8198-4896-98b0-1649f1f44ded",
+ "@id": "urn:7e90b8aa-1787-46fb-88cf-ae5ddc1b0750",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:623eb35c-21fa-4b31-8073-dfdba666871f"
+ "GeneratedBy": "urn:2d9ff369-4529-4847-81b1-9444562e5d64"
},
{
- "@id": "urn:52cfe718-8d39-42bd-9e65-221b5e1969e8",
+ "@id": "urn:fefe30f0-2f4a-4307-9cad-d79ba9e76530",
"Label": "sub-01_T1w.nii.gz",
"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
}
},
{
- "@id": "urn:030f431e-c8bd-4ad2-a374-1f115df2930e",
+ "@id": "urn:6bfc100c-c4f0-447a-9e02-461e126840ac",
"Label": "sub-01_T1w",
"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:e9dcd1ce-f9a5-4c85-8831-8e2118f3e436"
+ "GeneratedBy": "urn:9a05342f-5bd5-43c7-ad4c-c0335f9a38fb"
},
{
- "@id": "urn:0c66e2d5-902c-44fa-b9ac-fed0bf0f581f",
+ "@id": "urn:9723d944-903b-4c04-8a8f-b4d78556e8b4",
"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
}
},
{
- "@id": "urn:a5f0a28c-5544-4428-87a1-a296cda93f56",
+ "@id": "urn:a49c2b75-473b-4726-93c3-d0327ef97cd4",
"Label": "pb00.$subj.r01.tcat",
"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:57c70746-bc5d-4d0f-ac6b-cf37f0e790d1"
+ "GeneratedBy": "urn:96a73f71-358d-457f-8892-670c9b5e4c54"
},
{
- "@id": "urn:591e78c6-f12c-49e6-b053-b365d9daf3b8",
+ "@id": "urn:7b77f6cf-4ed2-464a-90d4-623dd12ada75",
"Label": "pb00.$subj.r$run.tcat",
"AtLocation": "pb00.$subj.r$run.tcat+orig",
"digest": {
@@ -659,16 +659,16 @@
}
},
{
- "@id": "urn:f529c4f5-fab8-406d-98a0-0472739c6b6f",
+ "@id": "urn:7970c870-e51d-4fa9-9ea9-b98844305997",
"Label": "outcount.r$run.1D",
"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:1dc5978a-3a2c-41fe-93da-da44031facdc",
+ "GeneratedBy": "urn:f018e574-c168-4881-888c-9219e4b677b5",
"digest": {
"sha256": "63d9f539e5470badc625d557109f68bc4eecbb02ca2667483739d52f95e5d0dd"
}
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{
- "@id": "urn:0ae1180e-9758-449b-96a6-998f6c382716",
+ "@id": "urn:57568e78-c209-4703-8379-c145283e032f",
"Label": "outcount.r*.1D",
"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
}
},
{
- "@id": "urn:19f7f936-05fb-4194-a6d8-10d878641d10",
+ "@id": "urn:d371b84e-3f72-47e0-815d-60bda0e0ea20",
"Label": "outcount_rall.1D",
"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:771015e0-2dcd-4c90-b82f-1910bff41ca0",
+ "GeneratedBy": "urn:1b781f3e-d5fd-400c-89de-ff3f0fa207a7",
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"sha256": "cb887fd5e4d5e9acb3a24820d0f7a62ed38a5ffb0fdedd373440ac0219fb186a"
}
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{
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+ "@id": "urn:834348f8-d41c-407b-a7dd-0209297427d4",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:c11c7f24-d9c0-48d8-9db1-fe7b3d9f617f",
+ "GeneratedBy": "urn:c6a468b6-cc4a-43b3-ac27-31554da9d2fc",
"digest": {
"sha256": "c6bf01cea8d2eac1d7a866f80b865c6e7d4b4e012dbb63d480ac9a8551162d72"
}
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{
- "@id": "urn:d124a1ec-ede9-4c55-9f3b-5534ba2d4bf1",
+ "@id": "urn:0bbb1294-8273-4059-89d9-af92f4a71b99",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
}
},
{
- "@id": "urn:05e8ba57-1f57-44a5-bad6-794adef06065",
+ "@id": "urn:cb843ce6-4f3d-488c-8ca2-98c312821d59",
"Label": "pb01.$subj.r01.tshift",
"AtLocation": "pb01.$subj.r01.tshift+orig",
"digest": {
@@ -710,16 +710,16 @@
}
},
{
- "@id": "urn:8331d741-04e7-4367-ab1f-0e51decade3a",
+ "@id": "urn:ac767057-e6a1-4207-8818-bbb01d04b597",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:7d6b4ad3-03f6-4196-a307-35cc3bd624d6",
+ "GeneratedBy": "urn:c0a5b861-e47c-4344-9a73-9d2816eaea9c",
"digest": {
"sha256": "bd785a075a4c6446e1e54de9e628913f7f1c814e86b69a9fbfe933209e6d37b5"
}
},
{
- "@id": "urn:4d9e730a-a6b0-4067-8b79-32276517f8bc",
+ "@id": "urn:17e338e3-78a3-420f-ab4b-f48e30cbd207",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +727,7 @@
}
},
{
- "@id": "urn:987e241d-ef25-4cbc-a063-20943d5391b1",
+ "@id": "urn:4c92e3a4-6cf2-4fa0-9fa6-91e0dcda8b8d",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
}
},
{
- "@id": "urn:8e09f9b8-62f0-43fa-9be3-9d37b3e3ffb0",
+ "@id": "urn:24d65676-5458-4491-b14d-afc59bdc3e7c",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc::WARP_DATA",
"digest": {
@@ -743,16 +743,16 @@
}
},
{
- "@id": "urn:f7c6cade-4218-4595-9786-416f1729ab69",
+ "@id": "urn:91e6e90d-7fd9-4fe3-9c65-1029ada5d21f",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
+ "GeneratedBy": "urn:0f4d707a-72e8-42d9-bfe8-0c2db37553b3",
"digest": {
"sha256": "800633fb5b4e9be64078bc181c4d5510ffb73fc5cccaf364c7fb6a294aa06728"
}
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{
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+ "@id": "urn:f4d3c9da-afba-4300-bdb6-8b2eddc90883",
"Label": "pb01.$subj.r$run.tshift",
"AtLocation": "pb01.$subj.r$run.tshift+orig",
"digest": {
@@ -760,34 +760,34 @@
}
},
{
- "@id": "urn:10dfb433-94b4-4ea4-b283-3fec0ed1cbd2",
+ "@id": "urn:02ad2de3-ed26-4828-86dd-5090741065b4",
"Label": "mat.r$run.vr.aff12.1D",
"AtLocation": "mat.r$run.vr.aff12.1D",
- "GeneratedBy": "urn:8a10bc3b-8f5a-48c0-86e4-74a908ff2dff",
+ "GeneratedBy": "urn:fc13645c-7312-4383-ae53-acf45451ee3b",
"digest": {
"sha256": "2e6e6c2ce8089cfa3c6e11dc72fca0cc8497f7a55faae2ced402de4867466c91"
}
},
{
- "@id": "urn:a5e308d1-648c-48a2-80f6-91ea050a021c",
+ "@id": "urn:25b260b1-6825-40d3-b423-c05cca0747fb",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
+ "GeneratedBy": "urn:a39399d3-0741-43a7-9dfb-b26d5ad05a16",
"digest": {
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}
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{
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+ "@id": "urn:f58b2410-1003-4339-820b-f8d53e229a17",
"Label": "mat.r$run.warp.aff12.1D",
"AtLocation": "mat.r$run.warp.aff12.1D",
- "GeneratedBy": "urn:f8d879cd-b835-4036-a683-af5dccf73a8e",
+ "GeneratedBy": "urn:f22c9f55-f2c2-4817-92f3-730166d502e6",
"digest": {
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{
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+ "@id": "urn:43044f87-e488-43eb-8305-0ff802654d36",
"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+tlrc",
"digest": {
@@ -795,16 +795,16 @@
}
},
{
- "@id": "urn:d8dbbd9f-bb1b-4993-b567-a239b9bfc293",
+ "@id": "urn:4a25fd24-f3f5-4e89-8aec-1df8d599a71b",
"Label": "rm.epi.nomask.r$run",
"AtLocation": "rm.epi.nomask.r$run",
- "GeneratedBy": "urn:816a65be-5552-4100-89ab-2eb490723213",
+ "GeneratedBy": "urn:f19ccc20-154f-4cee-9abd-ec0a43848b3d",
"digest": {
"sha256": "03d6cba0426c5545e350e6b63a19b0e46f8dfa2223fd08691753e8914a479e36"
}
},
{
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+ "@id": "urn:b7bd3c57-1d8d-4cd8-9a1c-67c8b0962dfc",
"Label": "rm.epi.all1",
"AtLocation": "rm.epi.all1+orig",
"digest": {
@@ -812,16 +812,16 @@
}
},
{
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+ "@id": "urn:f0863245-95c7-43b5-9c32-469ebf21fa5c",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run",
- "GeneratedBy": "urn:3ac15d53-254f-4af7-9550-dbf93b032f0a",
+ "GeneratedBy": "urn:0b111a92-c24b-463f-b287-d4090823ed0c",
"digest": {
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}
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{
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+ "@id": "urn:91318679-1f06-4646-bf2f-168ab6ba91ed",
"Label": "rm.epi.1.r$run",
"AtLocation": "rm.epi.1.r$run+tlrc",
"digest": {
@@ -829,16 +829,16 @@
}
},
{
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+ "@id": "urn:f51d9744-f346-482a-ad1e-ff3c2c5e620c",
"Label": "rm.epi.min.r$run",
"AtLocation": "rm.epi.min.r$run",
- "GeneratedBy": "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "GeneratedBy": "urn:09963577-4d12-4c45-b9d1-d37b89b1772f",
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{
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+ "@id": "urn:1d22dfd7-820c-47f1-a56f-71c83fc51b1a",
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"AtLocation": "dfile.r*.1D",
"digest": {
@@ -846,16 +846,16 @@
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{
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"AtLocation": "dfile_rall.1D",
- "GeneratedBy": "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
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{
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+ "@id": "urn:09394dac-4d4d-4232-b1eb-73e58f8eb813",
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"digest": {
@@ -863,16 +863,16 @@
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{
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+ "@id": "urn:973d08db-2757-4255-a5df-d8705d9b523e",
"Label": "mask_epi_extents",
"AtLocation": "mask_epi_extents",
- "GeneratedBy": "urn:74469c27-c574-4f02-9288-00dcb5161c82",
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{
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"digest": {
@@ -880,7 +880,7 @@
}
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{
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+ "@id": "urn:4d096062-937a-423a-b156-281a3a0a9777",
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"digest": {
@@ -888,34 +888,34 @@
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{
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"AtLocation": "pb02.$subj.r$run.volreg",
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@@ -939,25 +939,25 @@
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@@ -1255,16 +1255,16 @@
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@@ -1272,16 +1272,16 @@
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- "GeneratedBy": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
+ "GeneratedBy": "urn:bbc46cf1-2945-44ae-a29d-9453d9dc7d90",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:f6d1f866-f52d-40b0-a893-4ba09265a1ce",
+ "@id": "urn:a8cb53b6-104c-4d2f-be09-f14150ec2a23",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:5b1e5792-a7c3-4fd3-a40e-1f56638ead1c",
+ "@id": "urn:92eb5d77-cf54-4cc9-bc54-d83c7d463e05",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:7e5081e7-c009-4256-9c58-49b629cdadd5",
+ "GeneratedBy": "urn:12b01b25-f812-4a96-b44f-5de5c04b952a",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:afa442fa-9ff3-4bea-8b48-6677515236e4",
+ "@id": "urn:fa2200bb-fb7c-4e93-af75-14a37b278ed7",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:2afece4b-1134-467c-b01a-33d391048b34",
+ "GeneratedBy": "urn:8067fd08-5f7e-4f27-9136-ac7073d14839",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:6bbcef9d-c59c-420e-af06-7b51ccae0169",
+ "@id": "urn:309094d0-38c7-4b73-b683-aebd81f546ff",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:39f1ca8b-66d3-4d02-b1e6-5af2de7b426a",
+ "GeneratedBy": "urn:3ce0d53d-6b9c-4ee6-9c0d-426ad9f2ce5d",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:053adfcf-45e4-4b25-a9cd-5da93c03211d",
+ "@id": "urn:3c62785c-8c8b-41d2-8681-a25cfc8feab1",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:19fb39c5-b85c-4be4-8f4a-c8be81315b19",
+ "GeneratedBy": "urn:cd429bbc-d81b-4918-ae96-ded7b7e18ce3",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:164dec41-95f0-4393-bd4e-a73b5b698322",
+ "@id": "urn:98b8d939-2139-43fe-9809-aff688aedb64",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:60e714fe-8ee1-42e7-a6da-d0bd9dde8c93",
+ "GeneratedBy": "urn:ba63182a-d2c9-4442-8ebf-8702b0055293",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:7875fa28-0d90-44a1-a518-b16af69727f1",
+ "@id": "urn:e6e749e0-26ba-4cdb-9160-a7fc1b49740e",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:0b5d9f6c-e4eb-4ece-a250-cd75da76911c",
+ "@id": "urn:efc88b68-bb5c-4444-9fbc-2714e3c64014",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:608b662d-4757-4c39-94d5-44c28ff93938",
+ "GeneratedBy": "urn:5ab6aa9e-0882-49b0-8c88-f1d550948dd0",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png
index c4382609c..ea6b76c30 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
new file mode 100644
index 000000000..bce0b14eb
--- /dev/null
+++ b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:1320e946-ac94-4740-9e0c-b6f97ad0d99b",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_clusterwise_fwe/tone_counting_onset_times.txt ./afni_clusterwise_fwe/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:63f29e1b-4b6c-4457-80a6-3d1fbd4cce36",
+ "urn:e2baa3ee-4e71-4167-8fa6-2a24869d3bf3",
+ "urn:989551bd-89f0-41fd-b83d-ff7f03e47600"
+ ]
+ },
+ {
+ "@id": "urn:8db107d7-034d-4963-a81d-edf6a4c19ab2",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:091391a5-1062-44cc-b7b6-4e2e5f2e005a"
+ ]
+ },
+ {
+ "@id": "urn:59ad2686-bf03-4c54-ab58-52d3e36e159d",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:da5aa1af-62a9-4d38-b211-b84e477282bf",
+ "urn:b9f762ec-b84c-448f-8d10-a7ce9720420d"
+ ]
+ },
+ {
+ "@id": "urn:3ffb5f05-4a19-4865-b981-909b041426bb",
+ "Label": "tshift",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:da5aa1af-62a9-4d38-b211-b84e477282bf"
+ ]
+ },
+ {
+ "@id": "urn:d867fd7f-631d-420b-900e-78f8937f4436",
+ "Label": "align",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:7c054844-b870-48f3-a56d-0958618d172d",
+ "urn:c0281cc6-41ae-4afb-8712-bdddf923860a"
+ ]
+ },
+ {
+ "@id": "urn:065fd0da-dec5-43b9-89bd-2e28490b2920",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:27cbef79-02e5-4f56-a288-ea546ba6a2b1",
+ "urn:38c736a6-4fc6-4073-bb81-f2c369f76e4c",
+ "urn:52020508-61e6-4dfe-a196-64f7e40dc726"
+ ]
+ },
+ {
+ "@id": "urn:10f8b075-1fca-472e-b140-189ba027fbad",
+ "Label": "volreg",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:cb896b82-c1f6-4b6e-8517-e6b9b39074f0",
+ "urn:cb896b82-c1f6-4b6e-8517-e6b9b39074f0",
+ "urn:52020508-61e6-4dfe-a196-64f7e40dc726",
+ "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "urn:cb896b82-c1f6-4b6e-8517-e6b9b39074f0",
+ "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "urn:bd0e45d1-072d-4eb7-bf69-3fda63ddfba9",
+ "urn:5deae2c5-d728-4f5b-9d1e-3ac865f0e162",
+ "urn:b281ae59-f7ca-40e4-a206-7c9fc41d6a24",
+ "urn:babf96d9-d90b-478d-b086-b723089322ff",
+ "urn:21589409-ca27-4422-bb77-ea4dca81d049",
+ "urn:e3486423-f966-4ef5-be39-ed9946ed911d",
+ "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "urn:c2cf42dc-0dd5-4be2-8ffc-e5d8352d94ed"
+ ]
+ },
+ {
+ "@id": "urn:6f2a8768-dd51-49f4-b29b-badf9cbd2355",
+ "Label": "blur",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:564f19b7-406c-4518-a908-47569202ac15",
+ "urn:a372b104-9942-4b0f-93bf-e99787eab67b"
+ ]
+ },
+ {
+ "@id": "urn:4f8e64ff-f2e7-4b80-b21d-aab197e3b643",
+ "Label": "mask",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:6fb270cb-246a-489a-9655-358899756167",
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "urn:439ab190-6f31-45d3-b781-9cd272040fb4",
+ "urn:86081194-0636-47f1-9e3b-b68114def1d2",
+ "urn:9649d954-d3f8-4d7f-9749-43c44cfb4870",
+ "urn:f71aba7e-cfbf-475d-a938-f89e03affa34",
+ "urn:9649d954-d3f8-4d7f-9749-43c44cfb4870",
+ "urn:f71aba7e-cfbf-475d-a938-f89e03affa34",
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "urn:d351d30f-a4e9-40b2-9de0-e697ad8f4e22",
+ "urn:df9d2191-8a3a-45c5-9650-403521b23e4d"
+ ]
+ },
+ {
+ "@id": "urn:d3ee1eb9-ba34-4c1b-be52-8fb9737bcae5",
+ "Label": "scale",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:6fb270cb-246a-489a-9655-358899756167",
+ "urn:6fb270cb-246a-489a-9655-358899756167",
+ "urn:c9c0d4d9-bd85-425e-b9c7-bb4537311f58",
+ "urn:e3486423-f966-4ef5-be39-ed9946ed911d"
+ ]
+ },
+ {
+ "@id": "urn:c612758d-292e-4c5c-9f22-09f64fa14d84",
+ "Label": "regress",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
+ "Used": [
+ "urn:46735ade-270f-473e-91ff-d89229e04697",
+ "urn:46735ade-270f-473e-91ff-d89229e04697",
+ "urn:46735ade-270f-473e-91ff-d89229e04697",
+ "urn:5066b42d-c30f-4ef9-bcd0-3a0d0fe6ad41",
+ "urn:5066b42d-c30f-4ef9-bcd0-3a0d0fe6ad41",
+ "urn:26c558ba-8b6d-4b5c-bf5b-936db5ea9a5f",
+ "urn:5b8c4638-771b-45cf-843f-eed11904b166",
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "urn:e1ae001c-ae9b-4f3a-93c6-0c1645cc0cc6",
+ "urn:e5cde463-e48d-484b-b743-a9a652b0f3bb",
+ "urn:f825b81b-a359-4837-9ddd-1c429b57df18",
+ "urn:ada01202-ea7b-4b88-b337-d7350ee0a693",
+ "urn:da3d5f91-9e99-4368-8202-f07e1a5015c0",
+ "urn:7f43852f-2d85-4cbc-9406-b5d27f469302",
+ "urn:29c076d5-a462-4488-977b-958e22f360a9",
+ "urn:c0e2232b-3121-49e4-9765-abca3e931e90",
+ "urn:9256a39d-9dd7-4cc1-9cf9-d82a3e799545",
+ "urn:9256a39d-9dd7-4cc1-9cf9-d82a3e799545"
+ ]
+ },
+ {
+ "@id": "urn:f6388f61-a430-4ddb-8dc8-558e2ef8b0ac",
+ "Label": "blur estimation",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
+ "Used": [
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3",
+ "urn:1a4cacfc-6c2f-4960-8b86-7bcda40db9b3"
+ ]
+ },
+ {
+ "@id": "urn:29e1c19f-538c-4342-9e76-a6866ccd580f",
+ "Label": "auto block: generate review scripts",
+ "AssociatedWith": "urn:456e30ed-525d-48d5-b2b9-99e3b490e311",
+ "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
+ "Used": [
+ "urn:02fb5596-8669-4c2a-9df6-600488e892b5"
+ ]
+ }
+ ],
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diff --git a/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png
new file mode 100644
index 000000000..f80fd4f65
Binary files /dev/null and b/examples/from_parsers/afni/afni_thr_clustfwep05_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
index ed6e595f6..30809bd71 100644
--- a/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_clustunck10_proc.jsonld
@@ -4,7 +4,7 @@
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- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:cd4eb98c-0ee8-4e24-bcf5-30ca3bb9157b"
+ "urn:d59e4156-cfd3-425b-aabf-92519931fc2c"
]
},
{
- "@id": "urn:b3855205-d04b-4532-bba8-743d0b93c2d3",
+ "@id": "urn:fab5364a-1378-4e37-9a8b-cf22f60a9a30",
"Label": "cat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:53e2ece8-f99e-4cd5-a1c8-2b01c724d863"
+ "urn:fbc4b24a-d16d-4e16-b839-a4b3f2de8748"
]
},
{
- "@id": "urn:ec47503c-521d-422e-acf3-853d8bc6eef8",
+ "@id": "urn:a50a026c-f2ea-4900-81c3-2f3577e6a7c2",
"Label": "3dTshift",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:cd4eb98c-0ee8-4e24-bcf5-30ca3bb9157b"
+ "urn:d59e4156-cfd3-425b-aabf-92519931fc2c"
]
},
{
- "@id": "urn:65ca8ac9-e460-4bb4-b988-c0e8b640d0f6",
+ "@id": "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:21f0889a-2884-47bb-96d9-844dbb3cacb2",
- "urn:8429cb3a-f417-48a2-87c8-7eef3f8cecea"
+ "urn:4037cdbc-a9fa-42df-984c-8469028aa60a",
+ "urn:c6bb8b00-5a11-4ad3-9079-e3e04b49cb2f"
]
},
{
- "@id": "urn:0c3e5b35-2012-4f1e-8082-d52f69234d96",
+ "@id": "urn:f2c84bf5-9702-4567-8403-cfa1b8cffc1e",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:7dd9eb6e-2c26-4aef-bbdd-27155171191f",
- "urn:eba70185-e536-493c-9a67-e36a17e85583"
+ "urn:529cf71a-5021-4ba3-8f9b-5d0f3ac8187d",
+ "urn:afb7ccbc-ae02-4cf5-a4ad-e90da3838f67"
]
},
{
- "@id": "urn:6ef2fa60-155f-45b3-8ea3-cfcd906b43b9",
+ "@id": "urn:686a8225-b31f-4025-9b31-c2c64bb0c114",
"Label": "cat_matvec",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:b9fa590e-c9a7-4755-baaf-fdfbd9adbf5b"
+ "urn:79061e66-aeab-4d4a-863d-f657c20101a1"
]
},
{
- "@id": "urn:0dd0e641-9d9b-44e8-b602-7a0ea3ba1b56",
+ "@id": "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
"Label": "3dvolreg",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:8322775b-62fc-4344-b93d-fa8dad3d9fe0"
+ "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a"
]
},
{
- "@id": "urn:48f9cdad-094a-41e9-bacd-4d5e0a8d9639",
+ "@id": "urn:c74ef101-704e-4506-ae89-a363ce40b2db",
"Label": "3dcalc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:8322775b-62fc-4344-b93d-fa8dad3d9fe0"
+ "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a"
]
},
{
- "@id": "urn:766cf6f0-051b-45c6-8451-c590708c3122",
+ "@id": "urn:97b6c82e-f1d3-48dc-82b4-17bfeb916d8b",
"Label": "cat_matvec",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:b9fa590e-c9a7-4755-baaf-fdfbd9adbf5b"
+ "urn:79061e66-aeab-4d4a-863d-f657c20101a1"
]
},
{
- "@id": "urn:b801e693-611b-478e-810f-18890efe7473",
+ "@id": "urn:81af6e38-e763-4d07-822f-34aacf80459e",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:8322775b-62fc-4344-b93d-fa8dad3d9fe0",
- "urn:e72dcc3e-adcd-4dbe-8641-3498938eeada",
- "urn:f972fd76-8fb6-4a2d-a066-35b0affd6195"
+ "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
+ "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a",
+ "urn:b5a834c1-6209-4d61-82c6-3409448659ea"
]
},
{
- "@id": "urn:de54b09c-420b-496f-95e9-77180f2ea2a3",
+ "@id": "urn:ebf46ff4-7980-4938-a4bc-f6536d7e3282",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:b89b4e42-4d72-4ccf-aec4-9ac21339fc1c",
- "urn:e72dcc3e-adcd-4dbe-8641-3498938eeada",
- "urn:f972fd76-8fb6-4a2d-a066-35b0affd6195"
+ "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3",
+ "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
+ "urn:b5a834c1-6209-4d61-82c6-3409448659ea"
]
},
{
- "@id": "urn:194448dc-d2cd-43cc-ad82-8054b1ba2df5",
+ "@id": "urn:4bb24dcb-7e84-4293-af56-cf0afe4d1ca9",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:30b89792-f8a9-4f81-8734-f482347fb96d"
+ "urn:dbbfca19-1a7b-4b70-ae99-015594ee8ce4"
]
},
{
- "@id": "urn:957cf01d-7c97-4b54-8c82-b2e3330f5935",
+ "@id": "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8",
"Label": "cat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:2925e014-5c3f-4f83-bf81-5437b7478cba"
+ "urn:e51aba5a-f2b9-40e1-b125-5dab00b3a511"
]
},
{
- "@id": "urn:8692a4e7-d9de-4618-85f7-76adfee80306",
+ "@id": "urn:2cb3b422-c0d9-4b55-a7ac-8742884b0264",
"Label": "3dcopy",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:238ee357-9664-4341-89fe-87da449145ba"
+ "urn:165c0ff2-9c2e-4375-bdcf-6b231aa78151"
]
},
{
- "@id": "urn:375bd401-f59d-41f9-9554-3e3844f1e172",
+ "@id": "urn:a3ee6471-60a9-481e-b3fc-2fab7ace82a2",
"Label": "3dcalc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:64f3a5a9-a8b3-4de3-9b4c-89e46e6bdf39",
- "urn:81320ff0-3c04-46f5-82a0-2096247086bc"
+ "urn:34aa7f5c-1db3-458e-9bee-ebc98626d3b1",
+ "urn:d23d365d-bc81-4feb-aa92-49f60ef280ac"
]
},
{
- "@id": "urn:7d12b8f2-8f4b-4cec-b9f5-320f51af16ef",
+ "@id": "urn:a8ddfdef-39e3-40e4-9746-bbe17c8576c2",
"Label": "3dcopy",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:f972fd76-8fb6-4a2d-a066-35b0affd6195"
+ "urn:b5a834c1-6209-4d61-82c6-3409448659ea"
]
},
{
- "@id": "urn:2b669e28-a0cf-4fca-b868-ad8e89b90e48",
+ "@id": "urn:cd0ed143-f19d-46c3-803c-78ed75e36935",
"Label": "3dAllineate",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:4f6fe1ef-7874-449b-85a1-edc1ce3063db"
+ "urn:834a2563-5bec-469a-9210-671fe38ba63c"
]
},
{
- "@id": "urn:13b80b23-36fb-4b06-ba8e-d2739470fb8a",
+ "@id": "urn:9334173e-be89-47f0-b122-4b20dc4548ea",
"Label": "3dmerge",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:7cdfe3ab-fac6-4fc5-88cf-6f8b3dfcd272",
- "urn:ef75cf7f-49b6-459f-92ee-a356d4649a17"
+ "urn:499896cf-cadc-47e3-bc6d-f191317c50b9",
+ "urn:b8ddd52a-bbf4-4fc6-92fd-5dce1f764117"
]
},
{
- "@id": "urn:c3e40dc5-8e40-4a7e-b0f2-415dd8b846ef",
+ "@id": "urn:6bbb13fb-8238-47f3-887a-4305acacb258",
"Label": "3dAutomask",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:457e2c3b-290a-4d49-b677-77424fc164e0"
+ "urn:1544c31e-843b-4eda-a65d-83f079e3454c"
]
},
{
- "@id": "urn:218ffa82-8cd0-4624-9995-7d9b9da621f0",
+ "@id": "urn:99e7a814-3df2-4296-97a5-cc45eaf22414",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:02fa4dac-b13e-47ef-8390-9b5f37135c15",
+ "@id": "urn:57907561-aabf-43fd-ab44-4d130188cf3e",
"Label": "3dresample",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:b1c281e2-c739-46f8-a194-514e241747b2",
- "urn:f972fd76-8fb6-4a2d-a066-35b0affd6195"
+ "urn:ab757f74-c92c-4975-872c-4316678e0289",
+ "urn:b5a834c1-6209-4d61-82c6-3409448659ea"
]
},
{
- "@id": "urn:60d56e93-faf4-4101-be8b-18f457793b62",
+ "@id": "urn:129e5718-0a40-4429-a259-095c28c7a2d6",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:1f988b1a-d24f-425f-a9ae-e63df25e13c1"
+ "urn:b1d257f4-28f0-4e6e-b1d0-fa0dc15ca666"
]
},
{
- "@id": "urn:07715c6d-a301-48f9-b7e1-a44f5c4aec34",
+ "@id": "urn:28c52fef-260a-4cee-9b3b-c7af96752e12",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:32257d53-8603-40db-b02f-6002a5d6ee1a",
- "urn:84089e16-6209-4d72-ba0a-c9003f234966"
+ "urn:167795fc-87bc-4fa8-af0e-78391dd3aec1",
+ "urn:7693af36-0c01-4257-9531-d5e8d89bd197"
]
},
{
- "@id": "urn:75b192c7-da14-488c-93e9-6b6390ee73a9",
+ "@id": "urn:2ccd78dd-e38b-4537-a039-90c1a17501fb",
"Label": "3ddot",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:32257d53-8603-40db-b02f-6002a5d6ee1a",
- "urn:84089e16-6209-4d72-ba0a-c9003f234966"
+ "urn:167795fc-87bc-4fa8-af0e-78391dd3aec1",
+ "urn:7693af36-0c01-4257-9531-d5e8d89bd197"
]
},
{
- "@id": "urn:758476e6-7d68-4c13-968c-da2ed9657bd8",
+ "@id": "urn:dceaced7-8496-4699-9576-12b35f78fa94",
"Label": "3dresample",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
- "urn:b1c281e2-c739-46f8-a194-514e241747b2"
+ "urn:72b01569-8026-4ef1-9dd6-5d6da3f48b07",
+ "urn:ab757f74-c92c-4975-872c-4316678e0289"
]
},
{
- "@id": "urn:aa3da46b-70ce-43e9-9884-20dfe3b086b0",
+ "@id": "urn:6707d5a3-8854-4f88-ab6c-0084ee707e1b",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:38fb1c54-00fb-4ac6-a9dc-26c81c1cb409"
+ "urn:5599efc2-698a-43fd-8f94-8c596d69dc39"
]
},
{
- "@id": "urn:4f135819-17e3-44e5-bf60-cfa7e579b316",
+ "@id": "urn:6c55e71b-8928-46d6-9877-d304c2ba90b8",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:457e2c3b-290a-4d49-b677-77424fc164e0"
+ "urn:1544c31e-843b-4eda-a65d-83f079e3454c"
]
},
{
- "@id": "urn:0960d74a-45cf-420e-b77a-4d7caf1ea1c6",
+ "@id": "urn:35737c62-7629-4ffd-8d4e-5701ddd34404",
"Label": "3dcalc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:3dfd4a56-f366-4bd7-b140-c5252318e0cb",
- "urn:457e2c3b-290a-4d49-b677-77424fc164e0",
- "urn:81320ff0-3c04-46f5-82a0-2096247086bc"
+ "urn:1544c31e-843b-4eda-a65d-83f079e3454c",
+ "urn:d23d365d-bc81-4feb-aa92-49f60ef280ac",
+ "urn:d7651714-0e05-4d80-be6d-730cdf9412c9"
]
},
{
- "@id": "urn:b3730248-9b2b-49ed-9dee-45be3b2efa5d",
+ "@id": "urn:194f9b1b-1cb5-4d04-a5b7-3322a5ae77e0",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:1ac2c87f-eeb1-4e78-95d3-ea9b816d6ba5"
+ "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e"
]
},
{
- "@id": "urn:7b6220b4-8027-423d-a314-287932253b51",
+ "@id": "urn:c842ad68-03aa-4d56-a726-64bc81e2eb22",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:1ac2c87f-eeb1-4e78-95d3-ea9b816d6ba5"
+ "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e"
]
},
{
- "@id": "urn:8a659019-84c1-4c8e-9f06-1f02d1b401dd",
+ "@id": "urn:a8698c4b-51e2-4e42-9f7c-ad1f76aa06fc",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:1ac2c87f-eeb1-4e78-95d3-ea9b816d6ba5"
+ "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e"
]
},
{
- "@id": "urn:b5e9050f-4d3b-47f4-901a-7063ed55253f",
+ "@id": "urn:1a32d6b1-17e6-41d4-a670-17fad8f133a0",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:4c609c7f-beba-4c9c-99c9-cb6070983ebd"
+ "urn:5bf8c031-4fac-437e-94a9-70bd54096121"
]
},
{
- "@id": "urn:52b454bd-7e81-4ee7-ac1e-efe736cdd46c",
+ "@id": "urn:09966e3e-1647-482c-a3cc-853889509946",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:54d4205c-2755-4b93-8703-c1d55bea28be"
+ "urn:8885981b-cea7-4492-920a-1e5a26cbb875"
]
},
{
- "@id": "urn:f6eda669-13c2-412a-bad4-785ab23219d0",
+ "@id": "urn:ddefe5b8-47af-466b-a3e5-99a98409d213",
"Label": "3dTcat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:4c609c7f-beba-4c9c-99c9-cb6070983ebd"
+ "urn:5bf8c031-4fac-437e-94a9-70bd54096121"
]
},
{
- "@id": "urn:a094dcca-d44d-4beb-bdac-576804c53c44",
+ "@id": "urn:a5e6ae32-cb04-46f9-a999-7d0ebd8b8db9",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:530372d1-1692-44c6-8880-08936c1e3afc"
+ "urn:d0e2f63f-eaa2-4877-9fa2-bfb74ff511da"
]
},
{
- "@id": "urn:f237b0b8-0b29-478c-ac7f-2dc18976a994",
+ "@id": "urn:bee9f96d-0344-4880-b428-3c0d4fe9f451",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:81eb387a-a9f4-404a-89ac-8eb8bd0c328d"
+ "urn:92c3e4de-0ff4-4a84-bb19-096b59a10c02"
]
},
{
- "@id": "urn:6ff085a4-dd4b-413a-9701-e9ae6a37032f",
+ "@id": "urn:89ccbc96-0197-4eb7-b08c-980efea855eb",
"Label": "3dcalc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:6f06bfd7-b5d0-456c-af66-3db79158609f",
- "urn:b1c281e2-c739-46f8-a194-514e241747b2",
- "urn:dfde6c8e-d119-4215-b337-145bb3eef5f1"
+ "urn:6d333ab9-b325-4bde-b130-8685d6c388a2",
+ "urn:ab757f74-c92c-4975-872c-4316678e0289",
+ "urn:f4b9999c-6136-49d0-97a3-0d20890a86bc"
]
},
{
- "@id": "urn:1a0a096d-ee73-4243-afb5-5d33c6177308",
+ "@id": "urn:4a94eba4-13cf-43ef-bcf4-df58648e00e9",
"Label": "3dTnorm",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:51ee2018-45e8-49ce-a6ac-8202b01a4902"
+ "urn:bb43a681-4381-4ce8-b43a-53df91bc4374"
]
},
{
- "@id": "urn:ef1d1588-ae65-4d09-9c2f-4e241eed532c",
+ "@id": "urn:2d85d493-2f98-4769-b7f5-6f0388debfec",
"Label": "3dmaskave",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:f9ff08c4-87f3-4355-b509-a30ad6ac0bb7",
+ "@id": "urn:eea02eb9-3c81-47ac-8fa1-4541570610fa",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:7f98f463-6009-4719-8115-5e8ed110f410"
+ "urn:545d832b-aa4b-43c4-91f7-852908bcf351"
]
},
{
- "@id": "urn:1932e5b3-5d43-45cd-9a74-83f7db69b8b2",
+ "@id": "urn:e53e1630-eaf0-4075-9d40-b8dbdc32b896",
"Label": "3dcalc",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:87a19083-35ef-4e69-bcc2-a414ce65738f",
- "urn:f06804b1-350d-4114-a036-23dd4599b121"
+ "urn:4dc13e11-7a79-4297-a361-531cb7311a66",
+ "urn:fb7115e3-1ddf-4f35-9b8a-a51ef5ba0f6e"
]
},
{
- "@id": "urn:9c18c3d4-999e-4e35-af52-a2ab367c9566",
+ "@id": "urn:95fcd406-75cc-4d71-b892-179ebee27d02",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:a4052ff6-ac0e-4709-8ccf-096142900064"
+ "urn:bd6744b9-2023-4e53-9ed3-e67bd58bfd97"
]
},
{
- "@id": "urn:8b2f63d1-861e-4b43-97e4-6bbbff470320",
+ "@id": "urn:50bea5d4-4dc1-48df-aee1-7f8a209875e7",
"Label": "1dcat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:d6806031-87b7-40be-b276-bf0ebc9c7440"
+ "urn:f564409f-84db-4594-ac89-518f2d4b8373"
]
},
{
- "@id": "urn:9f7852ef-9692-4835-816e-224e3152c46a",
+ "@id": "urn:69b2efdd-746f-413f-a34e-d651b2d2fc13",
"Label": "1dcat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:800cb0d4-2427-4684-a00f-3cb9d52a9925"
+ "urn:a365a7e3-6f69-48f8-aca7-ae5d99434345"
]
},
{
- "@id": "urn:fb6b516a-fe10-4c47-b3d3-71d602d8b389",
+ "@id": "urn:7479bb7e-54b2-47ea-98d2-43c51aeaa2a4",
"Label": "3dTstat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:6506f02f-3be9-4a1a-af00-dec6938acd6f"
+ "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b"
]
},
{
- "@id": "urn:5cefbcb6-8854-49cd-9e25-46649309344b",
+ "@id": "urn:70d7cd80-32f6-4994-a4d4-c3fed4e02383",
"Label": "1dcat",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:6506f02f-3be9-4a1a-af00-dec6938acd6f"
+ "urn:e693c57c-65b6-445b-b9a2-bb2d67afd32b"
]
},
{
- "@id": "urn:70d45a51-a443-48f7-82c8-3542f0071288",
+ "@id": "urn:8967c63f-5fc7-44a6-a350-10e4d91420e5",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:b1c281e2-c739-46f8-a194-514e241747b2"
+ "urn:ab757f74-c92c-4975-872c-4316678e0289"
]
},
{
- "@id": "urn:14de7aef-a2bf-4a1e-8c16-47fb34f4d67c",
+ "@id": "urn:b04ba5a4-7187-414c-bf95-ec135e792a53",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:b1c281e2-c739-46f8-a194-514e241747b2"
+ "urn:ab757f74-c92c-4975-872c-4316678e0289"
]
},
{
- "@id": "urn:b08e3d70-dd9a-40fe-b019-685761dbc4b9",
+ "@id": "urn:b4cb0bba-46e0-4c70-b0ed-fc17fcc0c5d5",
"Label": "3dClustSim",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:b1c281e2-c739-46f8-a194-514e241747b2"
+ "urn:ab757f74-c92c-4975-872c-4316678e0289"
]
},
{
- "@id": "urn:53016baa-c6e5-4905-972c-da0a4f944e2c",
+ "@id": "urn:71935ebf-a6ab-4500-ad8b-7f5e8da5e05e",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:97cd560d-ae4f-434c-a666-628134b605a4"
+ "urn:877c6274-e93f-4843-8f27-6c3ba56bca0e"
]
},
{
- "@id": "urn:1b2b3cc3-b38b-4b56-9498-7aea3ffe98f9",
+ "@id": "urn:2b4f94e0-5fc5-4ffe-bef1-0aac47d21a99",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "AssociatedWith": "urn:bfd1983e-c301-4a2e-ace4-13091ebde405",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
{
- "@id": "urn:89f67975-ca98-45c5-9a5c-7a8259167d49",
+ "@id": "urn:f2718969-5393-4474-810c-18a55930c2b3",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:a78bed8b-8b1d-4170-86f6-a0597cea4fd9",
+ "GeneratedBy": "urn:926cfd79-5399-4ed5-a1ef-7ddac7372cb3",
"digest": {
"sha256": "9fa4c635e6533ddf2fed54295920052818d948c3ffe97bc753bd7336b453f8cb"
}
},
{
- "@id": "urn:ea12cbb8-ae5f-4a2e-b17f-47c484ceeaaa",
+ "@id": "urn:d4855f22-1f95-4735-9a85-8c55d4f931b4",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:2b558372-4a0d-42ac-8b26-6fbc2315e380"
+ "GeneratedBy": "urn:9c8cfdcd-ec35-49e0-956d-6cf35f72bd8d"
},
{
- "@id": "urn:4e77f001-0494-4dca-9fe7-200145f77608",
+ "@id": "urn:7a6ac72f-175e-48b5-82a7-24552b43801e",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
- "@id": "urn:8dbbca53-df2f-4b06-af4f-9676bed62dc2",
+ "@id": "urn:c81268eb-5e93-4ef2-a06f-12a37475e7f7",
"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_cluster_k10/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
- "@id": "urn:2698dc70-650e-477d-92ff-94d0c568bd35",
+ "@id": "urn:057aa3ca-32fa-4c88-98d3-5f6135ff173b",
"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:15de7fc4-4c26-42ab-bc52-486034377c0a"
+ "GeneratedBy": "urn:e49008ed-d256-4355-b47b-fc159cc53ed7"
},
{
- "@id": "urn:2585982e-0b08-44f0-b0c6-b38d9ac241e1",
+ "@id": "urn:bb970877-b8e1-4deb-bcd4-3241dcacc59e",
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@@ -631,13 +631,13 @@
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@@ -645,13 +645,13 @@
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@@ -659,16 +659,16 @@
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@@ -676,25 +676,25 @@
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@@ -702,7 +702,7 @@
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@@ -710,16 +710,16 @@
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@@ -727,7 +727,7 @@
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@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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@@ -760,34 +760,34 @@
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@@ -795,16 +795,16 @@
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -846,16 +846,16 @@
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@@ -863,16 +863,16 @@
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@@ -880,7 +880,7 @@
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@@ -888,34 +888,34 @@
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@@ -923,7 +923,7 @@
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@@ -931,7 +931,7 @@
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@@ -939,25 +939,25 @@
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@@ -965,16 +965,16 @@
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@@ -982,16 +982,16 @@
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@@ -999,7 +999,7 @@
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@@ -1007,7 +1007,7 @@
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diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png
index 6037db19e..5402ef6a5 100644
Binary files a/examples/from_parsers/afni/afni_thr_clustunck10_proc.png and b/examples/from_parsers/afni/afni_thr_clustunck10_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.jsonld
new file mode 100644
index 000000000..5311b92d5
--- /dev/null
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+ "Used": [
+ "urn:69b7b657-5c68-4486-a573-5e8f78e8ef2d",
+ "urn:e2161cb4-2cf0-4eea-b9fd-88b0157f0df4",
+ "urn:fc9b60b7-8c2b-41c5-9ae7-d4733436c333"
+ ]
+ },
+ {
+ "@id": "urn:083e7a48-1f1e-4a25-8049-d4b80641baae",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:f9d9798b-3574-4575-9644-32356a2670e4"
+ ]
+ },
+ {
+ "@id": "urn:105801bb-7b35-42d6-9ff2-4966a82149c5",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:800b2f42-62f7-43ab-aafe-a9c283857656",
+ "urn:3c8b9fce-ce3c-434a-918c-35889ca6823b"
+ ]
+ },
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+ "@id": "urn:dc28ed67-83ae-483a-9eeb-de245979553a",
+ "Label": "tshift",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:800b2f42-62f7-43ab-aafe-a9c283857656"
+ ]
+ },
+ {
+ "@id": "urn:1ae8f36b-01cf-4052-ac85-d10dc0aa6524",
+ "Label": "align",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:46f33eb6-7317-42e6-a994-c29dbc9faef0",
+ "urn:9dc87c3e-7da6-430a-bac5-dab5afbe300e"
+ ]
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+ {
+ "@id": "urn:45579f06-fc67-4a72-a435-4a2bde6046c2",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:aa411b08-993a-490e-b91a-8846bf69d918",
+ "urn:b76d1e93-8206-4b3c-b018-d3a8076cc796",
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+ "Label": "volreg",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
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+ "urn:f2112638-40a2-4662-b12e-b2519dfb950c",
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+ "Label": "blur",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:15455f94-530a-460a-a7b6-2130b0cc78ee",
+ "urn:4eb45450-e358-46a7-86ee-cfdb9902415e"
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+ {
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+ "Label": "mask",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
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+ "urn:f97e9638-f9aa-4f35-8225-62aeaa38350d",
+ "urn:2ec74de8-9ad4-49f3-8e6b-a2fd4c979565",
+ "urn:79f3e573-83e7-4024-b551-22bb4851003d",
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+ "Label": "scale",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
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+ "Label": "regress",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D; 1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}; 3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj; 1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt; 3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD; 3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"; 3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"; 3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj; 3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc; 3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D; 3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D; 3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP; 3dTstat -sum -prefix corr_brain rm.DP+tlrc; 1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D; 1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D; 3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"; 1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D; ",
+ "Used": [
+ "urn:8c1eca6e-2b08-4870-8d0b-25bc020fa0dd",
+ "urn:8c1eca6e-2b08-4870-8d0b-25bc020fa0dd",
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+ },
+ {
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+ "Label": "blur estimation",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D; 3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D; 3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim; ",
+ "Used": [
+ "urn:2ec74de8-9ad4-49f3-8e6b-a2fd4c979565",
+ "urn:2ec74de8-9ad4-49f3-8e6b-a2fd4c979565",
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+ "Label": "auto block: generate review scripts",
+ "AssociatedWith": "urn:b5a1e0ec-f429-4dad-8195-9e71c8861dae",
+ "Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD; gen_ss_review_scripts.py -mot_limit 0.3 -exit0; ",
+ "Used": [
+ "urn:0df00aab-8630-4a0a-87d4-d948ff20b516"
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+ "Entities": [
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+ "digest": {
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+ "Label": "tone_counting_probe_duration.txt",
+ "AtLocation": "./afni_cluster_k10/tone_counting_probe_duration.txt",
+ "digest": {
+ "sha256": "178ed9da232a5227ac0c7a34a87f4064bae90a329d448d7757304003c9043e2f"
+ }
+ },
+ {
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+ "digest": {
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+ "Label": "$output_dir",
+ "AtLocation": "$output_dir",
+ "GeneratedBy": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
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+ "Label": "stimuli",
+ "AtLocation": "$output_dir/stimuli",
+ "GeneratedBy": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb"
+ },
+ {
+ "@id": "urn:112723b4-9501-4fe9-aa4b-fa63a6c56252",
+ "Label": "stimuli",
+ "AtLocation": "$output_dir/stimuli",
+ "GeneratedBy": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb"
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+ "@id": "urn:8ae3884c-450f-43e5-b055-4b370616b43d",
+ "Label": "sub-01_T1w",
+ "AtLocation": "$output_dir/sub-01_T1w",
+ "GeneratedBy": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb"
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+ {
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+ "Label": "sub-01_task-tonecounting_bold.nii.gz",
+ "AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
+ "digest": {
+ "sha256": "86e5929f2610d2cfc3d7a81b513f39bdc818fe467085eb9174213ad1eefde8ca"
+ }
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+ "Label": "pb00.$subj.r01.tcat",
+ "AtLocation": "$output_dir/pb00.$subj.r01.tcat",
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+ "AtLocation": "outcount_rall.1D",
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+ "AtLocation": "pb01.$subj.r$run.tshift",
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+}
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diff --git a/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png
new file mode 100644
index 000000000..517a5ebba
Binary files /dev/null and b/examples/from_parsers/afni/afni_thr_clustunck10_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
index c7cb56eb8..185eda18e 100644
--- a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "@id": "urn:60181192-775f-4634-98d3-66d692c27341",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:60ac6427-f2f9-4df8-b0a4-2e52279ea854",
+ "@id": "urn:f3920868-80ba-4883-a1b3-ab0fb63e9d35",
"Label": "Make directory",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
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"Parameters": {},
"Used": []
},
{
- "@id": "urn:5c807607-6449-4770-b25b-5e78dc0d69c7",
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"Label": "Make directory",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
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"Parameters": {},
"Used": []
},
{
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- "urn:a305c30b-a37a-44ea-8c35-13978fc055af"
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]
},
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"Label": "3dcopy",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
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"Parameters": {},
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]
},
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},
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},
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"Used": [
- "urn:fef3aff5-1de5-4c25-8ff1-4d95a6ef5a30"
+ "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56"
]
},
{
- "@id": "urn:5ff1801c-9116-43a9-aa4a-c72b55bfef4e",
+ "@id": "urn:b27fcab0-8025-43f6-bc2b-e214f412c4f4",
"Label": "cat_matvec",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:678905c1-d3f9-4079-8e8a-ebeff7b289ba"
+ "urn:2fe607fe-5996-4abd-b270-e284373a4352"
]
},
{
- "@id": "urn:f0025fe9-879f-4469-a137-261e544d5478",
+ "@id": "urn:31493e8e-6002-4207-b099-de7f25d7df59",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
- "urn:1407a659-fd7a-4484-8d8e-01defef6f7b1",
- "urn:a41cf029-3f2e-42b7-bdbf-e8d710365518",
- "urn:fef3aff5-1de5-4c25-8ff1-4d95a6ef5a30"
+ "urn:05ca7568-0ad0-495e-8456-fbc9ff878699",
+ "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
]
},
{
- "@id": "urn:bc442431-361a-4ce5-971c-cf8eddac2c4c",
+ "@id": "urn:fa30e6eb-06b6-4084-8b84-2246196531dc",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
- "urn:1407a659-fd7a-4484-8d8e-01defef6f7b1",
- "urn:a41cf029-3f2e-42b7-bdbf-e8d710365518",
- "urn:ceeead2a-ad34-47d3-90e6-938a3309d894"
+ "urn:05ca7568-0ad0-495e-8456-fbc9ff878699",
+ "urn:a50b87fb-4dad-4045-af1b-5fb7218f58f6",
+ "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
]
},
{
- "@id": "urn:b71fd583-0674-4c89-a2f8-d444419c7562",
+ "@id": "urn:00be7c67-3470-4109-aac0-ce3457fe672f",
"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:fbc5b261-27ad-48b2-8d9d-f0abc6a2f421"
+ "urn:8c7cfc61-2fa9-45fe-a568-dacccb6e4bd5"
]
},
{
- "@id": "urn:bc34e799-ee74-412a-bfec-b63b237f82cb",
+ "@id": "urn:6244338e-5df1-4496-829a-7ee82e6af2cf",
"Label": "cat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:2b92b353-7620-4afd-871b-bfa460def5c6"
+ "urn:b85e4dd6-61b9-4c63-85f1-76c2718a8fc2"
]
},
{
- "@id": "urn:5eb20761-d530-43d3-94b9-5355fcf7f3d8",
+ "@id": "urn:df7bed39-e2be-4ad5-a90e-79193079851a",
"Label": "3dcopy",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:1c76f216-0aa4-4f8e-85f7-bfbced813d7d"
+ "urn:776e5668-c60d-4388-8c68-0ed9953b0a58"
]
},
{
- "@id": "urn:c7f1f41c-a405-40c0-944e-f6749c09aa9b",
+ "@id": "urn:7b9b59ac-2c07-45fc-9bd2-6f3602b9c7d6",
"Label": "3dcalc",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:a1818c62-2095-4959-86e3-ffb15482055e",
- "urn:a9909b0a-06e7-42d5-ae5b-699ba62cce5c"
+ "urn:bcd8bccb-c962-4602-bf5f-650419dcf0f2",
+ "urn:f00f6f70-9f59-463a-9315-37ec75568f19"
]
},
{
- "@id": "urn:9a843d97-01d0-4bd0-87f5-e2fa80b1b1db",
+ "@id": "urn:2c359c35-45bf-4507-9103-a3cb62eb98ab",
"Label": "3dcopy",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:1407a659-fd7a-4484-8d8e-01defef6f7b1"
+ "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267"
]
},
{
- "@id": "urn:298dc7d5-bb5b-4176-aebc-48c1081d2dac",
+ "@id": "urn:40f0ba7c-6c5e-41e3-be4d-cb51edc55892",
"Label": "3dAllineate",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:c9d42685-079c-4445-b83e-ce7178ddd0fa"
+ "urn:d9243bae-0e1c-48ea-b2b8-d670ffa89dcd"
]
},
{
- "@id": "urn:4b2b930b-628e-4e39-8f09-0c73566c0dfb",
+ "@id": "urn:26057a7a-635e-49cb-b254-4df7011e5db4",
"Label": "3dmerge",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:15b051f7-2e68-47b4-8c46-1d2ca75e246f",
- "urn:766c924e-2b0d-42fa-bb26-1f89e6182516"
+ "urn:49db383a-f7ce-4b02-b18a-301f09f8ca2e",
+ "urn:ffd8b61e-9219-4196-8acf-5c7e304172a6"
]
},
{
- "@id": "urn:70371069-142c-4e78-b151-6ec28fa99fc4",
+ "@id": "urn:53290d6f-b334-45f8-8be9-24c36e53bf4f",
"Label": "3dAutomask",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:46008793-da4c-4675-95a2-9665da5c4eda"
+ "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
]
},
{
- "@id": "urn:5f936fa4-b3cf-47d1-99ed-f6ed17e7d2e9",
+ "@id": "urn:8f056e6d-ce22-46c1-8a64-9b84414f4382",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:ea575ae5-8930-4141-a4c2-d8ef656487f6",
+ "@id": "urn:252da241-915a-4ff5-9164-23b45d8b6adb",
"Label": "3dresample",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:1407a659-fd7a-4484-8d8e-01defef6f7b1",
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:fbf7e4fe-124b-4f1f-8c16-6f23a9008267",
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:4209a343-3884-4554-9ebc-7ec0df1f26f7",
+ "@id": "urn:a44737d5-bbe8-45aa-bbda-e4e39c4fc2e4",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:8f5db629-7053-4922-b9f0-6bdf5a81ae52"
+ "urn:ca75045e-e6e1-4f42-b342-11111042cfd4"
]
},
{
- "@id": "urn:34b6df30-bd5a-4398-9342-1874c1deb96d",
+ "@id": "urn:f60325ef-133c-42ed-991d-cafc1d400a1c",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
- "urn:40f4de67-872c-4eb2-aa1b-fcd9d510265a"
+ "urn:216ca191-cc14-4478-a738-9d618364793e",
+ "urn:375dfc81-5906-4f37-869d-a5f3d511c1f1"
]
},
{
- "@id": "urn:b59ccf17-52ef-44e6-8967-572a84fccdb9",
+ "@id": "urn:f6ff0b38-f70a-4a10-b2da-eddaa63ba9d7",
"Label": "3ddot",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
- "urn:40f4de67-872c-4eb2-aa1b-fcd9d510265a"
+ "urn:216ca191-cc14-4478-a738-9d618364793e",
+ "urn:375dfc81-5906-4f37-869d-a5f3d511c1f1"
]
},
{
- "@id": "urn:380501ca-17d2-4ef6-b735-bdd2502c1fd6",
+ "@id": "urn:bcc78824-4e5f-4dec-a981-c78823d20545",
"Label": "3dresample",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:0d20d783-5c33-47b9-acc0-d7c6c576fd63",
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:62133b1c-e258-4578-8377-9c4c48a504b3",
+ "@id": "urn:bbc5cfa9-fc2a-4a19-b7cd-6eff9a5300b2",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:7c153386-680f-469c-9558-1ef58f5e9387"
+ "urn:57e1e447-c13d-4bd5-ac34-e7c12ee6ff0e"
]
},
{
- "@id": "urn:966bda3f-ef3a-4c6b-96f3-37a8f63317ac",
+ "@id": "urn:dd2943db-d18f-4c3b-b091-b2392fb26750",
"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:46008793-da4c-4675-95a2-9665da5c4eda"
+ "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
]
},
{
- "@id": "urn:f2718969-5393-4474-810c-18a55930c2b3",
+ "@id": "urn:9977a87f-a67e-46c5-9208-6d52284bb1ee",
"Label": "3dcalc",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:46008793-da4c-4675-95a2-9665da5c4eda",
- "urn:a9909b0a-06e7-42d5-ae5b-699ba62cce5c",
- "urn:d4855f22-1f95-4735-9a85-8c55d4f931b4"
+ "urn:02e6c51d-962c-4a4b-8b77-ca222c537f17",
+ "urn:bcd8bccb-c962-4602-bf5f-650419dcf0f2",
+ "urn:f2efbcb4-3695-485f-8ac7-d1ef7a54cd5f"
]
},
{
- "@id": "urn:c81268eb-5e93-4ef2-a06f-12a37475e7f7",
+ "@id": "urn:2906ce55-4d86-46f2-b57b-d2e79a77c30c",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:96298bd4-56d1-49ad-8c03-cecf40d46075"
+ "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2"
]
},
{
- "@id": "urn:bb970877-b8e1-4deb-bcd4-3241dcacc59e",
+ "@id": "urn:3cf0faa1-5214-43b0-8f2e-ea07771e161f",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:96298bd4-56d1-49ad-8c03-cecf40d46075"
+ "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2"
]
},
{
- "@id": "urn:91406eb5-1759-4dab-82d5-c0c43b5d80ef",
+ "@id": "urn:b1dfae7b-a755-4880-bb1b-2943bb5dabe6",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:96298bd4-56d1-49ad-8c03-cecf40d46075"
+ "urn:bc2c5ca3-552a-4da0-9bd1-0c16a94c5ac2"
]
},
{
- "@id": "urn:a20b66f5-dc52-4a8a-ab60-eab714ac4963",
+ "@id": "urn:edc4d342-e3a2-4a70-9590-c7cd4293922d",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:d59e4156-cfd3-425b-aabf-92519931fc2c"
+ "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857"
]
},
{
- "@id": "urn:fab5364a-1378-4e37-9a8b-cf22f60a9a30",
+ "@id": "urn:3181950d-f9a7-408e-945c-c9b5103e06a7",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:130be5b5-1d74-4f34-aa19-8883f9dc0198"
+ "urn:80914d4d-105b-4df0-80a9-5532aa1c7b13"
]
},
{
- "@id": "urn:2ddf06d7-bcb2-4949-b78b-7ebda1733463",
+ "@id": "urn:58eadaf7-7a2c-435b-aa5b-9e9e982ec4fb",
"Label": "3dTcat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:d59e4156-cfd3-425b-aabf-92519931fc2c"
+ "urn:5f654627-6b77-4c10-801f-0e3ed2cfe857"
]
},
{
- "@id": "urn:e413cb9e-66c0-45cb-a31f-541be143d96f",
+ "@id": "urn:b42bc9d6-e128-4b83-ad77-cfe2907081f6",
"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d"
+ "urn:e3b4c9b6-c534-42ec-b134-a78421c8db3e"
]
},
{
- "@id": "urn:4037cdbc-a9fa-42df-984c-8469028aa60a",
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"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23"
+ "urn:9244d50f-27f2-4a26-9f27-b728870aaefa"
]
},
{
- "@id": "urn:afb7ccbc-ae02-4cf5-a4ad-e90da3838f67",
+ "@id": "urn:aa053e5f-cbc9-42d8-abb9-b90d70044136",
"Label": "3dcalc",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
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- "urn:686a8225-b31f-4025-9b31-c2c64bb0c114",
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:5e66964f-ad8f-467e-b290-2956f00ef1a2",
+ "urn:6ef22af4-3ce3-4db5-9551-9b22e7d65ad8",
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
+ "@id": "urn:5c10fcbd-bf1a-4dec-8e9e-4731987020fa",
"Label": "3dTnorm",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a"
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]
},
{
- "@id": "urn:c74ef101-704e-4506-ae89-a363ce40b2db",
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"Label": "3dmaskave",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
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"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:081fa336-6cc1-4eb4-8b76-659180dbea4b",
+ "@id": "urn:4660f101-7e47-4dc9-a294-6f28a4bd6b5b",
"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:97b6c82e-f1d3-48dc-82b4-17bfeb916d8b"
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]
},
{
- "@id": "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
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"Label": "3dcalc",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
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"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
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- "urn:81af6e38-e763-4d07-822f-34aacf80459e"
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]
},
{
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"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:bde49ce6-af3e-4616-8f87-272181752a26"
+ "urn:f9c3593a-4a89-4d2a-8386-0f235a2c95b2"
]
},
{
- "@id": "urn:b749c781-f2ad-471d-a39c-effdffc69219",
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"Label": "1dcat",
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+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3"
+ "urn:77fed1bd-e7f7-40bf-b2fc-4db30628b65e"
]
},
{
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"Label": "1dcat",
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"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:4bb24dcb-7e84-4293-af56-cf0afe4d1ca9"
+ "urn:dc76cb9c-681c-4842-9207-8d88aa5a4e54"
]
},
{
- "@id": "urn:da3000b5-650b-4cb2-8cbb-dc42cabb876e",
+ "@id": "urn:92eee993-7765-4d39-a302-e4e7bd9e6e2d",
"Label": "3dTstat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8"
+ "urn:7da2e5ed-45c6-4bef-bbe6-aefef427df2c"
]
},
{
- "@id": "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e",
+ "@id": "urn:c1887097-aa8e-4ded-9839-159c05a8ff2c",
"Label": "1dcat",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8"
+ "urn:7da2e5ed-45c6-4bef-bbe6-aefef427df2c"
]
},
{
- "@id": "urn:1207013b-244d-4675-998f-ada93a74cded",
+ "@id": "urn:f416139d-e9f8-4692-b181-11e4888553af",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:d23d365d-bc81-4feb-aa92-49f60ef280ac",
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"Label": "3dFWHMx",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:f9850102-6111-4db5-9684-ff4deebda300",
+ "@id": "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
"Label": "3dClustSim",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:9afb0d8c-87de-47ba-8300-b53136b969a7"
+ "urn:fe869478-f885-406d-955b-bad539f054b8"
]
},
{
- "@id": "urn:58593ee7-e92c-41c8-abd4-db8f69e4a693",
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"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
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"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:9cc55ce2-65a9-469b-85ba-5ba4ded3cb2b"
+ "urn:be1edb32-3e58-45fa-a6af-df2d560cc972"
]
},
{
- "@id": "urn:9334173e-be89-47f0-b122-4b20dc4548ea",
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"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5",
+ "AssociatedWith": "urn:60181192-775f-4634-98d3-66d692c27341",
"Command": "gen_ss_review_scripts.py -mot_limit 0.3 -exit0",
"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
"Entities": [
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"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:60ac6427-f2f9-4df8-b0a4-2e52279ea854",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:5c807607-6449-4770-b25b-5e78dc0d69c7"
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{
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+ "@id": "urn:66a6c02a-7aed-4920-a165-fbbbefe73c7f",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
},
{
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
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{
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:ef4136f0-99bb-4107-ab16-e576bfffbdd3"
+ "GeneratedBy": "urn:b858ca8c-00ce-4220-b42b-9fdbce0c54c5"
},
{
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+ "@id": "urn:a9b05b37-91c1-4fc8-8744-6d437d5ca73b",
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"AtLocation": "sub-01_T1w.nii.gz",
"digest": {
@@ -631,13 +631,13 @@
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{
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:6c362f45-df32-43c4-8c57-d8456a54f0be"
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{
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"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
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{
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
- "GeneratedBy": "urn:784958c7-9655-4c6a-b6fe-1e9b2b5aa90c"
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{
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+ "@id": "urn:79638e82-9f85-4be7-b17a-4a2cce96034c",
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@@ -659,16 +659,16 @@
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{
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:fd5cfc88-112e-46d7-881f-f322692999a8",
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{
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+ "@id": "urn:b0be6445-9afb-4e3f-a7c1-33449fd2a793",
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"AtLocation": "outcount.r*.1D",
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@@ -676,25 +676,25 @@
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{
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"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:64f2b964-b55e-418f-acbf-fb9e9e0e8437",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:a9b6c421-df6f-4d8f-8949-e84066a596fc",
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+ "@id": "urn:35c1f502-94fe-4cbc-aef7-63f633acd45e",
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@@ -702,7 +702,7 @@
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{
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+ "@id": "urn:d888ce87-db52-42c4-86ec-7f5937747369",
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@@ -710,16 +710,16 @@
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{
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"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:9d08e256-18dc-49a0-aaf2-712b1d2f9058",
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{
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@@ -727,7 +727,7 @@
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@@ -735,7 +735,7 @@
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@@ -743,16 +743,16 @@
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@@ -760,34 +760,34 @@
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@@ -795,16 +795,16 @@
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -846,16 +846,16 @@
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@@ -863,16 +863,16 @@
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@@ -880,7 +880,7 @@
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@@ -888,34 +888,34 @@
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@@ -923,7 +923,7 @@
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@@ -931,7 +931,7 @@
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@@ -939,25 +939,25 @@
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@@ -965,16 +965,16 @@
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@@ -999,7 +999,7 @@
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@@ -1007,7 +1007,7 @@
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@@ -1015,16 +1015,16 @@
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@@ -1032,25 +1032,25 @@
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@@ -1058,34 +1058,34 @@
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@@ -1093,25 +1093,25 @@
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+ "@id": "urn:1b6bc660-3002-4209-b970-2bf3816c16f7",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj",
- "GeneratedBy": "urn:2ddf06d7-bcb2-4949-b78b-7ebda1733463",
+ "GeneratedBy": "urn:58eadaf7-7a2c-435b-aa5b-9e9e982ec4fb",
"digest": {
"sha256": "bcf27fc2e339e751d0ea9bba931674c21fd9d434ff411330f4df55f872a8cc7e"
}
},
{
- "@id": "urn:1617de95-9492-49a4-997c-c3fff2ae8c6d",
+ "@id": "urn:e3b4c9b6-c534-42ec-b134-a78421c8db3e",
"Label": "all_runs.$subj",
"AtLocation": "all_runs.$subj+tlrc\"[$ktrs]\"",
"digest": {
@@ -1119,16 +1119,16 @@
}
},
{
- "@id": "urn:c6bb8b00-5a11-4ad3-9079-e3e04b49cb2f",
+ "@id": "urn:4912dc91-d374-4b1e-b893-ce6cf0a9dc35",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all",
- "GeneratedBy": "urn:e413cb9e-66c0-45cb-a31f-541be143d96f",
+ "GeneratedBy": "urn:b42bc9d6-e128-4b83-ad77-cfe2907081f6",
"digest": {
"sha256": "bda68a16c0afd5e55d4d7415c8c959e61a9aad7898dd456b0f3bb597363dde31"
}
},
{
- "@id": "urn:e1f6cc09-c137-4859-894f-10d0a6bd0c23",
+ "@id": "urn:9244d50f-27f2-4a26-9f27-b728870aaefa",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc\"[$ktrs]\"",
"digest": {
@@ -1136,16 +1136,16 @@
}
},
{
- "@id": "urn:f2c84bf5-9702-4567-8403-cfa1b8cffc1e",
+ "@id": "urn:e3c8e006-f1fa-4f68-9ded-84f0ac9e44cd",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all",
- "GeneratedBy": "urn:4037cdbc-a9fa-42df-984c-8469028aa60a",
+ "GeneratedBy": "urn:7e255ee1-b542-4024-a4b3-323d68b5d8c3",
"digest": {
"sha256": "431314eb75d086ce08373b3a374427969e89414c4a2d607e449c1f6485c547af"
}
},
{
- "@id": "urn:529cf71a-5021-4ba3-8f9b-5d0f3ac8187d",
+ "@id": "urn:5e66964f-ad8f-467e-b290-2956f00ef1a2",
"Label": "rm.signal.all",
"AtLocation": "rm.signal.all+tlrc",
"digest": {
@@ -1153,7 +1153,7 @@
}
},
{
- "@id": "urn:686a8225-b31f-4025-9b31-c2c64bb0c114",
+ "@id": "urn:6ef22af4-3ce3-4db5-9551-9b22e7d65ad8",
"Label": "rm.noise.all",
"AtLocation": "rm.noise.all+tlrc",
"digest": {
@@ -1161,16 +1161,16 @@
}
},
{
- "@id": "urn:834a2563-5bec-469a-9210-671fe38ba63c",
+ "@id": "urn:4aa4cd22-277d-4275-a53e-46b3d6ae63b5",
"Label": "TSNR.$subj",
"AtLocation": "TSNR.$subj",
- "GeneratedBy": "urn:afb7ccbc-ae02-4cf5-a4ad-e90da3838f67",
+ "GeneratedBy": "urn:aa053e5f-cbc9-42d8-abb9-b90d70044136",
"digest": {
"sha256": "303f183145a1e295686c08335d3b70753777cf0fa0b3f9628cf8de5471359a00"
}
},
{
- "@id": "urn:a9c2c6b0-9fb1-4dce-86b7-7718a9ef3d1a",
+ "@id": "urn:bed41a63-8c25-475e-8018-c427a0c00a64",
"Label": "errts.${subj}",
"AtLocation": "errts.${subj}+tlrc",
"digest": {
@@ -1178,25 +1178,25 @@
}
},
{
- "@id": "urn:9c28481d-da26-44f6-9946-0fb9b7a7e96f",
+ "@id": "urn:23668e55-7db2-419a-ad69-9ebf9d5e2af3",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit",
- "GeneratedBy": "urn:8a71a648-4d87-4e46-a43a-e9bca7ce84ba",
+ "GeneratedBy": "urn:5c10fcbd-bf1a-4dec-8e9e-4731987020fa",
"digest": {
"sha256": "03b570ad773a00f51ab7e6cdedfebdeca45f5356de0c25f9e3be44d7bf2c7151"
}
},
{
- "@id": "urn:511ee360-0b7a-4223-946e-28c5c2cdec26",
+ "@id": "urn:64fe3794-20dd-46e0-90fc-56a8b309c17d",
"Label": "gmean.errts.unit.1D",
"AtLocation": "gmean.errts.unit.1D",
- "GeneratedBy": "urn:c74ef101-704e-4506-ae89-a363ce40b2db",
+ "GeneratedBy": "urn:9d494e57-2f2f-4ae9-9cee-f3fbb0da1e60",
"digest": {
"sha256": "a35a66cce2e2d487762823c197ca1edc450a9887f46f125826b69c5021662f95"
}
},
{
- "@id": "urn:97b6c82e-f1d3-48dc-82b4-17bfeb916d8b",
+ "@id": "urn:4ed3ae31-2469-4eea-8d7d-094dbe725b35",
"Label": "out.gcor.1D",
"AtLocation": "out.gcor.1D",
"digest": {
@@ -1204,16 +1204,16 @@
}
},
{
- "@id": "urn:b6337da7-d00d-4db1-b724-694325691d4d",
+ "@id": "urn:fb75466c-ea45-4159-9173-2a92b7963d0a",
"Label": "-",
"AtLocation": "-",
- "GeneratedBy": "urn:081fa336-6cc1-4eb4-8b76-659180dbea4b",
+ "GeneratedBy": "urn:4660f101-7e47-4dc9-a294-6f28a4bd6b5b",
"digest": {
"sha256": "dac304c9f20899ca1ef5aa403e565345fd0ff4ed80c35f82007c9b03a68292b3"
}
},
{
- "@id": "urn:81af6e38-e763-4d07-822f-34aacf80459e",
+ "@id": "urn:b4a0c70b-b21e-4841-9aa4-9162e50e00f8",
"Label": "rm.errts.unit",
"AtLocation": "rm.errts.unit+tlrc",
"digest": {
@@ -1221,16 +1221,16 @@
}
},
{
- "@id": "urn:8a5097be-6b13-4048-a042-c2b8783f4d08",
+ "@id": "urn:93a80c83-735c-49fe-a04f-eceeb9e9716c",
"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:83ae1c41-4e52-43b6-beef-857cab51b576",
+ "GeneratedBy": "urn:007db657-ae51-471b-bb1e-28dc9722171b",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:bde49ce6-af3e-4616-8f87-272181752a26",
+ "@id": "urn:f9c3593a-4a89-4d2a-8386-0f235a2c95b2",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:ebf46ff4-7980-4938-a4bc-f6536d7e3282",
+ "@id": "urn:3c93a0f8-9da1-4d13-8f7b-06e36b99e86e",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:1a014967-de1c-46ed-a37f-26cb3f7eda52",
+ "GeneratedBy": "urn:a6e8a9af-35b9-4280-a896-19c0ba402b50",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:69a3a04f-f0e7-428c-bf7f-98b6a0098ad3",
+ "@id": "urn:77fed1bd-e7f7-40bf-b2fc-4db30628b65e",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:6916c807-44ba-48eb-9a03-dfbf52c8a393",
+ "@id": "urn:1b82a18a-a7ff-46a9-afd5-53fbf7bfb66a",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:b749c781-f2ad-471d-a39c-effdffc69219",
+ "GeneratedBy": "urn:d6fc59d7-169a-41aa-90eb-ac368da47367",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:4bb24dcb-7e84-4293-af56-cf0afe4d1ca9",
+ "@id": "urn:dc76cb9c-681c-4842-9207-8d88aa5a4e54",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:dbbfca19-1a7b-4b70-ae99-015594ee8ce4",
+ "@id": "urn:05d99bd1-1aa9-452a-9162-19459c4a4c71",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:a9563344-2af3-4f9b-a158-b055df86882d",
+ "GeneratedBy": "urn:b277d6f4-0e05-454d-83ee-8ebd8be563a8",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:aa2d4900-01b1-4586-94b8-bee17c62e5b8",
+ "@id": "urn:7da2e5ed-45c6-4bef-bbe6-aefef427df2c",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:e51aba5a-f2b9-40e1-b125-5dab00b3a511",
+ "@id": "urn:176f5667-ceaa-47a1-ba89-54e565469876",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:da3000b5-650b-4cb2-8cbb-dc42cabb876e",
+ "GeneratedBy": "urn:92eee993-7765-4d39-a302-e4e7bd9e6e2d",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:165c0ff2-9c2e-4375-bdcf-6b231aa78151",
+ "@id": "urn:3e5999d6-e31d-4abf-be04-504c748c06aa",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:c97b4bb7-f8fa-4bc6-bcdf-8ab52723dc9e",
+ "GeneratedBy": "urn:c1887097-aa8e-4ded-9839-159c05a8ff2c",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:34aa7f5c-1db3-458e-9bee-ebc98626d3b1",
+ "@id": "urn:62724743-d128-48d9-b0a9-b8bb0f6800ac",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:1207013b-244d-4675-998f-ada93a74cded",
+ "GeneratedBy": "urn:f416139d-e9f8-4692-b181-11e4888553af",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:a8ddfdef-39e3-40e4-9746-bbe17c8576c2",
+ "@id": "urn:0ed6b3ac-dce1-4927-93ac-a8a05131d6c8",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:d23d365d-bc81-4feb-aa92-49f60ef280ac",
+ "GeneratedBy": "urn:4dc7b638-37ac-46f6-88e5-3e711bd3a4cc",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:cd0ed143-f19d-46c3-803c-78ed75e36935",
+ "@id": "urn:473dc7c2-1028-4a00-9592-5b20a96d2401",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:f9850102-6111-4db5-9684-ff4deebda300",
+ "GeneratedBy": "urn:7e5f43ce-add3-40a5-9912-007b2ad1623a",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:9cc55ce2-65a9-469b-85ba-5ba4ded3cb2b",
+ "@id": "urn:be1edb32-3e58-45fa-a6af-df2d560cc972",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:499896cf-cadc-47e3-bc6d-f191317c50b9",
+ "@id": "urn:7f0c37a4-8362-411a-9cab-3f45e445a60d",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:9334173e-be89-47f0-b122-4b20dc4548ea",
+ "GeneratedBy": "urn:28c080bc-7f9b-47fe-910f-db1304870e68",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png
index ba1fd0174..112ee3d8d 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
new file mode 100644
index 000000000..a0133b70b
--- /dev/null
+++ b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:cfd011d6-c6d4-4952-99b2-c5d7e9e2a217",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_fdr_p005/tone_counting_onset_times.txt ./afni_voxelwise_fdr_p005/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:4752a95b-fa74-4f9d-90b6-54cd74bf4c5e",
+ "urn:5ec203ef-e9b5-4e08-97a5-1a212b51a7c7",
+ "urn:fac605a0-fbab-47c9-bf38-7e7f3d8bacdb"
+ ]
+ },
+ {
+ "@id": "urn:cb873a01-1e2e-4677-8df0-64ead2637611",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:6ee4d50e-a3d9-4baa-8eca-fcc3e59e5f99"
+ ]
+ },
+ {
+ "@id": "urn:5f034d1d-132c-491b-b140-614cefd7f5d9",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9",
+ "urn:b59e9cce-8a28-4ecc-b68a-079d48cca2b7"
+ ]
+ },
+ {
+ "@id": "urn:2a385c37-816e-4440-b445-5ea777ad4416",
+ "Label": "tshift",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:27ca8d91-5360-4293-91fb-8ab8fb65ebf9"
+ ]
+ },
+ {
+ "@id": "urn:26a95a29-2208-4552-9804-5b275d6375e1",
+ "Label": "align",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:33b59642-b965-43a4-aca6-470c7a099750",
+ "urn:b3813f7b-85fb-4fbe-9def-1f72fb51ca15"
+ ]
+ },
+ {
+ "@id": "urn:53a88a84-37d2-4b4e-837c-5a6a19f96284",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:7ce340ba-17c6-4c36-a37d-86a8f491b8cf",
+ "urn:955d49ee-c29b-4540-aaed-88c8f23d06f9",
+ "urn:18499e02-4412-494a-b605-241f24b66ba5"
+ ]
+ },
+ {
+ "@id": "urn:6ec748e7-4e38-471c-a82a-e38f5e25f410",
+ "Label": "volreg",
+ "AssociatedWith": "urn:34ae61a6-bf83-4b75-94ac-80cd6ee10bb3",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:751652bc-9d36-4f1b-b279-5d118517ab48",
+ "urn:751652bc-9d36-4f1b-b279-5d118517ab48",
+ "urn:18499e02-4412-494a-b605-241f24b66ba5",
+ "urn:68d316be-cf42-4d78-9f7d-d2c54c8c323a",
+ "urn:751652bc-9d36-4f1b-b279-5d118517ab48",
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+ "@id": "urn:ade3d57c-127c-402f-afb6-ac39ac65237a",
+ "Label": "rm.DP",
+ "AtLocation": "rm.DP",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
+ }
+ },
+ {
+ "@id": "urn:8c230d32-2446-4dfb-9583-31f69475bd4e",
+ "Label": "corr_brain",
+ "AtLocation": "corr_brain",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
+ }
+ },
+ {
+ "@id": "urn:a5c3032a-5e00-4f6c-8ab2-ebf4dfe8c790",
+ "Label": "ideal_tone_counting.1D",
+ "AtLocation": "ideal_tone_counting.1D",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
+ }
+ },
+ {
+ "@id": "urn:d1910e3d-571c-4a0a-8b04-922051d2f700",
+ "Label": "ideal_probe.1D",
+ "AtLocation": "ideal_probe.1D",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
+ }
+ },
+ {
+ "@id": "urn:53f729e0-2ea7-4491-a1c0-5f1ab799f99a",
+ "Label": "sum_ideal.1D",
+ "AtLocation": "sum_ideal.1D",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
+ }
+ },
+ {
+ "@id": "urn:cd2030da-1726-4bf3-9f11-c0dd70456604",
+ "Label": "X.stim.xmat.1D",
+ "AtLocation": "X.stim.xmat.1D",
+ "GeneratedBy": "urn:9e64a06d-9dc5-4e38-803f-8758f650cd1c",
+ "digest": {
+ "sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
+ }
+ },
+ {
+ "@id": "urn:4e78aec3-0449-4957-9b2e-e2670d3c8eac",
+ "Label": "full_mask.$subj",
+ "AtLocation": "full_mask.$subj+tlrc",
+ "digest": {
+ "sha256": "5ccbeeeef88c323d4141cd242861d39ffb389015ad6e1d788a67a1851123fc36"
+ }
+ },
+ {
+ "@id": "urn:f731f008-2aec-4366-8549-b78118c71d5c",
+ "Label": "blur.epits.1D",
+ "AtLocation": "blur.epits.1D",
+ "GeneratedBy": "urn:2b653326-eaf9-47ae-bb22-6ec2544f4982",
+ "digest": {
+ "sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
+ }
+ },
+ {
+ "@id": "urn:a5fba92e-6d6c-4ae0-9c48-82fd19ec8872",
+ "Label": "blur.errts.1D",
+ "AtLocation": "blur.errts.1D",
+ "GeneratedBy": "urn:2b653326-eaf9-47ae-bb22-6ec2544f4982",
+ "digest": {
+ "sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
+ }
+ },
+ {
+ "@id": "urn:d479a642-5dc1-4d5b-8652-51477e4994d5",
+ "Label": "ClustSim",
+ "AtLocation": "ClustSim",
+ "GeneratedBy": "urn:2b653326-eaf9-47ae-bb22-6ec2544f4982",
+ "digest": {
+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:f8d71294-bbc9-4741-a763-9d92fe5a8415",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:5700cf6a-967c-4a79-9f3f-4aab63a7a4f4",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:5352d93c-8554-4dd8-b154-4c8a7732ed7b",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png
new file mode 100644
index 000000000..dfc603ffa
Binary files /dev/null and b/examples/from_parsers/afni/afni_thr_voxelfdrp05_proc_block.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
index 9bafb7c8e..63e8272f6 100644
--- a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
+++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "@id": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,569 +13,569 @@
],
"Activities": [
{
- "@id": "urn:a1805d3b-baeb-4707-b217-71a4d28ace1b",
+ "@id": "urn:153b277a-635d-42c0-a884-4bbfa0c6dd1b",
"Label": "Make directory",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "mkdir $output_dir",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:64758879-6b04-479d-8021-1385b8b85587",
+ "@id": "urn:d0b03493-daf8-4372-bd90-a7d591ad03a9",
"Label": "Make directory",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "mkdir $output_dir/stimuli",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:3190be3b-d808-4789-a6b2-90c5db0bb314",
+ "@id": "urn:ddb15529-6e64-418a-a74b-7a3d384dc0ab",
"Label": "cp",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli",
"Parameters": {},
"Used": [
- "urn:d8d7376b-a591-4123-974d-081e6e33896a",
- "urn:f0423d9e-54a2-4f80-a53f-e1dd94b3a947"
+ "urn:045781d1-9e75-4834-9b30-4978b76070da",
+ "urn:a4c09a62-cb31-4c2b-ba17-d95d8005b33d"
]
},
{
- "@id": "urn:2be229a2-3fbe-4acb-9aaf-e280530aa938",
+ "@id": "urn:66a1b6d8-088a-4ae0-83f8-e96e5151ae0b",
"Label": "3dcopy",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w",
"Parameters": {},
"Used": [
- "urn:454dc845-1967-46e8-9b90-69b929477b23"
+ "urn:91ed2886-1c20-431d-9c0f-8f3720ffea22"
]
},
{
- "@id": "urn:4963497e-481b-4679-a1f7-425b747b8db9",
+ "@id": "urn:210bf154-81f9-4db1-99d0-871ae70630ab",
"Label": "3dTcat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"Parameters": {},
"Used": [
- "urn:bade994c-bfbf-48ef-952e-593582deab90"
+ "urn:3f07d54e-e55d-4e7e-bc51-9c2e441a58b3"
]
},
{
- "@id": "urn:198081c3-d54d-4afa-8c05-56a43bd2ec90",
+ "@id": "urn:b5be0e1d-2eae-4498-ad71-9ee980856337",
"Label": "3dToutcount",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D",
"Parameters": {},
"Used": [
- "urn:8d068463-26b0-4236-8937-fcb1118a01eb"
+ "urn:50736079-de9a-432b-a2db-79a26b418d57"
]
},
{
- "@id": "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
+ "@id": "urn:7b8eadd4-f765-437a-ab0e-4824de937df0",
"Label": "cat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "cat outcount.r*.1D > outcount_rall.1D",
"Parameters": {},
"Used": [
- "urn:59f3a66a-275b-4a37-8479-b063366c1072"
+ "urn:969531e6-8e1f-4881-b5cb-ce83fe7ff1ac"
]
},
{
- "@id": "urn:8154353f-62f4-4f33-a5e0-b25cfb3e0bf4",
+ "@id": "urn:fe6ace26-ff04-4f79-91bd-71b9d2b0cdea",
"Label": "3dTshift",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig",
"Parameters": {},
"Used": [
- "urn:8d068463-26b0-4236-8937-fcb1118a01eb"
+ "urn:50736079-de9a-432b-a2db-79a26b418d57"
]
},
{
- "@id": "urn:91a429ee-f3b0-42e8-bec2-e8be934e327e",
+ "@id": "urn:93043d20-67f9-40c3-8a9b-e016f761f4fb",
"Label": "align_epi_anat.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off",
"Parameters": {},
"Used": [
- "urn:4a1f3cd3-d200-41dc-81d3-78b30258701e",
- "urn:c73fa496-d31f-4802-97a4-ed7e422f2b73"
+ "urn:30b563bf-fe85-4fb6-bab0-727a4acb3078",
+ "urn:c77d7191-0804-496c-b902-abaed4fcf96c"
]
},
{
- "@id": "urn:aa7b2f0c-211d-402d-9e28-14a87872319f",
+ "@id": "urn:7ac1a591-3185-4ce8-9d34-f3bf695c0fa7",
"Label": "@auto_tlrc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss",
"Parameters": {},
"Used": [
- "urn:13d034fa-73d1-442e-a6c5-5225daf2683f",
- "urn:faf886ff-9fee-4689-bf69-9d37f32c368c"
+ "urn:161541c6-24a8-4a72-a6ca-7fdd2db5f14b",
+ "urn:49d22c69-9349-492e-b053-62a1b6afa901"
]
},
{
- "@id": "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
+ "@id": "urn:08e4f79d-ea4f-4d46-ab8d-c778d5bb066c",
"Label": "cat_matvec",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D",
"Parameters": {},
"Used": [
- "urn:a020ff0c-b5e2-4414-a32c-0791ca1dd749"
+ "urn:7dcd3f5a-55fd-4255-b6b0-28e323804813"
]
},
{
- "@id": "urn:6e528fd8-b78c-42f5-824d-5b4adbf88e5b",
+ "@id": "urn:c40149f1-9ffe-4002-923e-896181a14e31",
"Label": "3dvolreg",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig",
"Parameters": {},
"Used": [
- "urn:34aa4304-4007-4181-a467-db010e088b05"
+ "urn:3629b3b4-6e9a-417f-9924-ee2d75ed4331"
]
},
{
- "@id": "urn:588a7629-618c-407b-ba9b-2f1ecac124d7",
+ "@id": "urn:f0a285b6-e50c-4693-a082-9633c0e895d2",
"Label": "3dcalc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1",
"Parameters": {},
"Used": [
- "urn:34aa4304-4007-4181-a467-db010e088b05"
+ "urn:3629b3b4-6e9a-417f-9924-ee2d75ed4331"
]
},
{
- "@id": "urn:acd0d873-2205-4bcf-8552-465bb5afba1f",
+ "@id": "urn:33178c77-5b3e-41fc-aa26-ed92811f912b",
"Label": "cat_matvec",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D",
"Parameters": {},
"Used": [
- "urn:a020ff0c-b5e2-4414-a32c-0791ca1dd749"
+ "urn:7dcd3f5a-55fd-4255-b6b0-28e323804813"
]
},
{
- "@id": "urn:c650b95a-c9bf-4612-b47a-eedf376d79f9",
+ "@id": "urn:033018b3-4611-4020-a838-513bb1247ebf",
"Label": "3dAllineate",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run",
"Parameters": {},
"Used": [
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- "urn:7365d26e-619c-4e80-a058-964fa937d9e5",
- "urn:8f99c180-e872-4b3d-b928-89da81c3d281"
+ "urn:3629b3b4-6e9a-417f-9924-ee2d75ed4331",
+ "urn:ce01820c-b433-4f27-9aec-66cb4e464837",
+ "urn:e409a3c1-44eb-47e1-a284-584feffca4ad"
]
},
{
- "@id": "urn:17c44a15-af08-4f20-80dc-8d6a00fb19a0",
+ "@id": "urn:5a4ec6c3-6a40-4923-b0e1-694232dc8e68",
"Label": "3dAllineate",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run",
"Parameters": {},
"Used": [
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- "urn:8f99c180-e872-4b3d-b928-89da81c3d281"
+ "urn:ce01820c-b433-4f27-9aec-66cb4e464837",
+ "urn:e1b2a3cf-5e2c-46cc-b65d-e2af1525ae24",
+ "urn:e409a3c1-44eb-47e1-a284-584feffca4ad"
]
},
{
- "@id": "urn:308ee1ba-15be-4db5-a4f2-9e4ad49adee8",
+ "@id": "urn:ffe63744-e200-4a3d-ab0a-e0de9bce6565",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc",
"Parameters": {},
"Used": [
- "urn:f19f51ad-5e08-412b-b80a-9023c70693b4"
+ "urn:f2c161b4-1387-4be1-9ce3-ada9ff68a987"
]
},
{
- "@id": "urn:0571739d-afb1-4fc4-85a8-64b608b3ddc1",
+ "@id": "urn:5716b79a-8e82-4d72-99ca-9f76d32cd29c",
"Label": "cat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "cat dfile.r*.1D > dfile_rall.1D",
"Parameters": {},
"Used": [
- "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20"
+ "urn:9fc0d954-4735-442b-ae00-bdb679132ef0"
]
},
{
- "@id": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
+ "@id": "urn:f92146da-059f-436e-9761-19148ff8a713",
"Label": "3dcopy",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcopy rm.epi.min.r01+tlrc mask_epi_extents",
"Parameters": {},
"Used": [
- "urn:d2838435-2817-4d99-8c5e-4adbd8852f73"
+ "urn:1c50905a-4352-408b-bc1e-3d511116b8ed"
]
},
{
- "@id": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
+ "@id": "urn:84b79c77-e8eb-471c-9e27-83ae9cd47563",
"Label": "3dcalc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg",
"Parameters": {},
"Used": [
- "urn:a0b6b6d8-e7c9-4497-8f03-00bb7ea256c8",
- "urn:cffb91c8-2c95-46ce-b44f-baf44b7e488d"
+ "urn:362c1805-a188-444b-a452-3cceae801bbe",
+ "urn:e93ede5a-a9ec-4c73-96ba-d3c0500250c5"
]
},
{
- "@id": "urn:51561c54-ad75-499d-9aa7-1cb5ab17a577",
+ "@id": "urn:2766bf06-a141-4e54-9682-cf3964690b32",
"Label": "3dcopy",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcopy sub-01_T1w_ns+tlrc anat_final.$subj",
"Parameters": {},
"Used": [
- "urn:7365d26e-619c-4e80-a058-964fa937d9e5"
+ "urn:ce01820c-b433-4f27-9aec-66cb4e464837"
]
},
{
- "@id": "urn:184be230-ca69-44e0-b9d5-937d940c1349",
+ "@id": "urn:c7c84640-688f-48ff-9839-f197cde472eb",
"Label": "3dAllineate",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped",
"Parameters": {},
"Used": [
- "urn:0a80926c-2513-4239-bf14-d648691c34ee"
+ "urn:19376406-be37-4a1b-abdd-6e0af87f6e14"
]
},
{
- "@id": "urn:d4cb83cd-6bf6-48e2-955f-122e6d0a0439",
+ "@id": "urn:b2b56fae-7e4b-49e8-9740-dffd4345b618",
"Label": "3dmerge",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc",
"Parameters": {},
"Used": [
- "urn:57479980-7201-4d14-9ce3-a5f778c62ba1",
- "urn:b2713b64-ed9c-4912-bde1-97d522fcdadb"
+ "urn:23b99033-a46e-43f2-a3ab-1c5e95297e0d",
+ "urn:fc5c4a28-6158-4746-b8bf-f7c0202a5825"
]
},
{
- "@id": "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f",
+ "@id": "urn:e378a996-728b-4549-9f8d-54a158de0dd9",
"Label": "3dAutomask",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:a2408b33-ec25-4dc5-8fee-7718d02a4182"
+ "urn:afbb0fcd-be1d-434d-80d0-8cf9f17e4d12"
]
},
{
- "@id": "urn:95f9e98f-16a1-4203-add4-aa09068c95cc",
+ "@id": "urn:1efd8246-be85-4097-9127-d0bfbd75fdc2",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:6dfbc9e7-edf1-4dfb-8913-3084e1f1b1d5",
+ "@id": "urn:8c7ca029-99fa-4b68-83ba-5fa681021c7f",
"Label": "3dresample",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat",
"Parameters": {},
"Used": [
- "urn:7365d26e-619c-4e80-a058-964fa937d9e5",
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0"
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee",
+ "urn:ce01820c-b433-4f27-9aec-66cb4e464837"
]
},
{
- "@id": "urn:e29d8494-1287-4ba6-a240-13d062db51c0",
+ "@id": "urn:b8c70f53-b7ac-4987-9c8c-344acef7b7f5",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj",
"Parameters": {},
"Used": [
- "urn:9861b3fa-f459-4b8e-b56f-00916d10574d"
+ "urn:7aab29db-76b4-40ce-9e9f-1cb4562fd756"
]
},
{
- "@id": "urn:ab2e43b9-23a9-4498-b928-4a757cf4c869",
+ "@id": "urn:65b0ba1e-2605-4c33-a061-bbe12d0a744d",
"Label": "3dABoverlap",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt",
"Parameters": {},
"Used": [
- "urn:77c559d3-63ce-44f4-bb26-91c7ddbe62f6",
- "urn:db45e346-70b9-4be1-8d3c-be40c2aa586b"
+ "urn:cffc88d3-d33a-458a-bb38-67d39e4fbad7",
+ "urn:f962b32f-0ab9-4c2b-861a-20ef51f06bed"
]
},
{
- "@id": "urn:9c6482f8-d86c-42e8-887e-a01c650d7f9d",
+ "@id": "urn:bf196f88-6dea-4184-84d9-0017dcb02539",
"Label": "3ddot",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt",
"Parameters": {},
"Used": [
- "urn:77c559d3-63ce-44f4-bb26-91c7ddbe62f6",
- "urn:db45e346-70b9-4be1-8d3c-be40c2aa586b"
+ "urn:cffc88d3-d33a-458a-bb38-67d39e4fbad7",
+ "urn:f962b32f-0ab9-4c2b-861a-20ef51f06bed"
]
},
{
- "@id": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "@id": "urn:ab0217cf-72be-4734-819d-2ea486fa0aad",
"Label": "3dresample",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc",
"Parameters": {},
"Used": [
- "urn:59104013-7df9-4454-925f-bdb123c22844",
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0"
+ "urn:84298b0b-a786-45a5-a871-c186fc0ecef3",
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee"
]
},
{
- "@id": "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a",
+ "@id": "urn:4a70628a-6a31-428b-900c-5b0adc7fd6d2",
"Label": "3dmask_tool",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group",
"Parameters": {},
"Used": [
- "urn:192e03df-9cbd-4758-a519-d36f7449d11e"
+ "urn:e2f7dab3-3815-40a2-80a3-31469ef2bd0b"
]
},
{
- "@id": "urn:6095f7d1-7e5e-483d-bf1a-5a4838cc9152",
+ "@id": "urn:7fb86442-2d63-437f-8793-4c6a0429e57b",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc",
"Parameters": {},
"Used": [
- "urn:a2408b33-ec25-4dc5-8fee-7718d02a4182"
+ "urn:afbb0fcd-be1d-434d-80d0-8cf9f17e4d12"
]
},
{
- "@id": "urn:4abf85b0-30e5-4e03-92bb-35fd73da6f1d",
+ "@id": "urn:adc6bb28-7a0f-4e1a-aa5f-8d5e426b25f2",
"Label": "3dcalc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale",
"Parameters": {},
"Used": [
- "urn:5a8ac39b-1335-4c41-889f-60783a5e2b84",
- "urn:a2408b33-ec25-4dc5-8fee-7718d02a4182",
- "urn:cffb91c8-2c95-46ce-b44f-baf44b7e488d"
+ "urn:362c1805-a188-444b-a452-3cceae801bbe",
+ "urn:afbb0fcd-be1d-434d-80d0-8cf9f17e4d12",
+ "urn:b6918ff4-2c46-44be-85c7-1e73d9b38eef"
]
},
{
- "@id": "urn:17f60b95-1e29-42f6-9f58-15348ca2b014",
+ "@id": "urn:6f3a674f-8971-406f-9ef8-25572058e010",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -demean -write motion_demean.1D",
"Parameters": {},
"Used": [
- "urn:30df620a-6022-4cb7-8b04-92b6ee439617"
+ "urn:b1ef77d7-a2f8-452d-af2c-fcc3d9929bcc"
]
},
{
- "@id": "urn:f21f492c-1ded-461d-a8ba-11cf5b61aacf",
+ "@id": "urn:78498ca4-4f81-4c3e-b0e7-f024d8f4a0ae",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -derivative -demean -write motion_deriv.1D",
"Parameters": {},
"Used": [
- "urn:30df620a-6022-4cb7-8b04-92b6ee439617"
+ "urn:b1ef77d7-a2f8-452d-af2c-fcc3d9929bcc"
]
},
{
- "@id": "urn:19f90103-0415-4e89-9031-04bc863b9076",
+ "@id": "urn:8fca2197-e562-4255-8856-e9bdc397846c",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1d_tool.py -infile dfile_rall.1D -set_nruns 1 -show_censor_count -censor_prev_TR -censor_motion 0.3 motion_${subj}",
"Parameters": {},
"Used": [
- "urn:30df620a-6022-4cb7-8b04-92b6ee439617"
+ "urn:b1ef77d7-a2f8-452d-af2c-fcc3d9929bcc"
]
},
{
- "@id": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
+ "@id": "urn:798cd8cd-c847-4542-a933-b6e74e79b7dc",
"Label": "3dDeconvolve",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD -censor motion_${subj}_censor.1D -polort 2 -num_stimts 8 -stim_times 1 stimuli/tone_counting_onset_times.txt 'BLOCK(4)' -stim_label 1 tone_counting -stim_times_AM1 2 stimuli/tone_counting_probe_duration.txt 'dmBLOCK' -stim_label 2 probe -stim_file 3 motion_demean.1D'[0]' -stim_base 3 -stim_label 3 roll -stim_file 4 motion_demean.1D'[1]' -stim_base 4 -stim_label 4 pitch -stim_file 5 motion_demean.1D'[2]' -stim_base 5 -stim_label 5 yaw -stim_file 6 motion_demean.1D'[3]' -stim_base 6 -stim_label 6 dS -stim_file 7 motion_demean.1D'[4]' -stim_base 7 -stim_label 7 dL -stim_file 8 motion_demean.1D'[5]' -stim_base 8 -stim_label 8 dP -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.$subj -errts errts.${subj} -bucket stats.$subj",
"Parameters": {},
"Used": [
- "urn:423da7a2-7b60-42aa-b8ab-02fed4206f6d"
+ "urn:7f8e1890-72fb-4b74-a656-e1390ae6742c"
]
},
{
- "@id": "urn:3e1129c4-1668-4d2a-86a6-ec65ba4cdf22",
+ "@id": "urn:dd14f724-7a25-4843-9968-5c9d366a24b1",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1d_tool.py -show_cormat_warnings -infile X.xmat.1D |& tee out.cormat_warn.txt",
"Parameters": {},
"Used": [
- "urn:59a1ea45-0220-470e-939b-f58dd721e19d"
+ "urn:2c613c87-e382-4a3e-931f-f58e2f93f0db"
]
},
{
- "@id": "urn:4eb29210-41a9-45a5-96b6-1222aa0ae290",
+ "@id": "urn:27dee2a5-d4fd-455a-a7ba-355c85466044",
"Label": "3dTcat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTcat -prefix all_runs.$subj pb04.$subj.r*.scale+tlrc.HEAD",
"Parameters": {},
"Used": [
- "urn:423da7a2-7b60-42aa-b8ab-02fed4206f6d"
+ "urn:7f8e1890-72fb-4b74-a656-e1390ae6742c"
]
},
{
- "@id": "urn:ae9cf233-1cae-4123-a0a2-7d87c41578fa",
+ "@id": "urn:a0d89fab-b0ab-4f2d-9190-54341930a4bb",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -mean -prefix rm.signal.all all_runs.$subj+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:ec5adfc3-1f39-4145-a708-6aaee3ff4ea1"
+ "urn:918eddc7-6f84-490a-ac14-1da947842f79"
]
},
{
- "@id": "urn:f1fd52b2-0cea-408d-86e1-3d09209e9366",
+ "@id": "urn:e0b7adb3-d38b-4fc0-873d-2d62ebec19ce",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -stdev -prefix rm.noise.all errts.${subj}+tlrc\"[$ktrs]\"",
"Parameters": {},
"Used": [
- "urn:884190c2-d08b-4691-a22d-6a606a505216"
+ "urn:d314992b-cac9-4ad4-bdc7-867f727169d0"
]
},
{
- "@id": "urn:c86b2317-ab5f-4ba3-afa9-3fbd93c338eb",
+ "@id": "urn:c408e374-5f90-48fe-95b2-5f7a05eee2f9",
"Label": "3dcalc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcalc -a rm.signal.all+tlrc -b rm.noise.all+tlrc -c full_mask.$subj+tlrc -expr 'c*a/b' -prefix TSNR.$subj",
"Parameters": {},
"Used": [
- "urn:810d1d25-c45f-487c-aece-3d12edc22e68",
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0",
- "urn:dbca62fd-97b2-444f-b31a-4ed6d5c82310"
+ "urn:19438905-b980-4480-8213-acd4f5503231",
+ "urn:3416c6db-daf7-42a9-a4ac-dcbd53a83ee4",
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee"
]
},
{
- "@id": "urn:ffda532d-a9a3-4afe-ae56-0c197afed2e5",
+ "@id": "urn:5f56037d-5953-41cb-8829-328f92f7c45d",
"Label": "3dTnorm",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTnorm -norm2 -prefix rm.errts.unit errts.${subj}+tlrc",
"Parameters": {},
"Used": [
- "urn:ad54aeea-950d-4781-96b7-9042c66660de"
+ "urn:361e2de5-bd42-4a16-ba04-46357201d7a9"
]
},
{
- "@id": "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631",
+ "@id": "urn:23d7ac15-7e72-4849-b3a1-851e58705883",
"Label": "3dmaskave",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dmaskave -quiet -mask full_mask.$subj+tlrc rm.errts.unit+tlrc > gmean.errts.unit.1D",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:d8cc0c56-0ddc-4d6b-aa2b-6b5f38ecee47",
+ "@id": "urn:aacd816b-767d-4f22-932d-c1cdf4a88f80",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -sos -prefix - gmean.errts.unit.1D\\' > out.gcor.1D",
"Parameters": {},
"Used": [
- "urn:f62083f2-8dde-4cc3-a24c-d446e46978ad"
+ "urn:0f745c76-0f78-49c5-8ff9-bccd8ba53898"
]
},
{
- "@id": "urn:e9aece2a-e134-463e-82bb-80691c416208",
+ "@id": "urn:077d0829-deb4-4be7-9579-f9895424327e",
"Label": "3dcalc",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dcalc -a rm.errts.unit+tlrc -b gmean.errts.unit.1D -expr 'a*b' -prefix rm.DP",
"Parameters": {},
"Used": [
- "urn:227413e0-9f8c-4ec6-8469-9de994444e70",
- "urn:c9d09354-17e6-47d9-9ed7-be2474d8a292"
+ "urn:07504cd3-5a91-4cd5-8a96-15593431d0fb",
+ "urn:2bb9fe99-68dd-49fd-ad73-be9c94e8b622"
]
},
{
- "@id": "urn:413e1783-c57d-416f-9594-1b82ef39aa74",
+ "@id": "urn:a58b6031-b05a-43df-ac36-de55634b6bc9",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -sum -prefix corr_brain rm.DP+tlrc",
"Parameters": {},
"Used": [
- "urn:fe451eab-ab28-4f5f-8e5f-98855e0ed4a8"
+ "urn:eb9c5a32-a971-4ebc-88fb-ab4245683a0e"
]
},
{
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+ "@id": "urn:ac1535dc-23a4-43ba-8b51-9327ee6d8e55",
"Label": "1dcat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1dcat X.nocensor.xmat.1D'[3]' > ideal_tone_counting.1D",
"Parameters": {},
"Used": [
- "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893"
+ "urn:5b4476b9-ab24-40e1-b68a-1f0513780348"
]
},
{
- "@id": "urn:af38b1c5-cfab-4f4c-a109-1cebae93f287",
+ "@id": "urn:1b2b75d0-b3d0-41a6-95d1-205880e86671",
"Label": "1dcat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1dcat X.nocensor.xmat.1D'[4]' > ideal_probe.1D",
"Parameters": {},
"Used": [
- "urn:619b94b1-3e0e-4b72-828a-317b7c6bebd4"
+ "urn:fcb34c2a-0ac1-410d-9eb4-0cf5fcc167cb"
]
},
{
- "@id": "urn:e78802d6-1bb2-429f-bd2e-590f9ca87a83",
+ "@id": "urn:822d23a6-e31f-4857-94e7-1096567473c5",
"Label": "3dTstat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dTstat -sum -prefix sum_ideal.1D X.nocensor.xmat.1D\"[$reg_cols]\"",
"Parameters": {},
"Used": [
- "urn:e2e2d08d-3f8e-4b33-878c-67d75e93a4fa"
+ "urn:588ac9fe-3fa0-485e-b22d-412e072bdc42"
]
},
{
- "@id": "urn:79564ced-7998-4380-8c8f-3269d12b864f",
+ "@id": "urn:c1980f5d-3fe2-4082-9506-41b0d1ddc28b",
"Label": "1dcat",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "1dcat X.nocensor.xmat.1D\"[$reg_cols]\" > X.stim.xmat.1D",
"Parameters": {},
"Used": [
- "urn:e2e2d08d-3f8e-4b33-878c-67d75e93a4fa"
+ "urn:588ac9fe-3fa0-485e-b22d-412e072bdc42"
]
},
{
- "@id": "urn:493995db-4752-45aa-a7fe-8c271ece8525",
+ "@id": "urn:e1b7b543-bd2b-4c78-845e-b12ccb707f04",
"Label": "3dFWHMx",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc all_runs.$subj+tlrc\"[$trs]\" >> blur.epits.1D",
"Parameters": {},
"Used": [
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0"
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee"
]
},
{
- "@id": "urn:1da1246e-8f5c-4ddb-a27f-be71f0701162",
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"Label": "3dFWHMx",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dFWHMx -detrend -mask full_mask.$subj+tlrc errts.${subj}+tlrc\"[$trs]\" >> blur.errts.1D",
"Parameters": {},
"Used": [
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0"
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee"
]
},
{
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+ "@id": "urn:d7059659-eda4-459d-a116-80bc35f12d1f",
"Label": "3dClustSim",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "3dClustSim -both -mask full_mask.$subj+tlrc -fwhmxyz $fxyz[1-3] -prefix ClustSim",
"Parameters": {},
"Used": [
- "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0"
+ "urn:94aaf97a-23d3-4684-b9e1-40299faf81ee"
]
},
{
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+ "@id": "urn:5b5097fc-32d9-43ea-9eeb-dfee8e748ae6",
"Label": "gen_epi_review.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
"Command": "gen_epi_review.py -script @epi_review.$subj -dsets pb00.$subj.r*.tcat+orig.HEAD",
"Parameters": {},
"Used": [
- "urn:05b977f9-3054-4c8c-bca4-36bab8c25375"
+ "urn:8e5ab35a-7669-4e51-adee-3f7e416010f6"
]
},
{
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+ "@id": "urn:04a712df-9c24-485f-8e45-4df1264e44f8",
"Label": "gen_ss_review_scripts.py",
- "AssociatedWith": "urn:f15fe524-f568-4e93-9286-fc790afe24eb",
+ "AssociatedWith": "urn:5aa6443e-a002-4c17-8478-d18de21fc8b8",
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"Parameters": {
"-mot_limit": "0.3",
@@ -586,22 +586,22 @@
],
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{
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+ "@id": "urn:a9fca6d2-d86c-450d-97a9-50415da048a5",
"Label": "$output_dir",
"AtLocation": "$output_dir",
- "GeneratedBy": "urn:a1805d3b-baeb-4707-b217-71a4d28ace1b",
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:64758879-6b04-479d-8021-1385b8b85587"
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+ "@id": "urn:045781d1-9e75-4834-9b30-4978b76070da",
"Label": "tone_counting_onset_times.txt",
"AtLocation": "./afni_voxelwise_t4/tone_counting_onset_times.txt",
"digest": {
@@ -609,7 +609,7 @@
}
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{
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"Label": "tone_counting_probe_duration.txt",
"AtLocation": "./afni_voxelwise_t4/tone_counting_probe_duration.txt",
"digest": {
@@ -617,13 +617,13 @@
}
},
{
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"Label": "stimuli",
"AtLocation": "$output_dir/stimuli",
- "GeneratedBy": "urn:3190be3b-d808-4789-a6b2-90c5db0bb314"
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{
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+ "@id": "urn:91ed2886-1c20-431d-9c0f-8f3720ffea22",
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"AtLocation": "sub-01_T1w.nii.gz",
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@@ -631,13 +631,13 @@
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{
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"AtLocation": "$output_dir/sub-01_T1w",
- "GeneratedBy": "urn:2be229a2-3fbe-4acb-9aaf-e280530aa938"
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{
- "@id": "urn:bade994c-bfbf-48ef-952e-593582deab90",
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"Label": "sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "sub-01_task-tonecounting_bold.nii.gz'[0..$]'",
"digest": {
@@ -645,13 +645,13 @@
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{
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"AtLocation": "$output_dir/pb00.$subj.r01.tcat",
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{
- "@id": "urn:8d068463-26b0-4236-8937-fcb1118a01eb",
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@@ -659,16 +659,16 @@
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"AtLocation": "outcount.r$run.1D",
- "GeneratedBy": "urn:198081c3-d54d-4afa-8c05-56a43bd2ec90",
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{
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+ "@id": "urn:969531e6-8e1f-4881-b5cb-ce83fe7ff1ac",
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"AtLocation": "outcount.r*.1D",
"digest": {
@@ -676,25 +676,25 @@
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"AtLocation": "outcount_rall.1D",
- "GeneratedBy": "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
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"AtLocation": "pb01.$subj.r$run.tshift",
- "GeneratedBy": "urn:8154353f-62f4-4f33-a5e0-b25cfb3e0bf4",
+ "GeneratedBy": "urn:fe6ace26-ff04-4f79-91bd-71b9d2b0cdea",
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+ "@id": "urn:30b563bf-fe85-4fb6-bab0-727a4acb3078",
"Label": "sub-01_T1w",
"AtLocation": "sub-01_T1w+orig",
"digest": {
@@ -702,7 +702,7 @@
}
},
{
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@@ -710,16 +710,16 @@
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{
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+ "@id": "urn:2b405121-a35c-4902-b87f-572b4bbdae74",
"Label": "_al_junk",
"AtLocation": "_al_junk",
- "GeneratedBy": "urn:91a429ee-f3b0-42e8-bec2-e8be934e327e",
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{
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+ "@id": "urn:161541c6-24a8-4a72-a6ca-7fdd2db5f14b",
"Label": "TT_N27",
"AtLocation": "TT_N27+tlrc",
"digest": {
@@ -727,7 +727,7 @@
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{
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"Label": "sub-01_T1w_ns",
"AtLocation": "sub-01_T1w_ns+orig",
"digest": {
@@ -735,7 +735,7 @@
}
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{
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@@ -743,16 +743,16 @@
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{
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+ "@id": "urn:19376406-be37-4a1b-abdd-6e0af87f6e14",
"Label": "warp.anat.Xat.1D",
"AtLocation": "warp.anat.Xat.1D",
- "GeneratedBy": "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
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@@ -760,34 +760,34 @@
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{
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"AtLocation": "rm.epi.all1",
- "GeneratedBy": "urn:588a7629-618c-407b-ba9b-2f1ecac124d7",
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+ "@id": "urn:e409a3c1-44eb-47e1-a284-584feffca4ad",
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"AtLocation": "mat.r$run.warp.aff12.1D",
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@@ -795,16 +795,16 @@
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+ "@id": "urn:e1b2a3cf-5e2c-46cc-b65d-e2af1525ae24",
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@@ -812,16 +812,16 @@
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@@ -829,16 +829,16 @@
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@@ -1093,25 +1093,25 @@
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@@ -1136,16 +1136,16 @@
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"Label": "rm.DP",
"AtLocation": "rm.DP",
- "GeneratedBy": "urn:e9aece2a-e134-463e-82bb-80691c416208",
+ "GeneratedBy": "urn:077d0829-deb4-4be7-9579-f9895424327e",
"digest": {
"sha256": "06a0bfbc609c1a06ecf93c479a3288d2911c7f5f3e93cf49c5d26f721c2035ed"
}
},
{
- "@id": "urn:fe451eab-ab28-4f5f-8e5f-98855e0ed4a8",
+ "@id": "urn:eb9c5a32-a971-4ebc-88fb-ab4245683a0e",
"Label": "rm.DP",
"AtLocation": "rm.DP+tlrc",
"digest": {
@@ -1238,16 +1238,16 @@
}
},
{
- "@id": "urn:b5a35ff9-0434-42f2-9b5c-ef7669c25f2b",
+ "@id": "urn:3ac68a81-17d1-4bb2-aabc-08c6e5f5247c",
"Label": "corr_brain",
"AtLocation": "corr_brain",
- "GeneratedBy": "urn:413e1783-c57d-416f-9594-1b82ef39aa74",
+ "GeneratedBy": "urn:a58b6031-b05a-43df-ac36-de55634b6bc9",
"digest": {
"sha256": "74e3aeae0da338b871ab5dc9e8859a4e81fcf1b3c0042cd22fe337eb7baf5eae"
}
},
{
- "@id": "urn:f32dd099-a3b9-4889-8fbb-8b2f4df56893",
+ "@id": "urn:5b4476b9-ab24-40e1-b68a-1f0513780348",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[3]'",
"digest": {
@@ -1255,16 +1255,16 @@
}
},
{
- "@id": "urn:1164d63b-cf24-42cc-9f8f-c0ffaee54e74",
+ "@id": "urn:196062b9-4d14-4f30-9fc2-44a5b79b8ce4",
"Label": "ideal_tone_counting.1D",
"AtLocation": "ideal_tone_counting.1D",
- "GeneratedBy": "urn:12efd317-2a31-4854-b0c0-60c333623961",
+ "GeneratedBy": "urn:ac1535dc-23a4-43ba-8b51-9327ee6d8e55",
"digest": {
"sha256": "9bb1cabac5ce7ca19dffa5cd6336a9bf82d362fea2ce9341978406e421b5333c"
}
},
{
- "@id": "urn:619b94b1-3e0e-4b72-828a-317b7c6bebd4",
+ "@id": "urn:fcb34c2a-0ac1-410d-9eb4-0cf5fcc167cb",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D'[4]'",
"digest": {
@@ -1272,16 +1272,16 @@
}
},
{
- "@id": "urn:0e8e8869-93db-4b86-8b5e-08ad3dc1982b",
+ "@id": "urn:9db9310b-c431-471f-885f-4d92835f3e88",
"Label": "ideal_probe.1D",
"AtLocation": "ideal_probe.1D",
- "GeneratedBy": "urn:af38b1c5-cfab-4f4c-a109-1cebae93f287",
+ "GeneratedBy": "urn:1b2b75d0-b3d0-41a6-95d1-205880e86671",
"digest": {
"sha256": "705d93afa8b6ded9f4f572db3f967b54e9906942669af51dd8287a9863bb4288"
}
},
{
- "@id": "urn:e2e2d08d-3f8e-4b33-878c-67d75e93a4fa",
+ "@id": "urn:588ac9fe-3fa0-485e-b22d-412e072bdc42",
"Label": "X.nocensor.xmat.1D",
"AtLocation": "X.nocensor.xmat.1D\"[$reg_cols]\"",
"digest": {
@@ -1289,52 +1289,52 @@
}
},
{
- "@id": "urn:88abf868-a869-49a3-8dc4-1b3553c7ce81",
+ "@id": "urn:a71e77db-a92b-413f-a03a-4242ae1ae6d7",
"Label": "sum_ideal.1D",
"AtLocation": "sum_ideal.1D",
- "GeneratedBy": "urn:e78802d6-1bb2-429f-bd2e-590f9ca87a83",
+ "GeneratedBy": "urn:822d23a6-e31f-4857-94e7-1096567473c5",
"digest": {
"sha256": "b2dccadcd84b2d26ec9685c4d1846baf2f11b867f31c36a08748d1c85467b01a"
}
},
{
- "@id": "urn:3ef5d45b-c17d-4f9d-8c55-18a52b42ee5d",
+ "@id": "urn:a559ffd4-5aeb-4597-9090-066211978da4",
"Label": "X.stim.xmat.1D",
"AtLocation": "X.stim.xmat.1D",
- "GeneratedBy": "urn:79564ced-7998-4380-8c8f-3269d12b864f",
+ "GeneratedBy": "urn:c1980f5d-3fe2-4082-9506-41b0d1ddc28b",
"digest": {
"sha256": "7c61b2f4bbb9eb0cecb19f81faa3a79b94d547b7fb4087ed18e368619e0004e6"
}
},
{
- "@id": "urn:11f9b53f-10ed-481a-bf7c-bb31594d0e05",
+ "@id": "urn:2618dc26-6b1b-47a6-bfa4-c219a8a49058",
"Label": "blur.epits.1D",
"AtLocation": "blur.epits.1D",
- "GeneratedBy": "urn:493995db-4752-45aa-a7fe-8c271ece8525",
+ "GeneratedBy": "urn:e1b7b543-bd2b-4c78-845e-b12ccb707f04",
"digest": {
"sha256": "623e70a42214e56babc1f1dca156e0b11ba09865dbd6ca9549d54ca2fc601515"
}
},
{
- "@id": "urn:990a8e8f-1603-40d5-9b7e-89e4292d2808",
+ "@id": "urn:3e2a1065-eb68-42af-8262-c15c24532510",
"Label": "blur.errts.1D",
"AtLocation": "blur.errts.1D",
- "GeneratedBy": "urn:1da1246e-8f5c-4ddb-a27f-be71f0701162",
+ "GeneratedBy": "urn:6b970f51-83db-4286-9ac6-f0639095e34d",
"digest": {
"sha256": "73969700079b5d3275536ac7eaf0e17571d7e74ec49553b6940f90d5718fc800"
}
},
{
- "@id": "urn:e3fc347c-23da-42f1-9c1e-0adba15a1643",
+ "@id": "urn:74884da0-1e79-4463-8ba6-1abd595cc3dd",
"Label": "ClustSim",
"AtLocation": "ClustSim",
- "GeneratedBy": "urn:a6fece11-f37d-4d67-86a2-f2789092ab56",
+ "GeneratedBy": "urn:d7059659-eda4-459d-a116-80bc35f12d1f",
"digest": {
"sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
}
},
{
- "@id": "urn:05b977f9-3054-4c8c-bca4-36bab8c25375",
+ "@id": "urn:8e5ab35a-7669-4e51-adee-3f7e416010f6",
"Label": "pb00.$subj.r*.tcat",
"AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
"digest": {
@@ -1342,10 +1342,10 @@
}
},
{
- "@id": "urn:e335ba2c-7aa9-42f2-9337-9d3fba7ccb43",
+ "@id": "urn:28ddef98-1123-4229-8523-1113ba28ee95",
"Label": "-exit0",
"AtLocation": "-exit0",
- "GeneratedBy": "urn:23b55492-978b-4682-9b1f-fdd6e001aa8a",
+ "GeneratedBy": "urn:04a712df-9c24-485f-8e45-4df1264e44f8",
"digest": {
"sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
}
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png
index 25ca098c7..1d0cdb469 100644
Binary files a/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc.png differ
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
new file mode 100644
index 000000000..d0356e85d
--- /dev/null
+++ b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.jsonld
@@ -0,0 +1,1000 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:348b02c5-3388-42a3-90af-a610d35d440d",
+ "Label": "auto block: setup",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "mkdir $output_dir; mkdir $output_dir/stimuli; cp ./afni_voxelwise_t4/tone_counting_onset_times.txt ./afni_voxelwise_t4/tone_counting_probe_duration.txt $output_dir/stimuli; 3dcopy sub-01_T1w.nii.gz $output_dir/sub-01_T1w; ",
+ "Used": [
+ "urn:1f03bef8-16e4-416d-a833-11890da768d2",
+ "urn:f0c9a6c3-06f6-4cf7-8a95-14b8dbdbe664",
+ "urn:8ae7c2aa-3fc9-45b4-b199-31ac2d6380a1"
+ ]
+ },
+ {
+ "@id": "urn:ec9d7980-1d0b-42f4-96b5-51a4ff6c86d0",
+ "Label": "auto block: tcat",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dTcat -prefix $output_dir/pb00.$subj.r01.tcat sub-01_task-tonecounting_bold.nii.gz'[0..$]'; ",
+ "Used": [
+ "urn:0da784c9-12e0-4732-b4de-2f7fac3a78b6"
+ ]
+ },
+ {
+ "@id": "urn:f4f9e3cd-9b48-4b47-bb15-6deaeaa2acb0",
+ "Label": "auto block: outcount",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dToutcount -automask -fraction -polort 2 -legendre pb00.$subj.r$run.tcat+orig > outcount.r$run.1D; cat outcount.r*.1D > outcount_rall.1D; ",
+ "Used": [
+ "urn:b18d15a5-a09a-4c39-b3b2-55e1eb31b5db",
+ "urn:cb2d5117-8e60-42fb-b3fa-2c5ac0a124b9"
+ ]
+ },
+ {
+ "@id": "urn:247ba477-f6f4-4359-bf5f-d3779573ecd7",
+ "Label": "tshift",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dTshift -tzero 0 -quintic -prefix pb01.$subj.r$run.tshift pb00.$subj.r$run.tcat+orig; ",
+ "Used": [
+ "urn:b18d15a5-a09a-4c39-b3b2-55e1eb31b5db"
+ ]
+ },
+ {
+ "@id": "urn:d401069b-da20-48be-afbb-31e098f3b3b2",
+ "Label": "align",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "align_epi_anat.py -anat2epi -anat sub-01_T1w+orig -save_skullstrip -suffix _al_junk -epi pb01.$subj.r01.tshift+orig -epi_base 2 -epi_strip 3dAutomask -volreg off -tshift off; ",
+ "Used": [
+ "urn:8e96504b-4dbe-4a58-95ca-d30dcc106298",
+ "urn:b06f7897-a1fb-4d07-a1da-28a0cb8c1f45"
+ ]
+ },
+ {
+ "@id": "urn:0ae21bc4-efb3-434e-a543-eac47f225762",
+ "Label": "tlrc",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "@auto_tlrc -base TT_N27+tlrc -input sub-01_T1w_ns+orig -no_ss; cat_matvec sub-01_T1w_ns+tlrc::WARP_DATA -I > warp.anat.Xat.1D; ",
+ "Used": [
+ "urn:085cb3e0-27a6-4dc3-bfd1-d70faa299d05",
+ "urn:93db0be2-3d8f-4f51-8b91-357d2785f7cd",
+ "urn:4164d714-de46-441d-9547-155ad3215532"
+ ]
+ },
+ {
+ "@id": "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37",
+ "Label": "volreg",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dvolreg -verbose -zpad 1 -base pb01.$subj.r01.tshift+orig'[2]' -1Dfile dfile.r$run.1D -prefix rm.epi.volreg.r$run -cubic -1Dmatrix_save mat.r$run.vr.aff12.1D pb01.$subj.r$run.tshift+orig; 3dcalc -overwrite -a pb01.$subj.r$run.tshift+orig -expr 1 -prefix rm.epi.all1; cat_matvec -ONELINE sub-01_T1w_ns+tlrc::WARP_DATA -I sub-01_T1w_al_junk_mat.aff12.1D -I mat.r$run.vr.aff12.1D > mat.r$run.warp.aff12.1D; 3dAllineate -base sub-01_T1w_ns+tlrc -input pb01.$subj.r$run.tshift+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -prefix rm.epi.nomask.r$run; 3dAllineate -base sub-01_T1w_ns+tlrc -input rm.epi.all1+orig -1Dmatrix_apply mat.r$run.warp.aff12.1D -mast_dxyz 3 -final NN -quiet -prefix rm.epi.1.r$run; 3dTstat -min -prefix rm.epi.min.r$run rm.epi.1.r$run+tlrc; cat dfile.r*.1D > dfile_rall.1D; 3dcopy rm.epi.min.r01+tlrc mask_epi_extents; 3dcalc -a rm.epi.nomask.r$run+tlrc -b mask_epi_extents+tlrc -expr 'a*b' -prefix pb02.$subj.r$run.volreg; 3dcopy sub-01_T1w_ns+tlrc anat_final.$subj; 3dAllineate -source sub-01_T1w+orig -master anat_final.$subj+tlrc -final wsinc5 -1Dmatrix_apply warp.anat.Xat.1D -prefix anat_w_skull_warped; ",
+ "Used": [
+ "urn:96b36d9b-c550-4dcc-a426-16925826d22d",
+ "urn:96b36d9b-c550-4dcc-a426-16925826d22d",
+ "urn:4164d714-de46-441d-9547-155ad3215532",
+ "urn:96b36d9b-c550-4dcc-a426-16925826d22d",
+ "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "urn:aa96021b-cc85-47e0-afd1-a427861606f0",
+ "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "urn:d191a56c-9c39-409d-a7f3-89bf42f57cc6",
+ "urn:162eba86-ca6b-40ce-90b8-82fc8a8aee10",
+ "urn:0f978606-b24a-49bb-bc30-6419c648087e",
+ "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b",
+ "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "urn:4b99f7af-3b64-4174-ac3f-cccc60966174"
+ ]
+ },
+ {
+ "@id": "urn:c28e8620-2d74-43ae-be27-e2028601d9bd",
+ "Label": "blur",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dmerge -1blur_fwhm 4.0 -doall -prefix pb03.$subj.r$run.blur pb02.$subj.r$run.volreg+tlrc; ",
+ "Used": [
+ "urn:28a7f0e5-cc3f-4d95-ab33-4effe28cfe77",
+ "urn:d3630e97-6933-464a-97bb-ab45131ac706"
+ ]
+ },
+ {
+ "@id": "urn:bc3e9f42-d4b1-4642-97b0-5e6677575a1f",
+ "Label": "mask",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dAutomask -dilate 1 -prefix rm.mask_r$run pb03.$subj.r$run.blur+tlrc; 3dmask_tool -inputs rm.mask_r*+tlrc.HEAD -union -prefix full_mask.$subj; 3dresample -master full_mask.$subj+tlrc -input sub-01_T1w_ns+tlrc -prefix rm.resam.anat; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.anat+tlrc -prefix mask_anat.$subj; 3dABoverlap -no_automask full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_overlap.txt; 3ddot -dodice full_mask.$subj+tlrc mask_anat.$subj+tlrc |& tee out.mask_ae_dice.txt; 3dresample -master full_mask.$subj+tlrc -prefix ./rm.resam.group -input /Users/u1591557/abin/TT_N27+tlrc; 3dmask_tool -dilate_input 5 -5 -fill_holes -input rm.resam.group+tlrc -prefix mask_group; ",
+ "Used": [
+ "urn:2b05ded6-ada3-4741-91ef-c43d763b40ca",
+ "urn:df0f0a0c-cfc4-4d8c-b572-856b120846f6",
+ "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "urn:6a09ed66-56d8-45c8-baab-c2417d274efe",
+ "urn:4c7e0766-bcb2-4baa-b971-d4766f468d5c",
+ "urn:8570c470-01d4-4c71-9c9a-61730f84d797",
+ "urn:4c7e0766-bcb2-4baa-b971-d4766f468d5c",
+ "urn:8570c470-01d4-4c71-9c9a-61730f84d797",
+ "urn:5cc18600-63ec-4312-882b-c70dbc2b79ff",
+ "urn:df0f0a0c-cfc4-4d8c-b572-856b120846f6",
+ "urn:3b925dfa-3c45-47cb-98eb-650acbb9f064"
+ ]
+ },
+ {
+ "@id": "urn:abfb5142-c999-4e6e-ae9e-27cbe9f09a1d",
+ "Label": "scale",
+ "AssociatedWith": "urn:eff9d632-d6e4-4d8e-a8e9-a9ae05f988c6",
+ "Command": "3dTstat -prefix rm.mean_r$run pb03.$subj.r$run.blur+tlrc; 3dcalc -a pb03.$subj.r$run.blur+tlrc -b rm.mean_r$run+tlrc -c mask_epi_extents+tlrc -expr 'c * min(200, a/b*100)*step(a)*step(b)' -prefix pb04.$subj.r$run.scale; ",
+ "Used": [
+ "urn:2b05ded6-ada3-4741-91ef-c43d763b40ca",
+ "urn:2b05ded6-ada3-4741-91ef-c43d763b40ca",
+ "urn:52ecd782-22ca-4d35-927b-3400bee24e28",
+ "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b"
+ ]
+ },
+ {
+ "@id": "urn:94571380-7577-41e6-a488-f0c5ea96db5e",
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+ "sha256": "2e0cdba2c91902ba12d742a39cb20df66cfd705ba8de767fbf68aae8eb65c6f0"
+ }
+ },
+ {
+ "@id": "urn:289c4b37-40fb-4979-ab4c-a1537a0f8550",
+ "Label": "pb00.$subj.r*.tcat",
+ "AtLocation": "pb00.$subj.r*.tcat+orig.HEAD",
+ "digest": {
+ "sha256": "7bfdd183d7a8172bab0929d792d5be6548eb83fbaff501bdc9be8822b5daf2a2"
+ }
+ },
+ {
+ "@id": "urn:956a31fd-030a-4e43-8e0b-eb06823cf052",
+ "Label": "-exit0",
+ "AtLocation": "-exit0",
+ "GeneratedBy": "urn:ae230fff-5fff-4021-9495-434681ac33b1",
+ "digest": {
+ "sha256": "871a4d3513ed2924cbb10c1c15a196eac4a46a05bdcc248e3bcdb23327b3ad90"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png
new file mode 100644
index 000000000..1d24d3077
Binary files /dev/null and b/examples/from_parsers/afni/afni_thr_voxelunct4_proc_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
index 802e79287..52d6ab9a0 100644
--- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
+++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "@id": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,53 +13,53 @@
],
"Activities": [
{
- "@id": "urn:90645147-6abd-4c8a-a8a5-517f8a8f21fe",
+ "@id": "urn:38c32689-25e4-4616-a55f-99f621b66dae",
"Label": "3dpc",
- "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
"Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}",
"Parameters": {},
"Used": [
- "urn:a68d7d7d-2892-4c73-8931-cb493bf3664b",
- "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451"
+ "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "urn:854a0da7-0140-4007-b23a-63c8036c2338"
]
},
{
- "@id": "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
+ "@id": "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd",
"Label": "3dresample",
- "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
"Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"",
"Parameters": {},
"Used": [
- "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
- "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451"
+ "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "urn:dee38932-e432-45ac-9034-ec463c0c71d4"
]
},
{
- "@id": "urn:31c67e59-a174-4acc-a9db-a84469c666cf",
+ "@id": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
"Label": "3dMatch",
- "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
"Command": "3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED",
"Parameters": {},
"Used": [
- "urn:0aff86a2-c424-420f-8105-3869a44750ba",
- "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
- "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04"
+ "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
+ "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c"
]
},
{
- "@id": "urn:e6b98c73-86e5-4eed-abdd-25d3eb6842f7",
+ "@id": "urn:f6360992-6c3c-4790-874c-7469907d535a",
"Label": "3dcalc",
- "AssociatedWith": "urn:b624270f-a3c2-46c6-a27c-89d37f792539",
+ "AssociatedWith": "urn:36139506-2e6f-4255-bbe7-49fb09a05bde",
"Command": "3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
"Parameters": {},
"Used": [
- "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04"
+ "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5"
]
}
],
"Entities": [
{
- "@id": "urn:dcd9b6d5-0d6c-44a8-b2a4-20746f3bf451",
+ "@id": "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
"Label": "${dset_mask}",
"AtLocation": "${dset_mask}",
"digest": {
@@ -67,7 +67,7 @@
}
},
{
- "@id": "urn:a68d7d7d-2892-4c73-8931-cb493bf3664b",
+ "@id": "urn:854a0da7-0140-4007-b23a-63c8036c2338",
"Label": "${grp_dset}",
"AtLocation": "${grp_dset}",
"digest": {
@@ -75,16 +75,16 @@
}
},
{
- "@id": "urn:1d44d844-c4ca-4840-9019-b9b7a5f712e2",
+ "@id": "urn:270d4b00-919d-46a5-8bd3-ba90ab4de77c",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}",
- "GeneratedBy": "urn:90645147-6abd-4c8a-a8a5-517f8a8f21fe",
+ "GeneratedBy": "urn:38c32689-25e4-4616-a55f-99f621b66dae",
"digest": {
"sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
}
},
{
- "@id": "urn:b0e85dbd-3264-414a-aad3-bded58a631c6",
+ "@id": "urn:dee38932-e432-45ac-9034-ec463c0c71d4",
"Label": "\"${ref_dset}\"",
"AtLocation": "\"${ref_dset}\"",
"digest": {
@@ -92,16 +92,16 @@
}
},
{
- "@id": "urn:0aff86a2-c424-420f-8105-3869a44750ba",
+ "@id": "urn:f653dfb6-d7f8-4895-8e06-573f04121f8c",
"Label": "tmp_REF_DSET.nii.gz",
"AtLocation": "tmp_REF_DSET.nii.gz",
- "GeneratedBy": "urn:3bbde2e2-3198-4f5e-a405-3dc2859a814d",
+ "GeneratedBy": "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd",
"digest": {
"sha256": "e943c60b478a75e89c043bc4a7a6e6c629c3f075007ff501f7b2ab3a253e8d3d"
}
},
{
- "@id": "urn:eaef0dcb-5236-4a45-9f31-8a11e2ed6b04",
+ "@id": "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
"Label": "PC_hyp${num}",
"AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
"digest": {
@@ -109,19 +109,19 @@
}
},
{
- "@id": "urn:a8a1a9f6-ef1a-480d-bdea-a1be759db9ea",
+ "@id": "urn:af09e210-3d42-4ab8-881e-63b8a79ac26f",
"Label": "tmp_MATCHED",
"AtLocation": "tmp_MATCHED",
- "GeneratedBy": "urn:31c67e59-a174-4acc-a9db-a84469c666cf",
+ "GeneratedBy": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
"digest": {
"sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
}
},
{
- "@id": "urn:40c7b3b1-aa1b-41ef-b09f-423be7a6600a",
+ "@id": "urn:11801d7e-8459-47fd-bfb3-024e9bf5501d",
"Label": "PC_hyp${num}_sign0.nii.gz",
"AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
- "GeneratedBy": "urn:e6b98c73-86e5-4eed-abdd-25d3eb6842f7",
+ "GeneratedBy": "urn:f6360992-6c3c-4790-874c-7469907d535a",
"digest": {
"sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
}
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png
index df13feb18..0ccdb6295 100644
Binary files a/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0.png differ
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld
index f6af5d0f3..bfca84b12 100644
--- a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld
+++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_bloc.jsonld
@@ -24,7 +24,7 @@
},
{
"@id": "urn:c5b45432-97f7-4d5d-9cb7-4468389c1014",
- "Label": "bloc ...",
+ "Label": "block ...",
"AssociatedWith": "urn:b42066b4-1ce6-4ef1-81c8-5b010b7b18a9",
"Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ",
"Used": [
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
new file mode 100644
index 000000000..1e43f0a02
--- /dev/null
+++ b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.jsonld
@@ -0,0 +1,109 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:a0ac5b56-4d0f-4af6-aea6-5c921500a958",
+ "Label": "",
+ "AssociatedWith": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+ "Command": "3dpc -overwrite -mask ${dset_mask} -pcsave 5 -prefix ${dir_hyp}/PC_hyp${num} ${grp_dset}; ",
+ "Used": [
+ "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "urn:8cb2d405-f78e-461f-a680-56abf991cd9e"
+ ]
+ },
+ {
+ "@id": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+ "Label": "block ...",
+ "AssociatedWith": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+ "Command": "3dresample -overwrite -prefix tmp_REF_DSET.nii.gz -master ${dset_mask} -input \"${ref_dset}\"; 3dMatch -echo_edu -overwrite -mask ${dset_mask} -refset ${dir_hyp}/PC_hyp${num}+tlrc -inset tmp_REF_DSET.nii.gz -prefix tmp_MATCHED; 3dcalc -echo_edu -overwrite -a ${dir_hyp}/PC_hyp${num}+tlrc -expr \"${signum}*a\" -prefix ${dir_hyp}/PC_hyp${num}_sign0.nii.gz; ",
+ "Used": [
+ "urn:3629a684-e3d0-4d02-b46c-ba0aa897ca06",
+ "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d",
+ "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d"
+ ]
+ }
+ ],
+ "Entities": [
+ {
+ "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "Label": "${dset_mask}",
+ "AtLocation": "${dset_mask}",
+ "digest": {
+ "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
+ }
+ },
+ {
+ "@id": "urn:8cb2d405-f78e-461f-a680-56abf991cd9e",
+ "Label": "${grp_dset}",
+ "AtLocation": "${grp_dset}",
+ "digest": {
+ "sha256": "b1baa298b8599a501c11bb588cf53f5f808f115ea112431351bbf5c494bb9298"
+ }
+ },
+ {
+ "@id": "urn:5bcbb31a-da10-4a45-b7eb-04dac91e5b3c",
+ "Label": "PC_hyp${num}",
+ "AtLocation": "${dir_hyp}/PC_hyp${num}",
+ "GeneratedBy": "urn:a0ac5b56-4d0f-4af6-aea6-5c921500a958",
+ "digest": {
+ "sha256": "915832134c7f76c64fd48179b53dfb05de128b50ef451380b440cff2ec1990fb"
+ }
+ },
+ {
+ "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "Label": "${dset_mask}",
+ "AtLocation": "${dset_mask}",
+ "digest": {
+ "sha256": "aad93a52efcf1938cc27b6cfe707fe2b1f74b1bd4b13217516525ff60fa0a2cd"
+ }
+ },
+ {
+ "@id": "urn:3629a684-e3d0-4d02-b46c-ba0aa897ca06",
+ "Label": "\"${ref_dset}\"",
+ "AtLocation": "\"${ref_dset}\"",
+ "digest": {
+ "sha256": "be3e8ce0897c76f6b02c76da87ee56fc125ab1ea836bd57f388f3caf2df02028"
+ }
+ },
+ {
+ "@id": "urn:1b27e140-7a1e-44d0-b08b-6050245e2a3d",
+ "Label": "PC_hyp${num}",
+ "AtLocation": "${dir_hyp}/PC_hyp${num}+tlrc",
+ "digest": {
+ "sha256": "c04239860983b8514d0cddedd56525b497ec99d5e4c48976b7cbea1d51baf3a8"
+ }
+ },
+ {
+ "@id": "urn:8c6a8fad-4a10-4e63-902e-cb713291e98b",
+ "Label": "tmp_MATCHED",
+ "AtLocation": "tmp_MATCHED",
+ "GeneratedBy": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+ "digest": {
+ "sha256": "a251065c7203a21b76c1fb6acd1edb6da1c29896ad2df1f5479c71e16a29c302"
+ }
+ },
+ {
+ "@id": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+ "Label": "PC_hyp${num}_sign0.nii.gz",
+ "AtLocation": "${dir_hyp}/PC_hyp${num}_sign0.nii.gz",
+ "GeneratedBy": "urn:cfaa20a5-21e5-49c6-bfed-2d23065164c6",
+ "digest": {
+ "sha256": "5f0818d820edebe892295ffc1dd6f69823f2fb843bc2c3b0b5304054fa227af0"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png
new file mode 100644
index 000000000..659443ec7
Binary files /dev/null and b/examples/from_parsers/afni/narps_do_02_pc_with_sign0_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
index 1bb842e3a..dd5302379 100644
--- a/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
+++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "@id": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,67 +13,67 @@
],
"Activities": [
{
- "@id": "urn:af37ed47-62d0-4033-aaf3-b1a9bff13185",
+ "@id": "urn:ac0a1582-d0e6-4c06-8f3c-f7e2371d9d71",
"Label": "Make directory",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "\\mkdir ${odir}",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:ed039280-27f5-4133-b5da-56c4aa37acde",
+ "@id": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
"Label": "@chauffeur_afni",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean",
"Parameters": {},
"Used": [
- "urn:0573bcfc-c7db-41bb-9a08-3709f030ecb3"
+ "urn:1f3aa16c-dba5-4a6a-be1f-070a6dd46a7c"
]
},
{
- "@id": "urn:471a60f2-312f-4b0a-bd18-6e25086c7503",
+ "@id": "urn:a0b6b6d8-e7c9-4497-8f03-00bb7ea256c8",
"Label": "@chauffeur_afni",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean",
"Parameters": {},
"Used": [
- "urn:0573bcfc-c7db-41bb-9a08-3709f030ecb3"
+ "urn:1f3aa16c-dba5-4a6a-be1f-070a6dd46a7c"
]
},
{
- "@id": "urn:a74a4155-f6eb-4f14-89cd-6c9af840b2c7",
+ "@id": "urn:51561c54-ad75-499d-9aa7-1cb5ab17a577",
"Label": "adjunct_calc_mont_dims.py",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}",
"Parameters": {},
"Used": [
- "urn:af89af9c-125e-4b55-a644-10be24d34fb7"
+ "urn:dfcf8feb-83e2-4f66-8074-59323dfd273b"
]
},
{
- "@id": "urn:52bd406f-d274-405c-9bd2-12ad2edf9eef",
+ "@id": "urn:184be230-ca69-44e0-b9d5-937d940c1349",
"Label": "2dcat",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*",
"Parameters": {},
"Used": [
- "urn:84f56de4-3465-4cf5-9217-cdfaa5a8257e"
+ "urn:5522f531-9075-4d8d-a654-6905c88ca539"
]
},
{
- "@id": "urn:4422b094-b875-4fd4-8a41-55e97ebcc7e0",
+ "@id": "urn:d4cb83cd-6bf6-48e2-955f-122e6d0a0439",
"Label": "2dcat",
- "AssociatedWith": "urn:c193ee69-a1b6-4368-9111-7d2e95762454",
+ "AssociatedWith": "urn:30df620a-6022-4cb7-8b04-92b6ee439617",
"Command": "2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*",
"Parameters": {},
"Used": [
- "urn:62de0566-6cb1-4a25-bee0-6b7ed491b2af"
+ "urn:57479980-7201-4d14-9ce3-a5f778c62ba1"
]
}
],
"Entities": [
{
- "@id": "urn:0573bcfc-c7db-41bb-9a08-3709f030ecb3",
+ "@id": "urn:1f3aa16c-dba5-4a6a-be1f-070a6dd46a7c",
"Label": "${ref}",
"AtLocation": "${ref}",
"digest": {
@@ -81,25 +81,25 @@
}
},
{
- "@id": "urn:55cac575-b451-483d-89fd-26175de93e13",
+ "@id": "urn:e0673b5d-bc02-467e-9f5a-8466ab995bf5",
"Label": "img_${nnn}_alpha_${iid}",
"AtLocation": "${odir}/img_${nnn}_alpha_${iid}",
- "GeneratedBy": "urn:ed039280-27f5-4133-b5da-56c4aa37acde",
+ "GeneratedBy": "urn:d2838435-2817-4d99-8c5e-4adbd8852f73",
"digest": {
"sha256": "a0e5cbd9fe17cb80fe572ff230c1433b6f007d58746205bc6cf4747a1da48d1e"
}
},
{
- "@id": "urn:437944b7-da8d-4fe2-9606-45329b04b990",
+ "@id": "urn:2f256f1e-c083-484a-949d-6f728a0acd2c",
"Label": "img_${nnn}_psi_${iid}",
"AtLocation": "${odir}/img_${nnn}_psi_${iid}",
- "GeneratedBy": "urn:471a60f2-312f-4b0a-bd18-6e25086c7503",
+ "GeneratedBy": "urn:a0b6b6d8-e7c9-4497-8f03-00bb7ea256c8",
"digest": {
"sha256": "7c339c3ad32d56d3fd94128ff49e2bd3d109fddaaaa46451e0a8d646ae23cfe3"
}
},
{
- "@id": "urn:af89af9c-125e-4b55-a644-10be24d34fb7",
+ "@id": "urn:dfcf8feb-83e2-4f66-8074-59323dfd273b",
"Label": "nallbase",
"AtLocation": "nallbase",
"digest": {
@@ -107,16 +107,16 @@
}
},
{
- "@id": "urn:d90ed920-e508-4dbc-8a15-28f8ca144fbc",
+ "@id": "urn:79386b89-5260-48ae-9ca8-585c2ffa0480",
"Label": "__tmp_",
"AtLocation": "__tmp_",
- "GeneratedBy": "urn:a74a4155-f6eb-4f14-89cd-6c9af840b2c7",
+ "GeneratedBy": "urn:51561c54-ad75-499d-9aa7-1cb5ab17a577",
"digest": {
"sha256": "cdd06e3421f1953c55722187ed4a54d26fbbdabf2b77d6ba9abce36f2a9a8bbb"
}
},
{
- "@id": "urn:84f56de4-3465-4cf5-9217-cdfaa5a8257e",
+ "@id": "urn:5522f531-9075-4d8d-a654-6905c88ca539",
"Label": "img_*_alpha*${ss}*",
"AtLocation": "${odir}/img_*_alpha*${ss}*",
"digest": {
@@ -124,16 +124,16 @@
}
},
{
- "@id": "urn:eae1ad4d-af8a-4315-9449-a5faf98f38ef",
+ "@id": "urn:a2fcc21f-bcf1-477c-9b63-18d475287023",
"Label": "ALL_alpha_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:52bd406f-d274-405c-9bd2-12ad2edf9eef",
+ "GeneratedBy": "urn:184be230-ca69-44e0-b9d5-937d940c1349",
"digest": {
"sha256": "b30960ff9bf2be10473ab3cdd82775a150362f0b714db8b55d263d0d94078ecf"
}
},
{
- "@id": "urn:62de0566-6cb1-4a25-bee0-6b7ed491b2af",
+ "@id": "urn:57479980-7201-4d14-9ce3-a5f778c62ba1",
"Label": "img_*_psi*${ss}*",
"AtLocation": "${odir}/img_*_psi*${ss}*",
"digest": {
@@ -141,10 +141,10 @@
}
},
{
- "@id": "urn:681749e2-d210-4fe2-bea3-c7f02908594a",
+ "@id": "urn:b2713b64-ed9c-4912-bde1-97d522fcdadb",
"Label": "ALL_psi_${hyp}_sview_${ss}.jpg",
"AtLocation": "${odir}/ALL_psi_${hyp}_sview_${ss}.jpg",
- "GeneratedBy": "urn:4422b094-b875-4fd4-8a41-55e97ebcc7e0",
+ "GeneratedBy": "urn:d4cb83cd-6bf6-48e2-955f-122e6d0a0439",
"digest": {
"sha256": "c9b97ba53a4832ccd96c2802949fe72dc1e3718be9fc91d8fd85375a99c4d290"
}
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png
index ef2dd914a..a19da11c0 100644
Binary files a/examples/from_parsers/afni/narps_do_04_make_imgs_A.png and b/examples/from_parsers/afni/narps_do_04_make_imgs_A.png differ
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_bloc.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A_bloc.jsonld
index 0c1dc53f0..f1f584d5b 100644
--- a/examples/from_parsers/afni/narps_do_04_make_imgs_A_bloc.jsonld
+++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A_bloc.jsonld
@@ -21,7 +21,7 @@
},
{
"@id": "urn:bf4ed4ca-115c-4320-bbfa-cf160080113d",
- "Label": "bloc ...",
+ "Label": "block ...",
"AssociatedWith": "urn:165a1602-9cae-4311-84b5-3834366b9b38",
"Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; @chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*; ",
"Used": [
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld
new file mode 100644
index 000000000..4ef7c06cb
--- /dev/null
+++ b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.jsonld
@@ -0,0 +1,116 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:eaf22111-0b26-47af-8627-b1e278e5914a",
+ "Label": "",
+ "AssociatedWith": "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f",
+ "Command": "\\mkdir ${odir}; ",
+ "Used": []
+ },
+ {
+ "@id": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "Label": "block ...",
+ "AssociatedWith": "urn:238b43bf-8fe0-40ba-a54d-1954ced0274f",
+ "Command": "@chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha Linear -olay_boxed Yes -opacity 7 -prefix ${odir}/img_${nnn}_alpha_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; @chauffeur_afni -ulay ${ref} -ulay_range \"2%\" \"110%\" -olay ${ff} -set_subbricks -1 0 0 -func_range 5 -thr_olay 3 -cbar Reds_and_Blues_Inv -olay_alpha No -olay_boxed No -opacity 7 -prefix ${odir}/img_${nnn}_psi_${iid} -montx 1 -monty 1 -set_dicom_xyz 5 18 18 -set_xhairs OFF -label_string \"::${iid}\" -label_mode 1 -label_size 3 -do_clean; adjunct_calc_mont_dims.py ${nallbase} __tmp_${hyp}; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg ${odir}/img_*_alpha*${ss}*; 2dcat -echo_edu -gap 5 -gap_col ${lcol} -ny ${dims[4]} -nx ${dims[3]} -zero_wrap -prefix ${odir}/ALL_psi_${hyp}_sview_${ss}.jpg ${odir}/img_*_psi*${ss}*; ",
+ "Used": [
+ "urn:95f9e98f-16a1-4203-add4-aa09068c95cc",
+ "urn:95f9e98f-16a1-4203-add4-aa09068c95cc",
+ "urn:e29d8494-1287-4ba6-a240-13d062db51c0",
+ "urn:ab2e43b9-23a9-4498-b928-4a757cf4c869",
+ "urn:9c6482f8-d86c-42e8-887e-a01c650d7f9d"
+ ]
+ }
+ ],
+ "Entities": [
+ {
+ "@id": "urn:95f9e98f-16a1-4203-add4-aa09068c95cc",
+ "Label": "${ref}",
+ "AtLocation": "${ref}",
+ "digest": {
+ "sha256": "b3aae23398e94e7f9555eb69ec16b2d9854ba497a7b961d7668dbc77cd728f79"
+ }
+ },
+ {
+ "@id": "urn:e29d8494-1287-4ba6-a240-13d062db51c0",
+ "Label": "nallbase",
+ "AtLocation": "nallbase",
+ "digest": {
+ "sha256": "b2fc0bab06ca5629bb7528c8bc293781bf7d1b3cd5b8f3895e9aa4629ab6d8ac"
+ }
+ },
+ {
+ "@id": "urn:ab2e43b9-23a9-4498-b928-4a757cf4c869",
+ "Label": "img_*_alpha*${ss}*",
+ "AtLocation": "${odir}/img_*_alpha*${ss}*",
+ "digest": {
+ "sha256": "0fb386b69f31317d86bd4d540c3b229d3692106a60482aa93852c7f9e217f4cc"
+ }
+ },
+ {
+ "@id": "urn:9c6482f8-d86c-42e8-887e-a01c650d7f9d",
+ "Label": "img_*_psi*${ss}*",
+ "AtLocation": "${odir}/img_*_psi*${ss}*",
+ "digest": {
+ "sha256": "e43f051c04188dc916ed1dc25e3e718aaa7b154e04a016b30a97f31e38fd8e29"
+ }
+ },
+ {
+ "@id": "urn:11378299-046e-469a-8dd0-04997311c70f",
+ "Label": "img_${nnn}_alpha_${iid}",
+ "AtLocation": "${odir}/img_${nnn}_alpha_${iid}",
+ "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "digest": {
+ "sha256": "a0e5cbd9fe17cb80fe572ff230c1433b6f007d58746205bc6cf4747a1da48d1e"
+ }
+ },
+ {
+ "@id": "urn:9b5c6e54-fbf8-4532-9adb-d5c75ab11be0",
+ "Label": "img_${nnn}_psi_${iid}",
+ "AtLocation": "${odir}/img_${nnn}_psi_${iid}",
+ "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "digest": {
+ "sha256": "7c339c3ad32d56d3fd94128ff49e2bd3d109fddaaaa46451e0a8d646ae23cfe3"
+ }
+ },
+ {
+ "@id": "urn:9861b3fa-f459-4b8e-b56f-00916d10574d",
+ "Label": "__tmp_",
+ "AtLocation": "__tmp_",
+ "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "digest": {
+ "sha256": "cdd06e3421f1953c55722187ed4a54d26fbbdabf2b77d6ba9abce36f2a9a8bbb"
+ }
+ },
+ {
+ "@id": "urn:77c559d3-63ce-44f4-bb26-91c7ddbe62f6",
+ "Label": "ALL_alpha_${hyp}_sview_${ss}.jpg",
+ "AtLocation": "${odir}/ALL_alpha_${hyp}_sview_${ss}.jpg",
+ "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "digest": {
+ "sha256": "b30960ff9bf2be10473ab3cdd82775a150362f0b714db8b55d263d0d94078ecf"
+ }
+ },
+ {
+ "@id": "urn:fd0b7203-0967-4d90-95ec-24ef3e0696f9",
+ "Label": "ALL_psi_${hyp}_sview_${ss}.jpg",
+ "AtLocation": "${odir}/ALL_psi_${hyp}_sview_${ss}.jpg",
+ "GeneratedBy": "urn:3199161a-bb31-491f-bd82-4b3283c53d48",
+ "digest": {
+ "sha256": "c9b97ba53a4832ccd96c2802949fe72dc1e3718be9fc91d8fd85375a99c4d290"
+ }
+ }
+ ]
+ }
+}
\ No newline at end of file
diff --git a/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png
new file mode 100644
index 000000000..23a3e5fba
Binary files /dev/null and b/examples/from_parsers/afni/narps_do_04_make_imgs_A_block.png differ
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
index dc684021e..a08fcd5ba 100644
--- a/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
+++ b/examples/from_parsers/afni/narps_do_13_view_zoom.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "@id": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "AFNI",
@@ -13,35 +13,35 @@
],
"Activities": [
{
- "@id": "urn:3d49be80-4c79-4766-92cc-527c8883aeea",
+ "@id": "urn:5f9b6c63-f114-4763-a153-e4ba8a4c510e",
"Label": "Make directory",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "mkdir -p ${odir}",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:15284312-25a6-4da3-ad47-1a67b02f42ff",
+ "@id": "urn:01ddd7c2-68e7-46d1-a2f0-0754251c9b70",
"Label": "IsoSurface",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "IsoSurface -overwrite -isorois+dsets -input ${ivol} -o_gii cc_${pref_surf} -Tsmooth 0 0 -remesh 1",
"Parameters": {},
"Used": []
},
{
- "@id": "urn:8fe7b445-0304-4ef0-856c-250d561641e8",
+ "@id": "urn:af6179ab-9c22-4d4a-bf0e-222d6c572bb8",
"Label": "1d_tool.py",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "1d_tool.py -csim_pthr ${pthr} -csim_alpha ${alpha} -infile ${file_1D}",
"Parameters": {},
"Used": [
- "urn:d496b07a-2b8e-4fb6-94cd-63999e83692a"
+ "urn:d38b98e8-3e70-4650-a496-8fc444b4e061"
]
},
{
- "@id": "urn:6edb1340-d225-442b-bb95-c272df01c0da",
+ "@id": "urn:957b0079-9662-4836-b6d5-563dd2d7b239",
"Label": "plugout_drive",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "plugout_drive -echo_edu -npb $portnum -com \"SWITCH_UNDERLAY ${dset_ref:t}\" -com \"SWITCH_OVERLAY ${dset_ttest:t}\" -com \"SET_XHAIRS OFF\" -com \"SET_SUBBRICKS ${subbb}\" -com \"SET_PBAR_ALL -99 1.0 ${cbar}\" -com \"SET_FUNC_ALPHA ${olay_alpha}\" -com \"SET_FUNC_BOXED ${olay_boxed}\" -com \"$coor_type $coors\" -com \"SET_THRESHNEW ${thr}\" -com \"SET_FUNC_VISIBLE +\" -com \"SET_FUNC_RANGE $frange\" -com \"$OW sagittalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[1]}:${mgap}:${mcolor}\" -com \"$OW coronalimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[2]}:${mgap}:${mcolor}\" -com \"$OW axialimage ifrac=${ifrac} opacity=${opac} mont=${mx}x${my}:${gapord[3]}:${mgap}:${mcolor}\" &",
"Parameters": {
"-echo_edu": true,
@@ -50,23 +50,23 @@
"-99": "1.0"
},
"Used": [
- "urn:6faaf304-eef3-4519-9bbf-6acbcf3f74db"
+ "urn:30eff423-d391-4db7-a391-898d50dc8e92"
]
},
{
- "@id": "urn:2ccdf1c9-e316-48ef-a874-202db6a99cb0",
+ "@id": "urn:1c858060-3800-44dc-bcab-8a540f7d215c",
"Label": "suma",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "suma -echo_edu -npb $portnum -onestate -niml -i cc*.k*.gii -vol ${dset_ref} -sv ${dset_ref} &",
"Parameters": {},
"Used": [
- "urn:06218a45-987c-4f75-a5f4-435d2ea0711b"
+ "urn:ab98154a-24fa-47a8-84ea-d6eac5c8387d"
]
},
{
- "@id": "urn:bb805b8f-6cfc-429c-bb90-ecc678fe02a4",
+ "@id": "urn:44ed666d-a01c-4385-9f30-438c6db3b2d7",
"Label": "DriveSuma",
- "AssociatedWith": "urn:a1be5f37-d9a7-47fd-a1c0-59675f968edb",
+ "AssociatedWith": "urn:c9f93d13-28f2-4940-8f5b-e03bcf9f67a7",
"Command": "DriveSuma -npb $portnum -com viewer_cont -key \"t\" -key \".\" &",
"Parameters": {
"-npb": "$portnum",
@@ -78,25 +78,25 @@
],
"Entities": [
{
- "@id": "urn:905e6eb8-4f3a-4882-9f63-f57573383505",
+ "@id": "urn:ec283808-c37d-4153-868a-acac76f311bf",
"Label": "${odir}",
"AtLocation": "${odir}",
- "GeneratedBy": "urn:3d49be80-4c79-4766-92cc-527c8883aeea",
+ "GeneratedBy": "urn:5f9b6c63-f114-4763-a153-e4ba8a4c510e",
"digest": {
"sha256": "b1fc5ec0acec0bf1a5d6697b7f63ed3b4c8e33adcb77445bc544e124ade50c60"
}
},
{
- "@id": "urn:899e1e7d-41f3-4043-bd72-e83b444ed18d",
+ "@id": "urn:fe55b2a7-0de1-499d-a868-a5dc04c73443",
"Label": "cc_${pref_surf}",
"AtLocation": "cc_${pref_surf}",
- "GeneratedBy": "urn:15284312-25a6-4da3-ad47-1a67b02f42ff",
+ "GeneratedBy": "urn:01ddd7c2-68e7-46d1-a2f0-0754251c9b70",
"digest": {
"sha256": "5e02dacb1f0d92310532c03d04b14d6bdc19634a71800752df6d2e4f1adadf06"
}
},
{
- "@id": "urn:d496b07a-2b8e-4fb6-94cd-63999e83692a",
+ "@id": "urn:d38b98e8-3e70-4650-a496-8fc444b4e061",
"Label": "${file_1D}",
"AtLocation": "${file_1D}",
"digest": {
@@ -104,7 +104,7 @@
}
},
{
- "@id": "urn:6faaf304-eef3-4519-9bbf-6acbcf3f74db",
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"digest": {
@@ -112,16 +112,16 @@
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{
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- "GeneratedBy": "urn:6edb1340-d225-442b-bb95-c272df01c0da",
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"sha256": "a757facd6497c040401a26469144a2df7ad28984bf0e7688a2f32d607fcd6797"
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{
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+ "@id": "urn:ab98154a-24fa-47a8-84ea-d6eac5c8387d",
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"AtLocation": "cc*.k*.gii",
"digest": {
diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom.png b/examples/from_parsers/afni/narps_do_13_view_zoom.png
index 1e9a4748d..9b1c16353 100644
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diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_bloc.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom_bloc.jsonld
index a1da5a34c..87ed0d33c 100644
--- a/examples/from_parsers/afni/narps_do_13_view_zoom_bloc.jsonld
+++ b/examples/from_parsers/afni/narps_do_13_view_zoom_bloc.jsonld
@@ -21,7 +21,7 @@
},
{
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- "Label": "bloc ...",
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diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld
new file mode 100644
index 000000000..b6a07d122
--- /dev/null
+++ b/examples/from_parsers/afni/narps_do_13_view_zoom_block.jsonld
@@ -0,0 +1,88 @@
+{
+ "@context": "https://raw.githubusercontent.com/bids-standard/BEP028_BIDSprov/master/context.json",
+ "BIDSProvVersion": "dev",
+ "Records": {
+ "Software": [
+ {
+ "@id": "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83",
+ "RRID": "RRID:SCR_007037",
+ "@type": "prov:SoftwareAgent",
+ "Label": "AFNI",
+ "Version": "afni24"
+ }
+ ],
+ "Activities": [
+ {
+ "@id": "urn:e9ae82db-e47b-4e45-954e-a7e7d27708c1",
+ "Label": "",
+ "AssociatedWith": "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83",
+ "Command": "mkdir -p ${odir}; ",
+ "Used": []
+ },
+ {
+ "@id": "urn:1756ff39-a0cf-41b2-a7c8-d940ea52eaab",
+ "Label": "block ...",
+ "AssociatedWith": "urn:21b70068-0e68-4cfa-afd4-f6103efb8b83",
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+ "Used": [
+ "urn:cb16d235-37c7-44c2-bf6c-770d642ec8f8",
+ "urn:448c001b-fbf0-4915-b959-b7b87a921c7c",
+ "urn:65628bdc-1cf9-43c5-99eb-74f20c8e7278"
+ ]
+ }
+ ],
+ "Entities": [
+ {
+ "@id": "urn:15bea182-294d-4fe1-9350-ae103cb0dddb",
+ "Label": "${odir}",
+ "AtLocation": "${odir}",
+ "GeneratedBy": "urn:e9ae82db-e47b-4e45-954e-a7e7d27708c1",
+ "digest": {
+ "sha256": "b1fc5ec0acec0bf1a5d6697b7f63ed3b4c8e33adcb77445bc544e124ade50c60"
+ }
+ },
+ {
+ "@id": "urn:cb16d235-37c7-44c2-bf6c-770d642ec8f8",
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+ "AtLocation": "${file_1D}",
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+ "sha256": "1ceba5dd08283170f6a477b939a39fb36475056b3d34302ed53ba3a87f0273e5"
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+ "sha256": "8316e018f1f924e85f980916c33a30b32d50cb56a113fd4e4e12a21d24c192bd"
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+ "Label": "cc_${pref_surf}",
+ "AtLocation": "cc_${pref_surf}",
+ "GeneratedBy": "urn:1756ff39-a0cf-41b2-a7c8-d940ea52eaab",
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+ "sha256": "5e02dacb1f0d92310532c03d04b14d6bdc19634a71800752df6d2e4f1adadf06"
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+}
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diff --git a/examples/from_parsers/afni/narps_do_13_view_zoom_block.png b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png
new file mode 100644
index 000000000..b9082f474
Binary files /dev/null and b/examples/from_parsers/afni/narps_do_13_view_zoom_block.png differ
diff --git a/examples/from_parsers/context_2023_09_29_08h04m29s.txt b/examples/from_parsers/context_2024_05_21_13h48m55s.txt
similarity index 98%
rename from examples/from_parsers/context_2023_09_29_08h04m29s.txt
rename to examples/from_parsers/context_2024_05_21_13h48m55s.txt
index 4714ee86f..2565478b2 100644
--- a/examples/from_parsers/context_2023_09_29_08h04m29s.txt
+++ b/examples/from_parsers/context_2024_05_21_13h48m55s.txt
@@ -1,72 +1,72 @@
-Date : 2023_09_29_08h04m29s
+Date : 2024_05_21_13h48m55s
Processing files...
- file= nidmresults-examples/fsl_group_ols_report_log.html
- file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
- file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
- file= nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
- file= nidmresults-examples/spm_temporal_derivative_batch.m
- file= nidmresults-examples/spm_thr_clustfwep05_batch.m
file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
file= nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
- file= nidmresults-examples/fsl_contrast_mask_report_log.html
file= nidmresults-examples/afni_con_f_proc.sub_001
file= nidmresults-examples/afni_con_f_proc.sub_001
- file= nidmresults-examples/spm_group_wls_batch.m
- file= nidmresults-examples/fsl_motion_reg_der_report_log.html
- file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
- file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
+ file= nidmresults-examples/spm_thr_voxelfdrp05_batch.m
+ file= nidmresults-examples/fsl_gamma_basis_report_log.html
+ file= nidmresults-examples/fsl_group_wls_report_log.html
+ file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+ file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+ file= nidmresults-examples/fsl_con_f_multiple_report_log.html
+ file= nidmresults-examples/fsl_group_ols_report_log.html
file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
file= nidmresults-examples/afni_thr_clustunck10_proc.sub_001
+ file= nidmresults-examples/fsl_motion_reg_report_log.html
+ file= nidmresults-examples/fsl_motion_reg_der_report_log.html
+ file= nidmresults-examples/afni_hrf_tent_proc.sub_001
+ file= nidmresults-examples/afni_hrf_tent_proc.sub_001
+ file= nidmresults-examples/fsl_hrf_fir_report_log.html
+ file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
+ file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
+ file= nidmresults-examples/spm_group_ols_batch.m
+ file= nidmresults-examples/spm_thr_voxelfwep05_batch.m
+ file= nidmresults-examples/afni_gam_proc.sub_001
+ file= nidmresults-examples/afni_gam_proc.sub_001
+ file= nidmresults-examples/afni_clustconn_18_proc.sub_001
+ file= nidmresults-examples/afni_clustconn_18_proc.sub_001
+ file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
+ file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
+ file= nidmresults-examples/spm_hrf_fir_batch.m
+ file= nidmresults-examples/fsl_full_examples001_report_log.html
+ file= nidmresults-examples/afni_default_proc.sub_001
+ file= nidmresults-examples/afni_default_proc.sub_001
+ file= nidmresults-examples/spm_thr_clustfwep05_batch.m
+ file= nidmresults-examples/afni_clustconn_26_proc.sub_001
+ file= nidmresults-examples/afni_clustconn_26_proc.sub_001
+ file= nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
+ file= nidmresults-examples/spm_partial_conjunction_batch.m
+ file= nidmresults-examples/spm_explicit_mask_batch.m
file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
file= nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
- file= nidmresults-examples/spm_con_f_batch.m
- file= nidmresults-examples/spm_contrast_mask_batch.m
+ file= nidmresults-examples/spm_thr_clustunck10_batch.m
+ file= nidmresults-examples/spm_temporal_derivative_batch.m
+ file= nidmresults-examples/spm_2_t_test_batch.m
+ file= nidmresults-examples/fsl_thr_clustfwep05_report_log.html
+ file= nidmresults-examples/spm_conjunction_batch.m
+ file= nidmresults-examples/spm_default_batch.m
+ file= nidmresults-examples/spm_HRF_informed_basis_batch.m
+ file= nidmresults-examples/fsl_default_report_log.html
file= nidmresults-examples/narps_do_13_view_zoom.tcsh
file= nidmresults-examples/narps_do_13_view_zoom.tcsh
- file= nidmresults-examples/spm_hrf_fir_batch.m
+ file= nidmresults-examples/fsl_hrf_gammadiff_report_log.html
+ file= nidmresults-examples/spm_covariate_batch.m
file= nidmresults-examples/fsl_group_btw_report_log.html
+ file= nidmresults-examples/spm_non_sphericity_batch.m
file= nidmresults-examples/fsl_gaussian_report_log.html
- file= nidmresults-examples/fsl_motion_reg_report_log.html
- file= nidmresults-examples/afni_gam_proc.sub_001
- file= nidmresults-examples/afni_gam_proc.sub_001
- file= nidmresults-examples/spm_thr_clustunck10_batch.m
- file= nidmresults-examples/spm_HRF_informed_basis_batch.m
- file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
- file= nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+ file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
+ file= nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
+ file= nidmresults-examples/spm_contrast_mask_batch.m
file= nidmresults-examples/afni_alt_onesided_proc.sub_001
file= nidmresults-examples/afni_alt_onesided_proc.sub_001
- file= nidmresults-examples/spm_non_sphericity_batch.m
+ file= nidmresults-examples/spm_con_f_batch.m
+ file= nidmresults-examples/spm_group_wls_batch.m
+ file= nidmresults-examples/afni_other_template_proc.sub_001
+ file= nidmresults-examples/afni_other_template_proc.sub_001
file= nidmresults-examples/spm_thr_voxelunct4_batch.m
- file= nidmresults-examples/fsl_thr_clustfwep05_report_log.html
- file= nidmresults-examples/spm_default_batch.m
- file= nidmresults-examples/fsl_gamma_basis_report_log.html
file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
file= nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
- file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
- file= nidmresults-examples/narps_do_04_make_imgs_A.tcsh
- file= nidmresults-examples/fsl_full_examples001_report_log.html
- file= nidmresults-examples/afni_clustconn_26_proc.sub_001
- file= nidmresults-examples/afni_clustconn_26_proc.sub_001
- file= nidmresults-examples/fsl_hrf_gammadiff_report_log.html
- file= nidmresults-examples/afni_hrf_tent_proc.sub_001
- file= nidmresults-examples/afni_hrf_tent_proc.sub_001
- file= nidmresults-examples/fsl_default_report_log.html
+ file= nidmresults-examples/fsl_contrast_mask_report_log.html
file= nidmresults-examples/fsl_con_f_report_log.html
- file= nidmresults-examples/spm_group_ols_batch.m
- file= nidmresults-examples/afni_other_template_proc.sub_001
- file= nidmresults-examples/afni_other_template_proc.sub_001
- file= nidmresults-examples/fsl_con_f_multiple_report_log.html
- file= nidmresults-examples/spm_conjunction_batch.m
- file= nidmresults-examples/spm_2_t_test_batch.m
- file= nidmresults-examples/spm_partial_conjunction_batch.m
- file= nidmresults-examples/afni_default_proc.sub_001
- file= nidmresults-examples/afni_default_proc.sub_001
- file= nidmresults-examples/fsl_group_wls_report_log.html
- file= nidmresults-examples/spm_explicit_mask_batch.m
- file= nidmresults-examples/afni_clustconn_18_proc.sub_001
- file= nidmresults-examples/afni_clustconn_18_proc.sub_001
- file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
- file= nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
- file= nidmresults-examples/fsl_hrf_fir_report_log.html
- file= nidmresults-examples/spm_covariate_batch.m
-End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:00:02.155712
+End of processed files. Results in dir : 'examples/from_parsers'. Time required: 0:01:15.828609
diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
index 693151185..46b88afa6 100644
--- a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "@id": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,1134 +13,1134 @@
],
"Activities": [
{
- "@id": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
+ "@id": "urn:95dbbb1a-af6d-4133-8620-a928beb28b2c",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:86648548-ef86-4c65-acb2-f66f919cd602"
+ "urn:00d2cbcd-88c4-495d-a56c-9c436669c375"
]
},
{
- "@id": "urn:f5c8f6a7-13a4-431b-b55a-15d9f2c3c417",
+ "@id": "urn:f219d288-e9d1-4f13-9536-893d46332f3b",
"Label": "fslroi",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:dcea32e9-2cae-4ca0-9633-d89c8f6be7cf"
+ "urn:e4eab963-3f85-4099-b44a-7c31510246e3"
]
},
{
- "@id": "urn:b084ad3a-cf4b-47a4-83e6-06f3eae198c9",
+ "@id": "urn:7f264260-0859-4fd4-80a8-03136d9e1dd1",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
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- "urn:d1b9bc98-a253-4e9f-b88e-3c5199b9250d",
- "urn:ebfc60aa-ebdc-489d-b125-9a6ebd44b366"
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]
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{
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+ "@id": "urn:362a9b21-aaf4-43be-8ae2-e9676da61333",
"Label": "Make directory",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/reg",
"Used": []
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:d1b9bc98-a253-4e9f-b88e-3c5199b9250d"
+ "urn:92dd3a7a-0a15-443b-b85f-3201f38e7d41"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres_head",
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]
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{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain standard",
"Used": [
- "urn:ebfc60aa-ebdc-489d-b125-9a6ebd44b366"
+ "urn:dced5c1d-04b9-4ce8-9f1f-929ef0c1d8c7"
]
},
{
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"Label": "epi_reg",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:ae890394-01bf-44f5-a3b2-d08ca303ddc6",
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"Label": "convert_xfm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:717c4883-95a6-438b-a1e4-8cb4424a168c"
+ "urn:5125d2d9-6492-4c8b-adf2-c5705cc01a67"
]
},
{
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"Label": "slicer",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:5bc060d9-573c-49a3-8f8c-52ede444f022",
- "urn:cf43315f-7f8b-49ff-8cba-1e89b75df518"
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]
},
{
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"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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]
},
{
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"Label": "slicer",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:cf43315f-7f8b-49ff-8cba-1e89b75df518"
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]
},
{
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"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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]
},
{
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"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
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- "urn:ca299055-a662-4998-b793-5b0a8ffc6237"
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]
},
{
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"Label": "rm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
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- "urn:ca299055-a662-4998-b793-5b0a8ffc6237"
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]
},
{
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"Label": "rm",
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+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:2f7bcf43-f434-49be-8f47-e1b2424331f9"
+ "urn:4a199e13-d903-4746-8a05-4c28d3f24786"
]
},
{
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"Label": "flirt",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
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- "urn:b286b508-ccb9-409b-aa7d-5629f06e613e"
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]
},
{
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"Label": "convert_xfm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
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]
},
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"Label": "slicer",
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"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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]
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"Label": "pngappend",
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]
},
{
- "@id": "urn:af33c7b9-c0cb-4b14-b3b8-f3834419057c",
+ "@id": "urn:a78bed8b-8b1d-4170-86f6-a0597cea4fd9",
"Label": "slicer",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:0c7a2191-32e9-426b-8217-610f6a30b173",
- "urn:b286b508-ccb9-409b-aa7d-5629f06e613e"
+ "urn:1d44d844-c4ca-4840-9019-b9b7a5f712e2",
+ "urn:c9a17754-68bd-4d33-9e11-d660c14d86a5"
]
},
{
- "@id": "urn:93ba5941-eb9b-4d62-8502-5f902957b70d",
+ "@id": "urn:cd4eb98c-0ee8-4e24-bcf5-30ca3bb9157b",
"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
"Used": [
- "urn:02f1c791-5c7d-43a6-8e2f-f2536baa26d0",
- "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
- "urn:1170b37b-767e-4327-8f76-f61b204c411c",
- "urn:17b70280-d407-407f-820c-85dbabbdcd62",
- "urn:2cb826db-6e4d-4c03-ae37-39e153fd415f",
- "urn:2fcd8594-4286-4cdf-9100-4477f5bdce8f",
- "urn:374840d1-759f-4a7e-babe-e91ec845f206",
- "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
- "urn:831bf263-33b5-4b62-aa16-89c91b9a5dc5",
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47",
- "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
- "urn:d3666d78-32c0-424a-b170-f25ad8f10722"
+ "urn:13f7d6e4-de0c-411e-a8e5-36e80edb89ff",
+ "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "urn:47e324b7-183c-44e8-9f43-dc1008b8693a",
+ "urn:52207409-b5c7-42a2-a9f3-13fcebc29fa2",
+ "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0",
+ "urn:9aa8be1f-d7bd-4ade-9c20-192c16d8b960",
+ "urn:a06e91f3-8542-4272-a179-a66a7156b03a",
+ "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3",
+ "urn:c3c5639a-2d61-43e6-811e-33cac6c4b0ed",
+ "urn:fdecdbd0-25b4-4a8f-a3d3-e9908b473677"
]
},
{
- "@id": "urn:88ec6d95-8360-4138-8165-6d28f9b84980",
+ "@id": "urn:7dd9eb6e-2c26-4aef-bbdd-27155171191f",
"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
"Used": [
- "urn:8f3a6781-ee2f-445d-99bd-29309e221c13",
- "urn:b1782bbc-0ad8-4cf5-a5ce-d586bc629dfa"
+ "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b",
+ "urn:eba70185-e536-493c-9a67-e36a17e85583"
]
},
{
- "@id": "urn:ef52ae7f-9d76-4245-bd24-56a59d5a6dc3",
+ "@id": "urn:0dd0e641-9d9b-44e8-b602-7a0ea3ba1b56",
"Label": "rm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm -f sl?.png highres2standard2.png",
"Used": [
- "urn:61c4bfe5-74e0-4a0b-9e2f-35b78911266c",
- "urn:8f3a6781-ee2f-445d-99bd-29309e221c13"
+ "urn:9c283eeb-3683-4f35-966a-6cee22e62921",
+ "urn:eba70185-e536-493c-9a67-e36a17e85583"
]
},
{
- "@id": "urn:7b5de754-3451-4c33-96b1-ab7d2f389dda",
+ "@id": "urn:48f9cdad-094a-41e9-bacd-4d5e0a8d9639",
"Label": "rm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm highres2standard1.png",
"Used": [
- "urn:b1782bbc-0ad8-4cf5-a5ce-d586bc629dfa"
+ "urn:b91f86cb-9b9c-4e19-b29b-b444ace62d1b"
]
},
{
- "@id": "urn:ee4d2236-e8f8-40a9-87da-519574228dc2",
+ "@id": "urn:c174428c-bad9-4a34-ab52-f34e3680dc6a",
"Label": "convert_xfm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
"Used": [
- "urn:717c4883-95a6-438b-a1e4-8cb4424a168c"
+ "urn:5125d2d9-6492-4c8b-adf2-c5705cc01a67"
]
},
{
- "@id": "urn:c6e21f69-c865-4c72-8480-f4f6ada95937",
+ "@id": "urn:e72dcc3e-adcd-4dbe-8641-3498938eeada",
"Label": "flirt",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
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- "urn:521d474c-ce81-4a45-bc60-cc7d7fdfb117",
- "urn:b286b508-ccb9-409b-aa7d-5629f06e613e"
+ "urn:760ad209-0e8d-4380-9167-6790e6cdbef4",
+ "urn:b36b46ae-3d4e-4679-941f-63535c755e22",
+ "urn:c9a17754-68bd-4d33-9e11-d660c14d86a5"
]
},
{
- "@id": "urn:c753575e-7e2c-429d-9954-ee2103b515de",
+ "@id": "urn:b540995f-3dce-433c-9c41-c68e3df4d976",
"Label": "convert_xfm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
"Used": [
- "urn:521d474c-ce81-4a45-bc60-cc7d7fdfb117"
+ "urn:b36b46ae-3d4e-4679-941f-63535c755e22"
]
},
{
- "@id": "urn:8df94599-756d-4d89-a734-7c5ba65cf55d",
+ "@id": "urn:b89b4e42-4d72-4ccf-aec4-9ac21339fc1c",
"Label": "slicer",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:7936f9c4-88e8-41ee-bcf2-58b62401fc96",
- "urn:b286b508-ccb9-409b-aa7d-5629f06e613e"
+ "urn:511e7350-cc76-4097-8a2e-3b9bf291179b",
+ "urn:c9a17754-68bd-4d33-9e11-d660c14d86a5"
]
},
{
- "@id": "urn:2034611a-b421-4b03-95c2-2bc31bf78150",
+ "@id": "urn:180eb118-7aa1-44a2-a00b-32045330e858",
"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
"Used": [
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- "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
- "urn:1170b37b-767e-4327-8f76-f61b204c411c",
- "urn:17b70280-d407-407f-820c-85dbabbdcd62",
- "urn:2cb826db-6e4d-4c03-ae37-39e153fd415f",
- "urn:2fcd8594-4286-4cdf-9100-4477f5bdce8f",
- "urn:374840d1-759f-4a7e-babe-e91ec845f206",
- "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
- "urn:831bf263-33b5-4b62-aa16-89c91b9a5dc5",
- "urn:8a7d6591-f208-4564-b14f-dbda25796f47",
- "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
- "urn:d3666d78-32c0-424a-b170-f25ad8f10722"
+ "urn:13f7d6e4-de0c-411e-a8e5-36e80edb89ff",
+ "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "urn:47e324b7-183c-44e8-9f43-dc1008b8693a",
+ "urn:52207409-b5c7-42a2-a9f3-13fcebc29fa2",
+ "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0",
+ "urn:9aa8be1f-d7bd-4ade-9c20-192c16d8b960",
+ "urn:a06e91f3-8542-4272-a179-a66a7156b03a",
+ "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3",
+ "urn:c3c5639a-2d61-43e6-811e-33cac6c4b0ed",
+ "urn:fdecdbd0-25b4-4a8f-a3d3-e9908b473677"
]
},
{
- "@id": "urn:b166d860-3725-4ea1-95cf-f69ec640b968",
+ "@id": "urn:881b5b72-472b-4797-835d-2294ffb4917a",
"Label": "slicer",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:7936f9c4-88e8-41ee-bcf2-58b62401fc96",
- "urn:b286b508-ccb9-409b-aa7d-5629f06e613e"
+ "urn:511e7350-cc76-4097-8a2e-3b9bf291179b",
+ "urn:c9a17754-68bd-4d33-9e11-d660c14d86a5"
]
},
{
- "@id": "urn:a565191b-1db3-4743-bd31-6b8b2cbf88c2",
+ "@id": "urn:0b1ddf27-54b0-4851-8e40-50f09b403ec4",
"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
"Used": [
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- "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
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- "urn:17b70280-d407-407f-820c-85dbabbdcd62",
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- "urn:2fcd8594-4286-4cdf-9100-4477f5bdce8f",
- "urn:374840d1-759f-4a7e-babe-e91ec845f206",
- "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
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- "urn:8a7d6591-f208-4564-b14f-dbda25796f47",
- "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
- "urn:d3666d78-32c0-424a-b170-f25ad8f10722"
+ "urn:13f7d6e4-de0c-411e-a8e5-36e80edb89ff",
+ "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "urn:3b9828af-25bc-4463-b18a-2b842e1f91ff",
+ "urn:47e324b7-183c-44e8-9f43-dc1008b8693a",
+ "urn:52207409-b5c7-42a2-a9f3-13fcebc29fa2",
+ "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0",
+ "urn:9aa8be1f-d7bd-4ade-9c20-192c16d8b960",
+ "urn:a06e91f3-8542-4272-a179-a66a7156b03a",
+ "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3",
+ "urn:c3c5639a-2d61-43e6-811e-33cac6c4b0ed",
+ "urn:fdecdbd0-25b4-4a8f-a3d3-e9908b473677"
]
},
{
- "@id": "urn:34acc4e6-eeea-4eeb-8ef6-2f617abe7a79",
+ "@id": "urn:b3730248-9b2b-49ed-9dee-45be3b2efa5d",
"Label": "pngappend",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
"Used": [
- "urn:642b00c2-5f79-420a-a212-45cdd7dcba33",
- "urn:ed74188c-0a4a-4b0a-a0a1-47234ed3304f"
+ "urn:218ffa82-8cd0-4624-9995-7d9b9da621f0",
+ "urn:d56b4f90-3293-4027-990f-c954c816480a"
]
},
{
- "@id": "urn:6b32a0e3-f00f-4e9e-b8be-372ad5720d41",
+ "@id": "urn:fdfb15e4-17f6-48f7-b24e-edf1e2394938",
"Label": "rm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm -f sl?.png example_func2standard2.png",
"Used": [
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- "urn:ed74188c-0a4a-4b0a-a0a1-47234ed3304f"
+ "urn:9c283eeb-3683-4f35-966a-6cee22e62921",
+ "urn:d56b4f90-3293-4027-990f-c954c816480a"
]
},
{
- "@id": "urn:748557d0-dbf8-439f-9638-1d4963f93d52",
+ "@id": "urn:c12f783b-27ea-44e4-aaab-d818c36d5272",
"Label": "mcflirt",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:dcea32e9-2cae-4ca0-9633-d89c8f6be7cf"
+ "urn:e4eab963-3f85-4099-b44a-7c31510246e3"
]
},
{
- "@id": "urn:331dfb2c-c758-481e-b71f-20b131f2ed23",
+ "@id": "urn:54d4205c-2755-4b93-8703-c1d55bea28be",
"Label": "Make directory",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3",
+ "@id": "urn:7735b3ca-2f92-43b2-ae95-4ef18acc796b",
"Label": "mv",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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- "urn:5efb5d23-6a8b-467e-8bed-0141cc4c6d0e",
- "urn:94daf206-c9e2-45d9-95d0-6be1bbff9cc5",
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- "urn:e242c59b-d93e-41c9-8735-d0be6238883a"
+ "urn:3aa79963-75fc-45c4-838b-653210bd3857",
+ "urn:530372d1-1692-44c6-8880-08936c1e3afc",
+ "urn:91a99f75-a4b5-434e-b5fc-cd05fae1fad9",
+ "urn:a094dcca-d44d-4beb-bdac-576804c53c44",
+ "urn:d5fc324a-1aa6-4bb9-bf50-5348c8468ba1",
+ "urn:f6eda669-13c2-412a-bad4-785ab23219d0"
]
},
{
- "@id": "urn:e9492988-1bcb-4a89-b6e6-3c1925e1b1fc",
+ "@id": "urn:81eb387a-a9f4-404a-89ac-8eb8bd0c328d",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
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- "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
+ "urn:91a99f75-a4b5-434e-b5fc-cd05fae1fad9"
]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
+ "urn:91a99f75-a4b5-434e-b5fc-cd05fae1fad9"
]
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{
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+ "@id": "urn:606c5072-51fb-4143-a52a-2b73db9adcb5",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
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+ "urn:1a0a096d-ee73-4243-afb5-5d33c6177308"
]
},
{
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+ "@id": "urn:41ef447f-fccd-4aff-ae40-399d14ad3aa0",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
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- "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b"
+ "urn:4c609c7f-beba-4c9c-99c9-cb6070983ebd"
]
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{
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+ "@id": "urn:f9ff08c4-87f3-4355-b509-a30ad6ac0bb7",
"Label": "bet2",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/bet2 mean_func mask -f 0.3 -n -m",
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+ "urn:87a19083-35ef-4e69-bcc2-a414ce65738f"
]
},
{
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+ "@id": "urn:1932e5b3-5d43-45cd-9a74-83f7db69b8b2",
"Label": "immv",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/immv mask_mask mask",
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+ "urn:f06804b1-350d-4114-a036-23dd4599b121"
]
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{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b"
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]
},
{
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+ "@id": "urn:8b2f63d1-861e-4b43-97e4-6bbbff470320",
"Label": "fslstats",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:460f0b95-3f6c-4c96-81a3-ddc96e1ec5d5"
+ "urn:ea0d85a1-0495-4651-a4e2-e7b844affa2d"
]
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{
- "@id": "urn:45ccc0d7-d6a4-4e62-9efe-15b59b96354c",
+ "@id": "urn:aa64aea4-5eb2-4c2d-b8fb-dd510fa63edb",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:460f0b95-3f6c-4c96-81a3-ddc96e1ec5d5"
+ "urn:ea0d85a1-0495-4651-a4e2-e7b844affa2d"
]
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{
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"Label": "fslstats",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b"
+ "urn:4c609c7f-beba-4c9c-99c9-cb6070983ebd"
]
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{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths mask -dilF mask",
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+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:27631186-d180-49fa-9893-de9761f4e3b1",
- "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b"
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]
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{
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+ "@id": "urn:4debf022-96fd-4557-ad7c-380ace811d40",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:7aa13188-2509-40a0-9f80-8816b8cc8f68"
+ "urn:4846c2a0-8a5e-452e-8445-48caead091df"
]
},
{
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"Label": "susan",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:7aa13188-2509-40a0-9f80-8816b8cc8f68"
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:9b699ea3-8ad8-49af-83ff-7505506ab96c"
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]
},
{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
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+ "urn:6a61799d-2599-4916-80ef-4883143bc617"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3"
+ "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4"
]
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{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3"
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]
},
{
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"Label": "imrm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/imrm tempMean",
"Used": [
- "urn:307b8e93-4018-4034-b02d-3b761ef5558a"
+ "urn:761d8304-1910-4af4-9bcc-748950048e05"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:263e3610-fc97-46a1-a70f-f475bc13917d"
+ "urn:0381843b-eb04-4177-9a55-a98f65fb3262"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:5daf1c03-fc28-4693-b72d-04cd580ab021"
+ "urn:5092984f-5d20-4ec0-817f-5992ffdcb2c9"
]
},
{
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+ "@id": "urn:599f48e7-16cb-41c8-9af7-3e9523a18a89",
"Label": "rm",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
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+ "urn:ae057ca4-c2cc-4fd9-8c26-73e9f56c8b0d"
]
},
{
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+ "@id": "urn:507a8da5-9f2f-4616-ad3e-679eaad090d9",
"Label": "Make directory",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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+ "@id": "urn:a74e0bd9-a76a-408d-9d6d-1b406eeb73dc",
"Label": "fslFixText",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:e057248b-dd5d-4c40-bd31-8505d330fb13"
+ "urn:4f7198d4-27d5-4774-a8be-0493629b20c4"
]
},
{
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+ "@id": "urn:01c533ac-888f-4efc-a3c7-9a21bb0032c9",
"Label": "Make directory",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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+ "@id": "urn:f565cf28-54ed-4c08-ad1c-4c86fbd4209a",
"Label": "fslFixText",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:2f900215-15bd-4a15-8c21-a8ab51007afb"
+ "urn:783f0bfe-bc17-4fd3-86e4-5265722f4f3f"
]
},
{
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+ "@id": "urn:d51f009a-c70a-46d4-b88f-f68e1961fbdf",
"Label": "film_gls",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
"Used": []
},
{
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+ "@id": "urn:8e7d0070-8079-4c57-aede-ac31ab3d2c61",
"Label": "smoothest",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
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- "urn:31c406c9-e772-4346-bc0d-e20ecfc2a8a8"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
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]
},
{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
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- "urn:27631186-d180-49fa-9893-de9761f4e3b1"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "urn:ae6c30bd-7165-4aa1-bb31-3af82ba212fa"
]
},
{
- "@id": "urn:b5870dff-e3fe-4ef7-a78c-3f71f29e7942",
+ "@id": "urn:96c4c10a-78de-41e9-819c-cee215f36d3c",
"Label": "echo",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:a906578f-aa09-42aa-aab9-8716786196b3",
+ "@id": "urn:299f734f-30b4-43e4-8613-7fc79f324cfd",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:27631186-d180-49fa-9893-de9761f4e3b1",
- "urn:7052b74a-50e0-439c-81df-db12832c1a44"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "urn:ec7e16a9-e3a7-4bbe-9f6a-b36e67c48ec7"
]
},
{
- "@id": "urn:eb840ac1-a07c-458f-bc27-72a72f9c3be1",
+ "@id": "urn:ed752a0c-4414-4ed9-9dec-4e4f5fcff34d",
"Label": "echo",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:cd620add-4300-4d26-8e71-f9bd37cb0b8e",
+ "@id": "urn:e16d69a9-cb22-4fa6-93e3-3f382186da83",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:27631186-d180-49fa-9893-de9761f4e3b1",
- "urn:96707788-783b-4a32-88cc-425b7e5cc0a2"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "urn:b50d8309-9587-4c3d-8b68-eafea4254b96"
]
},
{
- "@id": "urn:8a7f70e5-e173-4ec2-944c-7b27e4f9ec29",
+ "@id": "urn:e8f6b5c8-2fca-43dd-bd0f-121ec5da6cce",
"Label": "echo",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:af85eb98-f60a-48ca-85fc-72ebed7a0c95",
+ "@id": "urn:92d3b2a1-dba6-4edc-93c6-11c3082b306f",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
"Used": [
- "urn:27631186-d180-49fa-9893-de9761f4e3b1",
- "urn:e5b6247c-0f74-4751-939f-af60b86ae6ca"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "urn:8dd263d5-5ca0-470a-b2ea-56225b421ea3"
]
},
{
- "@id": "urn:71d4b62d-e181-4b29-9cef-04ef856047a4",
+ "@id": "urn:b1f4fe7b-5e69-4b1f-8a3c-256fe2edb512",
"Label": "echo",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "echo 38352 > thresh_zfstat2.vol",
"Used": []
},
{
- "@id": "urn:dfea9359-ff55-4f9f-80a3-b053d6b53085",
+ "@id": "urn:6ca79a28-ccba-4ed7-9c3e-b723a3384c43",
"Label": "fslmaths",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/fslmaths stats/zfstat3 -mas mask thresh_zfstat3",
"Used": [
- "urn:27631186-d180-49fa-9893-de9761f4e3b1",
- "urn:75c61345-a8ea-4382-bfdb-d6d0c98ed84c"
+ "urn:294e434c-6bd8-47c2-ae75-bb719ea79b78",
+ "urn:3ed0a019-09cf-43fc-8a4d-a3b823fc25ad"
]
},
{
- "@id": "urn:56f6d5d1-4f72-4ea2-b1a6-2fa78a941026",
+ "@id": "urn:29be423e-dd92-4371-8292-a47c133dbab8",
"Label": "echo",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "echo 38352 > thresh_zfstat3.vol",
"Used": []
},
{
- "@id": "urn:2aaa0e60-f652-4176-af2f-3b0f09c14266",
+ "@id": "urn:b8bea1b6-d3a6-4051-98f1-1a65f739b6f3",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:932fc7fe-6a48-438b-9df6-9a150e9142d3",
+ "@id": "urn:27316f60-9bb2-44a4-92e3-10550fd887e9",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:38c32689-25e4-4616-a55f-99f621b66dae",
- "urn:cdc2d3c8-eace-4a0f-99ee-54b0afbb95e0"
+ "urn:0ab3aafa-76ca-4e3a-8379-e94368eed76a",
+ "urn:6f8300aa-44d9-4384-99b3-e51129ac29ab"
]
},
{
- "@id": "urn:270d4b00-919d-46a5-8bd3-ba90ab4de77c",
+ "@id": "urn:4aa8a051-839e-42db-9cd2-590565abf862",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd"
+ "urn:f3689c31-ae2f-4947-a2cf-9b34744341b9"
]
},
{
- "@id": "urn:dee38932-e432-45ac-9034-ec463c0c71d4",
+ "@id": "urn:e31fdb15-9bb3-4157-8090-92da89cfac7e",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:6c7c5ceb-8f8a-4126-931f-3e45b2fc80f0",
+ "@id": "urn:ddf90615-d0eb-4158-8692-b9628e86d510",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
- "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f"
+ "urn:2aa858d0-c72e-4263-aa8f-f09a66258e4c",
+ "urn:517a7515-49ec-465b-a678-5b2a2f9bb21c"
]
},
{
- "@id": "urn:ca4ee33e-ec88-4ec0-9662-9065d7cc4734",
+ "@id": "urn:bf214b29-acb3-4c15-bf07-61fae1e0c4bc",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:af09e210-3d42-4ab8-881e-63b8a79ac26f"
+ "urn:a9cb952e-31b9-43a4-817f-3dc1683dc1e8"
]
},
{
- "@id": "urn:f6360992-6c3c-4790-874c-7469907d535a",
+ "@id": "urn:d0ff6f02-8181-41b5-909b-f0b23781c1f9",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:fff5c382-53bd-4b97-a58a-1fe3dbded5df",
+ "@id": "urn:f7b23cf4-c8f9-4b58-9b0e-e0e62ffbccb7",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:5ecde4d0-c081-4835-aa9f-906b48bc746d"
+ "urn:04745c1c-681d-4ecd-99f5-96d342aae6ed"
]
},
{
- "@id": "urn:c99ec4d0-f9ca-4425-b9f4-c87db03772be",
+ "@id": "urn:21806867-325b-4362-8799-c3525d3f0a6c",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a"
+ "urn:d39efdca-98e2-420d-9c11-781542369bd7"
]
},
{
- "@id": "urn:8cb2d405-f78e-461f-a680-56abf991cd9e",
+ "@id": "urn:7708af65-3664-4ba3-b0eb-852b1312c3eb",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:5bcbb31a-da10-4a45-b7eb-04dac91e5b3c",
+ "@id": "urn:cab74723-0ee9-4288-958e-063720df47d4",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
"Used": [
- "urn:18e2f45e-748e-4659-9dd3-fd58912f36ba"
+ "urn:ae74e9d6-f37c-4fb2-9b4c-461f3c4b7919"
]
},
{
- "@id": "urn:c105ae15-b7b6-45a1-998a-edabc1944c3e",
+ "@id": "urn:56cebd72-711b-493a-8abc-9f859a81e659",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2",
"Used": [
- "urn:6f371063-f2c7-47dd-8a3b-6d0d986e115e"
+ "urn:08f73c1c-6be9-45f3-a4d7-396d919f2879"
]
},
{
- "@id": "urn:b1d963a1-adde-478c-9572-0e6491214316",
+ "@id": "urn:593ce871-0708-4cde-bd2a-be90a20aad38",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:49ef5b81-19e3-4c4e-b711-c5adb8849ec0",
+ "@id": "urn:08a36ae1-a3be-494d-94c5-20e993aafadc",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zfstat3 -t 3.090232 --othresh=thresh_zfstat3 -o cluster_mask_zfstat3 --connectivity=26 --olmax=lmax_zfstat3.txt --scalarname=Z --voxuncthresh > cluster_zfstat3.txt",
"Used": [
- "urn:1662b1a2-1679-4d8d-b615-c41a992926ca"
+ "urn:44e6ae47-f94d-4f63-b751-deb9963deff6"
]
},
{
- "@id": "urn:8c6a8fad-4a10-4e63-902e-cb713291e98b",
+ "@id": "urn:d1bbf2f0-8f57-4537-8e7d-a4f1f2046f1c",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat3",
"Used": [
- "urn:debeb16c-5b95-4d17-bf55-7b5f67d88815"
+ "urn:8c4c3b13-4c9e-41e0-a695-b0506ea60e3a"
]
},
{
- "@id": "urn:ac72bb00-f067-43c0-93f1-c19535495c63",
+ "@id": "urn:41e319a6-a2f0-471e-8f54-2328f979e712",
"Label": "ptoz",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+ "@id": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z --voxuncthresh > cluster_zstat1_std.txt",
"Used": [
- "urn:38c32689-25e4-4616-a55f-99f621b66dae",
- "urn:cdc2d3c8-eace-4a0f-99ee-54b0afbb95e0"
+ "urn:0ab3aafa-76ca-4e3a-8379-e94368eed76a",
+ "urn:6f8300aa-44d9-4384-99b3-e51129ac29ab"
]
},
{
- "@id": "urn:0a2bd5ea-a64e-42a0-ae31-150e7a1257b4",
+ "@id": "urn:3ffe526e-cf08-407d-b9b8-6fa4e7cb5345",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat1 -std",
"Used": [
- "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd"
+ "urn:f3689c31-ae2f-4947-a2cf-9b34744341b9"
]
},
{
- "@id": "urn:cf18c935-d808-4855-94c8-ab1e8af5e711",
+ "@id": "urn:5ac4155b-5684-4290-ab9b-2b6ad1bce005",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster -i thresh_zstat2 -c stats/cope2 -t 3.090232 -d 0.70114 --volume=38352 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat2_std.txt --scalarname=Z --voxuncthresh > cluster_zstat2_std.txt",
"Used": [
- "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
- "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f"
+ "urn:2aa858d0-c72e-4263-aa8f-f09a66258e4c",
+ "urn:517a7515-49ec-465b-a678-5b2a2f9bb21c"
]
},
{
- "@id": "urn:d9c5d9f6-d211-47e7-993d-ca16b373b789",
+ "@id": "urn:3fff3811-db41-42c4-ae1f-ab839e77e67f",
"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zstat2 -std",
"Used": [
- "urn:af09e210-3d42-4ab8-881e-63b8a79ac26f"
+ "urn:a9cb952e-31b9-43a4-817f-3dc1683dc1e8"
]
},
{
- "@id": "urn:b25b166c-87b5-473b-a60f-ad6c25f3622e",
+ "@id": "urn:1fb60e81-b476-46e6-b75d-ded62428c57d",
"Label": "cluster",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
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"Used": [
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]
},
{
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"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat1 -std",
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]
},
{
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"Used": [
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]
},
{
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"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/cluster2html . cluster_zfstat2 -std",
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]
},
{
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"Used": [
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]
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{
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"Label": "cluster2html",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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]
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{
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]
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{
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]
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]
},
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"Label": "fslstats",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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]
},
{
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"Command": "/usr/local/packages/fsl-5.0.8/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
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]
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]
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]
},
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},
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"Used": []
},
{
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- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
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"Used": [
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]
},
{
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+ "@id": "urn:b0f62f63-a5e4-428e-8d12-236f6b41d2f8",
"Label": "Make directory",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "mkdir -p tsplot",
"Used": []
},
{
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+ "@id": "urn:94a480db-59e3-43e5-866e-82fe1c3fbb5c",
"Label": "tsplot",
- "AssociatedWith": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
+ "AssociatedWith": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
"Command": "/usr/local/packages/fsl-5.0.8/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
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+ "@id": "urn:00d2cbcd-88c4-495d-a56c-9c436669c375",
"Label": "sub-01_task-tonecounting_bold",
"AtLocation": "/home/tommaullin/Documents/Data/ds011/sub-01/func/sub-01_task-tonecounting_bold",
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@@ -1148,25 +1148,25 @@
}
},
{
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+ "@id": "urn:e4eab963-3f85-4099-b44a-7c31510246e3",
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"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
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+ "@id": "urn:760ad209-0e8d-4380-9167-6790e6cdbef4",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:f5c8f6a7-13a4-431b-b55a-15d9f2c3c417",
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_con_f_multiple_test.feat/example_func.nii.gz",
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@@ -1174,7 +1174,7 @@
}
},
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"digest": {
@@ -1182,7 +1182,7 @@
}
},
{
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"digest": {
@@ -1190,46 +1190,46 @@
}
},
{
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- "GeneratedBy": "urn:b084ad3a-cf4b-47a4-83e6-06f3eae198c9"
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- "GeneratedBy": "urn:d29f9314-7a2c-4522-b097-5402aba8a5b4",
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@@ -1237,16 +1237,16 @@
}
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@@ -1254,250 +1254,250 @@
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@@ -1505,565 +1505,565 @@
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{
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{
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- "GeneratedBy": "urn:b166d860-3725-4ea1-95cf-f69ec640b968",
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{
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{
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{
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{
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{
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"AtLocation": "example_func2standard2.png",
- "GeneratedBy": "urn:a565191b-1db3-4743-bd31-6b8b2cbf88c2",
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"AtLocation": "example_func2standard.png",
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{
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"AtLocation": "prefiltered_func_data_mcf",
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{
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -2071,7 +2071,7 @@
}
},
{
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+ "@id": "urn:91a99f75-a4b5-434e-b5fc-cd05fae1fad9",
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"AtLocation": "prefiltered_func_data_mcf.par",
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@@ -2079,7 +2079,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_abs.rms",
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@@ -2087,7 +2087,7 @@
}
},
{
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+ "@id": "urn:a094dcca-d44d-4beb-bdac-576804c53c44",
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"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -2095,7 +2095,7 @@
}
},
{
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@@ -2103,7 +2103,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -2111,34 +2111,34 @@
}
},
{
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- "GeneratedBy": "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3",
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{
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- "GeneratedBy": "urn:725ce964-546e-4bc3-b142-d8c544ff20fb",
+ "GeneratedBy": "urn:dfde6c8e-d119-4215-b337-145bb3eef5f1",
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{
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"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -2146,34 +2146,34 @@
}
},
{
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- "GeneratedBy": "urn:dab0a08b-dacf-4844-a891-6ef77087c0aa",
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{
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"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:f1669840-b2b3-444f-a7d7-833c7e46505d",
+ "GeneratedBy": "urn:41ef447f-fccd-4aff-ae40-399d14ad3aa0",
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{
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- "GeneratedBy": "urn:582ba438-47f5-434f-a321-cfe55992160a",
+ "GeneratedBy": "urn:f9ff08c4-87f3-4355-b509-a30ad6ac0bb7",
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{
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@@ -2181,106 +2181,106 @@
}
},
{
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:47831ace-48c1-422e-a87d-97ecf3810601",
+ "GeneratedBy": "urn:4a850400-1f9e-471b-ba9a-add8e4a5671d",
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{
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- "GeneratedBy": "urn:45ccc0d7-d6a4-4e62-9efe-15b59b96354c",
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{
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{
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"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:711029e7-1a0b-4010-b6df-ed04fa5e35c1",
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}
},
{
- "@id": "urn:ea8de012-dce4-4e09-b850-ed1d8f0a2896",
+ "@id": "urn:953da91d-fdcc-4eb3-8b57-5f3f17727bc0",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:926ed1ec-af3b-452a-9b53-ca78b6f581bb",
+ "GeneratedBy": "urn:4debf022-96fd-4557-ad7c-380ace811d40",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:9b699ea3-8ad8-49af-83ff-7505506ab96c",
+ "@id": "urn:6a61799d-2599-4916-80ef-4883143bc617",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:3ee9492d-501c-49fa-8f15-d96306e9c0c6",
+ "GeneratedBy": "urn:9887c94f-91b2-4240-a36a-eadb5aa3c924",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:5d1a543b-6df9-4541-ae83-2c723b8c6368",
+ "@id": "urn:1b2b3cc3-b38b-4b56-9498-7aea3ffe98f9",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:917c58f5-3975-4e53-a51e-95ab439f33d7",
+ "GeneratedBy": "urn:8cf5d2ac-cc2a-44e7-8eb2-c32e0dbb77df",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3",
+ "@id": "urn:f412f5d1-816b-440b-9539-e4500dd9a7f4",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:c87eee96-f587-4647-b19b-c4e391998eff",
+ "GeneratedBy": "urn:933a06df-d189-4d77-8890-8ccf53fd1c0f",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:307b8e93-4018-4034-b02d-3b761ef5558a",
+ "@id": "urn:761d8304-1910-4af4-9bcc-748950048e05",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:78fdae39-e08e-4f0d-a442-3fe26d9438a2",
+ "GeneratedBy": "urn:40f105b4-d402-4298-9c9c-4c6535c9422f",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:367458e3-16bb-4dd1-ae1f-db628fdc3a0d",
+ "@id": "urn:ae9dab48-a818-43a0-be2b-28a9a4d076da",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:73f3d293-8378-44e5-b97f-f0d210d07474",
+ "GeneratedBy": "urn:1bb4ff15-fc4a-4873-a7af-ecad0fd620ac",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:263e3610-fc97-46a1-a70f-f475bc13917d",
+ "@id": "urn:0381843b-eb04-4177-9a55-a98f65fb3262",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -2288,25 +2288,25 @@
}
},
{
- "@id": "urn:5daf1c03-fc28-4693-b72d-04cd580ab021",
+ "@id": "urn:5092984f-5d20-4ec0-817f-5992ffdcb2c9",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:fe3d820b-4db4-4e2d-adcd-292735b69254",
+ "GeneratedBy": "urn:e06d0fe1-fc81-4ef3-b839-41a4a2c1ff71",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:1145ef1c-602d-4806-bfa5-39cb20e1394f",
+ "@id": "urn:c87a3172-8501-4620-87eb-5dfa686b2f8b",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:b807382f-c648-42ed-85a4-e308b783d419",
+ "GeneratedBy": "urn:4b785bbf-7f93-4aa1-a136-19df513b097d",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:d75904a1-7cd3-4610-a894-e6c3c5d76011",
+ "@id": "urn:ae057ca4-c2cc-4fd9-8c26-73e9f56c8b0d",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -2314,16 +2314,16 @@
}
},
{
- "@id": "urn:9a46fc84-5d80-45d6-beb8-5860b5ed50c5",
+ "@id": "urn:183130da-2404-4f2f-ab61-76892ddfb75c",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:961fc3ea-0194-4640-a8b7-8774f193fee2",
+ "GeneratedBy": "urn:507a8da5-9f2f-4616-ad3e-679eaad090d9",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:e057248b-dd5d-4c40-bd31-8505d330fb13",
+ "@id": "urn:4f7198d4-27d5-4774-a8be-0493629b20c4",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -2331,22 +2331,22 @@
}
},
{
- "@id": "urn:435a68ac-72e9-4d77-8ee2-9eb12b1468c4",
+ "@id": "urn:ad79dd69-ed1b-4779-9661-bdeccfa262ee",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:18783c49-a892-4343-83e7-86b8183d3e83"
+ "GeneratedBy": "urn:a74e0bd9-a76a-408d-9d6d-1b406eeb73dc"
},
{
- "@id": "urn:158a8fa0-2415-4647-98be-add728d66819",
+ "@id": "urn:66e2b8c9-38e4-419a-bc3a-b1730de5c887",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:551995e2-978b-482d-afd6-fe48b36f14c7",
+ "GeneratedBy": "urn:01c533ac-888f-4efc-a3c7-9a21bb0032c9",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:2f900215-15bd-4a15-8c21-a8ab51007afb",
+ "@id": "urn:783f0bfe-bc17-4fd3-86e4-5265722f4f3f",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -2354,13 +2354,13 @@
}
},
{
- "@id": "urn:1610add2-fdc2-479b-a927-1c15cee8cf73",
+ "@id": "urn:514b841f-0b5c-4fb1-aa1d-30d5a5ff174e",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:d68c27b7-672e-4f70-8746-fed40682c700"
+ "GeneratedBy": "urn:f565cf28-54ed-4c08-ad1c-4c86fbd4209a"
},
{
- "@id": "urn:31c406c9-e772-4346-bc0d-e20ecfc2a8a8",
+ "@id": "urn:6be892d4-a8b7-43cc-878f-266da06eca50",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -2368,16 +2368,16 @@
}
},
{
- "@id": "urn:d4ce1155-8e92-41de-ad87-a61a257d6e3f",
+ "@id": "urn:e69f4098-08d3-44bb-a7eb-cae49508103f",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:9eed7245-2062-4382-a312-e3700ce4e6ff",
+ "GeneratedBy": "urn:8e7d0070-8079-4c57-aede-ac31ab3d2c61",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:0d0dc84d-f553-4433-a38d-2c1056077f45",
+ "@id": "urn:ae6c30bd-7165-4aa1-bb31-3af82ba212fa",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -2385,16 +2385,16 @@
}
},
{
- "@id": "urn:cdc2d3c8-eace-4a0f-99ee-54b0afbb95e0",
+ "@id": "urn:6f8300aa-44d9-4384-99b3-e51129ac29ab",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:b68b9bc1-27cc-4c62-9d49-e1f70f7aa3a0",
+ "GeneratedBy": "urn:c41eeac9-b3fd-4ec4-8389-fd1c310222fc",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:7052b74a-50e0-439c-81df-db12832c1a44",
+ "@id": "urn:ec7e16a9-e3a7-4bbe-9f6a-b36e67c48ec7",
"Label": "zstat2",
"AtLocation": "stats/zstat2",
"digest": {
@@ -2402,16 +2402,16 @@
}
},
{
- "@id": "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f",
+ "@id": "urn:517a7515-49ec-465b-a678-5b2a2f9bb21c",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:a906578f-aa09-42aa-aab9-8716786196b3",
+ "GeneratedBy": "urn:299f734f-30b4-43e4-8613-7fc79f324cfd",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:96707788-783b-4a32-88cc-425b7e5cc0a2",
+ "@id": "urn:b50d8309-9587-4c3d-8b68-eafea4254b96",
"Label": "zfstat1",
"AtLocation": "stats/zfstat1",
"digest": {
@@ -2419,16 +2419,16 @@
}
},
{
- "@id": "urn:5ecde4d0-c081-4835-aa9f-906b48bc746d",
+ "@id": "urn:04745c1c-681d-4ecd-99f5-96d342aae6ed",
"Label": "thresh_zfstat1",
"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:cd620add-4300-4d26-8e71-f9bd37cb0b8e",
+ "GeneratedBy": "urn:e16d69a9-cb22-4fa6-93e3-3f382186da83",
"digest": {
"sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
}
},
{
- "@id": "urn:e5b6247c-0f74-4751-939f-af60b86ae6ca",
+ "@id": "urn:8dd263d5-5ca0-470a-b2ea-56225b421ea3",
"Label": "zfstat2",
"AtLocation": "stats/zfstat2",
"digest": {
@@ -2436,16 +2436,16 @@
}
},
{
- "@id": "urn:18e2f45e-748e-4659-9dd3-fd58912f36ba",
+ "@id": "urn:ae74e9d6-f37c-4fb2-9b4c-461f3c4b7919",
"Label": "thresh_zfstat2",
"AtLocation": "thresh_zfstat2",
- "GeneratedBy": "urn:af85eb98-f60a-48ca-85fc-72ebed7a0c95",
+ "GeneratedBy": "urn:92d3b2a1-dba6-4edc-93c6-11c3082b306f",
"digest": {
"sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
}
},
{
- "@id": "urn:75c61345-a8ea-4382-bfdb-d6d0c98ed84c",
+ "@id": "urn:3ed0a019-09cf-43fc-8a4d-a3b823fc25ad",
"Label": "zfstat3",
"AtLocation": "stats/zfstat3",
"digest": {
@@ -2453,16 +2453,16 @@
}
},
{
- "@id": "urn:1662b1a2-1679-4d8d-b615-c41a992926ca",
+ "@id": "urn:44e6ae47-f94d-4f63-b751-deb9963deff6",
"Label": "thresh_zfstat3",
"AtLocation": "thresh_zfstat3",
- "GeneratedBy": "urn:dfea9359-ff55-4f9f-80a3-b053d6b53085",
+ "GeneratedBy": "urn:6ca79a28-ccba-4ed7-9c3e-b723a3384c43",
"digest": {
"sha256": "d146fc312c5094abf2cb41add06d96d79e5f36d27a64adea95365e8776a3707d"
}
},
{
- "@id": "urn:38c32689-25e4-4616-a55f-99f621b66dae",
+ "@id": "urn:0ab3aafa-76ca-4e3a-8379-e94368eed76a",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -2470,25 +2470,25 @@
}
},
{
- "@id": "urn:48891029-b785-4f4f-8860-7054ddcf78ca",
+ "@id": "urn:a2ad449d-4882-4dec-90e8-1a9f300f1dbd",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:932fc7fe-6a48-438b-9df6-9a150e9142d3",
+ "GeneratedBy": "urn:27316f60-9bb2-44a4-92e3-10550fd887e9",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:854a0da7-0140-4007-b23a-63c8036c2338",
+ "@id": "urn:fbcc0e0a-4131-487e-9e7e-baf9fee5e1a3",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:932fc7fe-6a48-438b-9df6-9a150e9142d3",
+ "GeneratedBy": "urn:27316f60-9bb2-44a4-92e3-10550fd887e9",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:40d467e3-1a17-401c-a6fe-fc6b2df21dfd",
+ "@id": "urn:f3689c31-ae2f-4947-a2cf-9b34744341b9",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -2496,7 +2496,7 @@
}
},
{
- "@id": "urn:50551edf-7b41-4868-96c8-6f50ef1afcc5",
+ "@id": "urn:2aa858d0-c72e-4263-aa8f-f09a66258e4c",
"Label": "cope2",
"AtLocation": "stats/cope2",
"digest": {
@@ -2504,25 +2504,25 @@
}
},
{
- "@id": "urn:bc4ed7c6-6801-4fc5-8242-4cca359734a6",
+ "@id": "urn:99750f1a-7d7d-4c62-8dbb-d96f90fce621",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:6c7c5ceb-8f8a-4126-931f-3e45b2fc80f0",
+ "GeneratedBy": "urn:ddf90615-d0eb-4158-8692-b9628e86d510",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:abaf539c-8c53-4d5b-81dd-c5c8dd66cef5",
+ "@id": "urn:2ece99e1-6677-4796-a80a-3775f3199700",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:6c7c5ceb-8f8a-4126-931f-3e45b2fc80f0",
+ "GeneratedBy": "urn:ddf90615-d0eb-4158-8692-b9628e86d510",
"digest": {
"sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
}
},
{
- "@id": "urn:af09e210-3d42-4ab8-881e-63b8a79ac26f",
+ "@id": "urn:a9cb952e-31b9-43a4-817f-3dc1683dc1e8",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -2530,16 +2530,16 @@
}
},
{
- "@id": "urn:544d0fc1-89f3-4a63-b15c-b845ef1a2a66",
+ "@id": "urn:c4fc115a-6e43-47e8-8064-cf6a59c5d9dc",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:fff5c382-53bd-4b97-a58a-1fe3dbded5df",
+ "GeneratedBy": "urn:f7b23cf4-c8f9-4b58-9b0e-e0e62ffbccb7",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:68638674-b35e-4ee2-ac81-93b0eed1dc4a",
+ "@id": "urn:d39efdca-98e2-420d-9c11-781542369bd7",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -2547,16 +2547,16 @@
}
},
{
- "@id": "urn:3629a684-e3d0-4d02-b46c-ba0aa897ca06",
+ "@id": "urn:50600ca9-626c-462a-a065-e43145b94a63",
"Label": "cluster_mask_zfstat2",
"AtLocation": "cluster_mask_zfstat2",
- "GeneratedBy": "urn:5bcbb31a-da10-4a45-b7eb-04dac91e5b3c",
+ "GeneratedBy": "urn:cab74723-0ee9-4288-958e-063720df47d4",
"digest": {
"sha256": "962ef7014f226d586c47fb23ebcde5968e55a03f06dae8514b358579d8457e7a"
}
},
{
- "@id": "urn:6f371063-f2c7-47dd-8a3b-6d0d986e115e",
+ "@id": "urn:08f73c1c-6be9-45f3-a4d7-396d919f2879",
"Label": "cluster_zfstat2",
"AtLocation": "cluster_zfstat2",
"digest": {
@@ -2564,16 +2564,16 @@
}
},
{
- "@id": "urn:384ac647-9ad8-446d-b8a7-23ec3b5875b1",
+ "@id": "urn:bb3b9fe4-d9bb-456f-b15e-532108af5130",
"Label": "cluster_mask_zfstat3",
"AtLocation": "cluster_mask_zfstat3",
- "GeneratedBy": "urn:49ef5b81-19e3-4c4e-b711-c5adb8849ec0",
+ "GeneratedBy": "urn:08a36ae1-a3be-494d-94c5-20e993aafadc",
"digest": {
"sha256": "997d113725899451840579d113cb9c7adc8de328aa80459f8a03d175003a0d8a"
}
},
{
- "@id": "urn:debeb16c-5b95-4d17-bf55-7b5f67d88815",
+ "@id": "urn:8c4c3b13-4c9e-41e0-a695-b0506ea60e3a",
"Label": "cluster_zfstat3",
"AtLocation": "cluster_zfstat3",
"digest": {
@@ -2581,88 +2581,88 @@
}
},
{
- "@id": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
+ "@id": "urn:42ec9200-79c7-484d-9a0f-b81fe7a820a5",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+ "GeneratedBy": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:b9dd4585-53b2-46d3-86ef-605a4028c435",
+ "@id": "urn:13e5b321-4fa2-4564-981e-90497af02801",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:2a27b562-f2c8-4d65-87e7-8324ee4b0b9a",
+ "GeneratedBy": "urn:388ac5f3-9da0-4574-8860-bc4c4ef8e2cf",
"digest": {
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{
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"AtLocation": "reg/example_func2standard.mat",
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"AtLocation": "reg/example_func2standard.mat",
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{
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+ "@id": "urn:e02b2957-be9a-46ac-992e-79c7f1221e7f",
"Label": "example_func2standard.mat",
"AtLocation": "reg/example_func2standard.mat",
- "GeneratedBy": "urn:3a2c9ee8-541c-4bc9-8e5b-13a00b8688c7",
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},
{
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"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:329d09d5-6a12-4729-a722-c6dc26a2fbe5",
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{
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"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:d809c990-23f3-4601-80f6-06be25447e95",
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{
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+ "@id": "urn:3065dbec-ebc3-4b27-b4e2-aec22d89dbdd",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.8/etc/luts/ramp.gif",
"digest": {
@@ -2670,100 +2670,100 @@
}
},
{
- "@id": "urn:2d7fbb57-9060-4d9b-88e3-daacd0134d99",
+ "@id": "urn:bd6df541-22ee-4ac9-877c-84ae4768a726",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:905e675b-0242-43eb-9763-4908abbe7de9",
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{
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"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:868803d2-f2c9-45ad-98ae-215da048aed3",
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{
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"AtLocation": "rendered_thresh_zstat2.png",
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"AtLocation": "rendered_thresh_zfstat1",
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+ "GeneratedBy": "urn:0b896bf7-dede-493e-8f82-49d59aa8d3ae",
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{
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"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:3ba5cd1f-fdfc-400a-a1ae-227bdfe70c50",
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{
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"AtLocation": "rendered_thresh_zfstat2",
- "GeneratedBy": "urn:e6575988-076c-4dac-868c-1cba20f3c597",
+ "GeneratedBy": "urn:fe0dab03-b97b-4c4e-920c-ec29d36e0707",
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{
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"AtLocation": "rendered_thresh_zfstat2.png",
- "GeneratedBy": "urn:231abdc8-7275-44f3-86b3-b8cd318f4207",
+ "GeneratedBy": "urn:7329dacf-1f1a-4421-b1c1-a186371bd08c",
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{
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"AtLocation": "rendered_thresh_zfstat3",
- "GeneratedBy": "urn:65603e13-f0b7-4788-91a0-dff5363681c9",
+ "GeneratedBy": "urn:de483b5e-e512-4f14-8ccf-ee7c4d380f26",
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{
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"AtLocation": "rendered_thresh_zfstat3.png",
- "GeneratedBy": "urn:b9ea35db-d498-431f-88a6-0669481d8bd2",
+ "GeneratedBy": "urn:c16ff10b-d98c-4f4d-b98e-7bd72518b8a2",
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}
},
{
- "@id": "urn:95e22684-0144-4cce-af19-97b1623d1b90",
+ "@id": "urn:5a9d2766-f0ce-470d-bd3a-02d3064285bf",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:fd4b3e64-5e6c-48aa-b561-2bea00747104",
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{
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"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:245ce441-cd96-4dc1-86cd-0a1e2723db8c",
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diff --git a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png
index fe3dbfec4..410a9bc61 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_multiple_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
index 3c1b9421b..a38d90265 100644
--- a/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_con_f_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "@id": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,607 +13,607 @@
],
"Activities": [
{
- "@id": "urn:9b654366-a76d-4764-b5c9-25583871e422",
+ "@id": "urn:c358f7b3-73cf-45d3-acf3-497f46cedbea",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:2a166a8b-0df5-48e7-885f-3dd1049a4a6e"
+ "urn:7e3db413-8335-4676-9cf6-1602a3b1f94f"
]
},
{
- "@id": "urn:d9519d20-c5f6-431a-a1dd-e10a3259b3eb",
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"Label": "fslroi",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:8f8fe587-dd5a-43d2-9792-8b372f66297e"
+ "urn:776184ac-3435-4832-bef8-2c899faf87b9"
]
},
{
- "@id": "urn:29ae19fc-3f10-4560-b622-06a4f38fc36e",
+ "@id": "urn:3360db04-b715-4330-b177-7ab1cbce8211",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
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]
},
{
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"Label": "Make directory",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_f_test.feat/reg",
"Used": []
},
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]
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"Used": [
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]
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},
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"Label": "convert_xfm",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
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"Used": [
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]
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+ "urn:432b8f41-0b8f-4a0f-a96e-ef80c4ddc637",
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"Label": "pngappend",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
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- "urn:e29308d3-e89c-4238-a244-1637a64a3c27",
- "urn:e784343f-88eb-4b8d-8447-9af21cf0b76a"
+ "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8",
+ "urn:3d08452f-2ec9-47ad-be79-1d9fd0c690c2",
+ "urn:458f7948-c301-43af-ae62-817a341f59da",
+ "urn:543ec73e-7a7b-4f1c-b0f2-5e4faa4a024a",
+ "urn:5e650fe4-797e-43ba-a8e5-78407a74f7b4",
+ "urn:65ba8e42-11a5-4a89-805d-2befe29d2c82",
+ "urn:736f8ab3-cae1-4022-9c97-ba8843782a36",
+ "urn:77123f02-8628-496b-ae8c-94d6cbb0a645",
+ "urn:94d83b6c-0071-40c5-b3ad-9687a6570107",
+ "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1",
+ "urn:ce99dac3-455e-42e6-97d0-708e6a12d120",
+ "urn:e5c4e54e-7449-4454-916d-ac095d2d8c98"
]
},
{
- "@id": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "@id": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
"Label": "slicer",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:52b1e261-fec0-4e34-a356-90ad7d4e1234",
- "urn:7f26712f-542f-4cab-b485-c34d61c39b26"
+ "urn:432b8f41-0b8f-4a0f-a96e-ef80c4ddc637",
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]
},
{
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+ "@id": "urn:6b5b4ba1-493c-4407-b105-4101706e05c3",
"Label": "pngappend",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
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- "urn:e29308d3-e89c-4238-a244-1637a64a3c27",
- "urn:e784343f-88eb-4b8d-8447-9af21cf0b76a"
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+ "urn:3d08452f-2ec9-47ad-be79-1d9fd0c690c2",
+ "urn:458f7948-c301-43af-ae62-817a341f59da",
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+ "urn:65ba8e42-11a5-4a89-805d-2befe29d2c82",
+ "urn:736f8ab3-cae1-4022-9c97-ba8843782a36",
+ "urn:77123f02-8628-496b-ae8c-94d6cbb0a645",
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+ "urn:ce99dac3-455e-42e6-97d0-708e6a12d120",
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]
},
{
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+ "@id": "urn:3ce38cf8-d9ad-4bb8-a6ee-d7c5c0a18511",
"Label": "pngappend",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
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- "urn:9ee7d045-60cc-4630-9ecb-3a0d2d2c9ce5"
+ "urn:577dbeef-ee03-40d7-aa64-023f1045a060",
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]
},
{
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"Label": "rm",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
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- "urn:d993fcfd-8fa4-405e-906a-3df84fda0fb4"
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]
},
{
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+ "@id": "urn:d66a89e0-e899-4368-b615-3138cf30c215",
"Label": "rm",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:7de17507-bdc9-4002-bf2d-2815ea50a192"
+ "urn:d1e011d7-e565-4bea-850c-263729ba79cd"
]
},
{
- "@id": "urn:e27ae9b4-0f62-4c4e-9c20-049a703eee03",
+ "@id": "urn:e386f822-5553-4832-8d3d-145ad7886285",
"Label": "mcflirt",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:8f8fe587-dd5a-43d2-9792-8b372f66297e"
+ "urn:776184ac-3435-4832-bef8-2c899faf87b9"
]
},
{
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+ "@id": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
"Label": "Make directory",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
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+ "@id": "urn:28cb7508-1b38-4619-b8bb-a2dc2b849553",
"Label": "mv",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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- "urn:f015120b-6635-4636-8f4e-0bc4e2972782",
- "urn:f150c860-a320-4b6a-bffb-3296f4a0d6df"
+ "urn:0af1248e-e25c-46f3-b05a-9b3b2a617c5a",
+ "urn:10492bfd-8ec0-4fe0-b867-bec8425d0dca",
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+ "urn:b6fa3c79-0f4b-43ca-9e68-105676040d46",
+ "urn:f6c94055-f898-470c-8498-e56004edcadd",
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]
},
{
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+ "@id": "urn:5c4586db-865a-4612-818d-aedbe8a7214c",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:f015120b-6635-4636-8f4e-0bc4e2972782"
+ "urn:b6fa3c79-0f4b-43ca-9e68-105676040d46"
]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:f015120b-6635-4636-8f4e-0bc4e2972782"
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]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
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]
},
{
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+ "@id": "urn:8387f2d4-1fd6-4431-b2d2-fb5c9be44109",
"Label": "bet2",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
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+ "urn:14538410-322b-433e-89a1-fb485be42a81"
]
},
{
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+ "@id": "urn:98f84370-938e-4751-9130-dacf85d9b5fd",
"Label": "immv",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
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+ "urn:3c1ac51f-9d28-4ce9-a5ee-787dc723fe39"
]
},
{
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+ "@id": "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540"
+ "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c",
+ "urn:c27daab7-7b46-4a97-aef8-e9def2558de6"
]
},
{
- "@id": "urn:a30e819a-5b66-4fb4-ada6-e07513b0c982",
+ "@id": "urn:83df4d40-0769-4504-832a-88276820c98a",
"Label": "fslstats",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
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+ "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11"
]
},
{
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+ "@id": "urn:14381320-683a-4404-9dcf-f73101d00876",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
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+ "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11"
]
},
{
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+ "@id": "urn:6b9530f5-6075-4b7d-873b-15df208d2e88",
"Label": "fslstats",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
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+ "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
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+ "urn:c27daab7-7b46-4a97-aef8-e9def2558de6"
]
},
{
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+ "@id": "urn:372bd721-7ab0-4667-b4b6-a5412ee5062f",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540"
+ "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c",
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
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+ "urn:ccb1560a-9028-47f0-ab4c-966f54c83553"
]
},
{
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"Label": "susan",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
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"Used": [
- "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4"
+ "urn:ccb1560a-9028-47f0-ab4c-966f54c83553"
]
},
{
- "@id": "urn:2bafc123-f535-4eb0-9d99-98ffd606e387",
+ "@id": "urn:14ddd282-4294-4c2e-a111-1bc95e4f5a39",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b"
+ "urn:8e23621e-af1f-4f36-aa91-fe74af747392",
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]
},
{
- "@id": "urn:868a5cd1-12a1-444b-be3a-5bc2304b75a4",
+ "@id": "urn:2461ed0f-a5f5-47b8-96f4-be8d20fc72ec",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b"
+ "urn:8e23621e-af1f-4f36-aa91-fe74af747392"
]
},
{
- "@id": "urn:68e68da7-bcca-452f-b6f2-f83c35290e9e",
+ "@id": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:2a0541ac-72b1-43f5-929b-fbbb9aae72ee"
+ "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc"
]
},
{
- "@id": "urn:8ff96632-d4d4-4fff-9a73-a76e6a9c355e",
+ "@id": "urn:ba3fdc68-178d-4cf7-ad77-704f1b52cedd",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:a9cc3337-7dfa-4f97-820f-bf23f4eb4e64"
+ "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7",
+ "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc"
]
},
{
- "@id": "urn:5a78e128-92b4-4fb3-a38b-559576fcda4c",
+ "@id": "urn:9403d5c6-51b2-46bd-9794-981da1e12b27",
"Label": "imrm",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:a9cc3337-7dfa-4f97-820f-bf23f4eb4e64"
+ "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7"
]
},
{
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+ "@id": "urn:4fbd6045-cae5-4f0a-8b65-857ef927274f",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:0874b92d-50eb-4f06-aa11-1b4c1a3d7f25"
+ "urn:75142b97-c286-40c1-a0df-a19fee33956c"
]
},
{
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+ "@id": "urn:fe68686f-5fe0-4994-a9b1-200e446ff6b9",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:d9762ba0-28f1-4f2b-8d48-d26a5b51e993"
+ "urn:d59db5b5-4ab3-4475-bb6e-9e3510819631"
]
},
{
- "@id": "urn:439b451c-3b96-4949-ad1d-5c2dff6aba46",
+ "@id": "urn:589b1c78-c52c-4441-951b-48ba0f8ae0bd",
"Label": "rm",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:3264d870-df93-44d9-b00d-1e80a6a58e24"
+ "urn:954dc233-a400-4356-98f9-d818f2b94a91"
]
},
{
- "@id": "urn:71f4a784-5e42-413d-a991-c4aa0bda779d",
+ "@id": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
"Label": "Make directory",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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+ "@id": "urn:d09a9e6e-3b93-45ac-bc47-55d3f9553c11",
"Label": "fslFixText",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:eee94271-3a18-4576-818c-4513e34e6363"
+ "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148"
]
},
{
- "@id": "urn:b58a4b95-7e2c-42ca-8cf1-12c9a3e329fa",
+ "@id": "urn:499b5597-193b-4c01-8748-0353d72e7812",
"Label": "Make directory",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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+ "@id": "urn:571a134a-fc64-4cdd-a0f4-2ce78588cf20",
"Label": "fslFixText",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:ee6840ba-f606-4ad9-9e69-5ff2713e44b9"
+ "urn:3de80e83-be49-40e6-9e70-c25dd5f971ad"
]
},
{
- "@id": "urn:351aa42f-fff6-4ad9-b528-7d19cf588dd6",
+ "@id": "urn:c32531f4-eacb-40a9-923b-70b1748c51c5",
"Label": "film_gls",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
"Used": []
},
{
- "@id": "urn:72ca6d99-b763-4a26-a7b5-27932336af26",
+ "@id": "urn:2d92b15d-ceb0-4828-90ca-44d8cb55b37f",
"Label": "smoothest",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
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- "urn:56324442-e0d7-4e0a-a988-0b3618c3a03e"
+ "urn:a4bcce4e-9230-4c91-afc0-6657745b8701",
+ "urn:c27daab7-7b46-4a97-aef8-e9def2558de6"
]
},
{
- "@id": "urn:2099be2a-b112-41ff-aad9-e1f1e8ecfe62",
+ "@id": "urn:3bdef291-db22-4670-b345-fff8811f30ac",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
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- "urn:14ac402f-5767-45a4-a042-2fd87833e03b",
- "urn:56324442-e0d7-4e0a-a988-0b3618c3a03e"
+ "urn:c27daab7-7b46-4a97-aef8-e9def2558de6",
+ "urn:cb81e16e-cab3-408f-93d8-37aefc195994"
]
},
{
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+ "@id": "urn:a7c0d8c8-7be5-4ebc-8f07-ebd395edf9a2",
"Label": "echo",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:debb46d4-54c3-48a6-a2b8-f17ebe1f8148",
+ "@id": "urn:012baa80-344e-4625-9fe2-288360cec634",
"Label": "fslmaths",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
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- "urn:9927e922-1c5a-494b-bd2b-4c757248f5b9"
+ "urn:8433fb76-022b-4846-b2d4-fdc2cbeae320",
+ "urn:c27daab7-7b46-4a97-aef8-e9def2558de6"
]
},
{
- "@id": "urn:14467495-b476-4aaf-a69f-83d5a7aef290",
+ "@id": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
"Label": "echo",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:da0f93a1-21e2-4c32-a1cc-b01b3dbb0974",
+ "@id": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
"Label": "ptoz",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:62e03cb0-08ac-4ca1-9da2-ddec7b358f8d",
+ "@id": "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79",
"Label": "cluster",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:33ada915-fc3b-480d-9981-cb1e137f6c75",
- "urn:b6e931d9-c40f-4f4a-a438-22174f068437"
+ "urn:ac224bd4-b45c-4ad9-a7c7-14bff747481d",
+ "urn:e289288b-2ab9-40af-bfb8-5ccf11862589"
]
},
{
- "@id": "urn:bdae09ab-3575-435e-b1f0-daa620099477",
+ "@id": "urn:7c2e9e77-f441-4a6e-a902-d2101c32b8eb",
"Label": "cluster2html",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:5ad8a67a-8993-45e4-ad9d-011a4ad6c0b8"
+ "urn:a424e26a-4756-4ebf-aee7-78caa8508f49"
]
},
{
- "@id": "urn:dd8d82c8-7151-4882-8ff2-1e28985144fd",
+ "@id": "urn:a9ba8f6c-c396-418e-a76a-08e1034d485c",
"Label": "ptoz",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:824f0992-a9ac-41bc-adc9-0af7ddf3a550",
+ "@id": "urn:c769e5d3-d624-487f-8403-8a811b38236f",
"Label": "cluster",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:468dc6f0-6861-4ff3-8d4d-58181a0180ae"
+ "urn:7c2dc4f8-24fc-4996-ab18-2e8059b863d6"
]
},
{
- "@id": "urn:2d23f131-3861-4ad5-bea0-b062e52a8b8f",
+ "@id": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5",
"Label": "cluster2html",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:65b6c37a-b6e7-4e98-adf9-673fbf302ff9"
+ "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772"
]
},
{
- "@id": "urn:02a43b91-931a-400f-a514-f6c0a53cc18c",
+ "@id": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
"Label": "fslstats",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:33ada915-fc3b-480d-9981-cb1e137f6c75"
+ "urn:e289288b-2ab9-40af-bfb8-5ccf11862589"
]
},
{
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+ "@id": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
"Label": "fslstats",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:468dc6f0-6861-4ff3-8d4d-58181a0180ae"
+ "urn:7c2dc4f8-24fc-4996-ab18-2e8059b863d6"
]
},
{
- "@id": "urn:ae858cc0-bd50-4fef-aa03-3cd358b91eb3",
+ "@id": "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
"Label": "overlay",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090250 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:5621d6ab-3b3c-4ce5-beee-f3b2ab86dd39",
+ "@id": "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21",
"Label": "slicer",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:15bedf62-df23-49b6-bbc8-1aa1713a09ea"
+ "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a"
]
},
{
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+ "@id": "urn:b3b270f2-332e-408c-9217-66156ffa79ff",
"Label": "cp",
- "AssociatedWith": "urn:52f6d3c6-539c-4296-999e-6c4388081a81",
+ "AssociatedWith": "urn:ff0e65a4-0e54-4c77-b24e-cf8ce0421e85",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:a2c97340-5cae-4aa3-a068-b2da6d76d29b"
+ "urn:b3ad7f23-b5b1-495b-bd54-c81324facbbf"
]
},
{
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@@ -621,25 +621,25 @@
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@@ -647,7 +647,7 @@
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@@ -655,7 +655,7 @@
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@@ -663,31 +663,31 @@
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@@ -695,13 +695,13 @@
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@@ -709,16 +709,16 @@
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+ "@id": "urn:eb164190-0156-408a-8695-eabc2105da90",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "GeneratedBy": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
"digest": {
"sha256": "12b578b66c0305ed3283d229408a1498ea405ccd95b3184ff523d4b36d3bbeca"
}
},
{
- "@id": "urn:9bc6ddb2-0e44-4319-9930-3448025da245",
+ "@id": "urn:24dc3cb9-8070-4c72-873b-7984f8bce111",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "GeneratedBy": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
"digest": {
"sha256": "e3417ca0a8c36a7c9572306e68b2837708e4dad049103ac2654e8f21082f261c"
}
},
{
- "@id": "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4",
+ "@id": "urn:1f8622e8-1b41-46db-8ea0-c302e1a18b83",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "GeneratedBy": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
"digest": {
"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:0f413d1b-22ea-42e5-9d8f-a8ed53c5e448",
+ "@id": "urn:12313157-10eb-4297-9463-d87018825ae9",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
+ "GeneratedBy": "urn:d9ee762f-9dd7-491b-82a6-000d8178f364",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:9ee7d045-60cc-4630-9ecb-3a0d2d2c9ce5",
+ "@id": "urn:577dbeef-ee03-40d7-aa64-023f1045a060",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:df900226-398d-422c-963e-eee25dd764b6",
+ "GeneratedBy": "urn:6b5b4ba1-493c-4407-b105-4101706e05c3",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:f2382eed-c3ed-4d76-a432-94fcaae0bfcc",
+ "@id": "urn:0ca949c1-667d-4f2c-899b-823a46887441",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:faa033ad-6397-4a90-9967-81e2735c7665",
+ "GeneratedBy": "urn:3ce38cf8-d9ad-4bb8-a6ee-d7c5c0a18511",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:d993fcfd-8fa4-405e-906a-3df84fda0fb4",
+ "@id": "urn:655ebf55-3871-401e-af6d-9b51b8475106",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -977,25 +977,25 @@
}
},
{
- "@id": "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540",
+ "@id": "urn:6e4f96b4-c210-48f8-92ab-727c45324f2c",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:e27ae9b4-0f62-4c4e-9c20-049a703eee03",
+ "GeneratedBy": "urn:e386f822-5553-4832-8d3d-145ad7886285",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:e0483247-a008-491a-8bb4-5b7c9e14dc17",
+ "@id": "urn:77b55fda-08f6-4167-aaa8-81a868cd06bb",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:774e8f06-f15d-4e68-a1f8-a836aea358c8",
+ "GeneratedBy": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:a9e05bff-7f86-441f-aea4-2b1431340600",
+ "@id": "urn:10492bfd-8ec0-4fe0-b867-bec8425d0dca",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1003,7 +1003,7 @@
}
},
{
- "@id": "urn:f015120b-6635-4636-8f4e-0bc4e2972782",
+ "@id": "urn:b6fa3c79-0f4b-43ca-9e68-105676040d46",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1011,7 +1011,7 @@
}
},
{
- "@id": "urn:514b91e5-0436-42ce-8c57-e5b70a35d201",
+ "@id": "urn:f6c94055-f898-470c-8498-e56004edcadd",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1019,7 +1019,7 @@
}
},
{
- "@id": "urn:bb6ab84c-76ed-43cc-a8fd-e3605bb6abbe",
+ "@id": "urn:0af1248e-e25c-46f3-b05a-9b3b2a617c5a",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1027,7 +1027,7 @@
}
},
{
- "@id": "urn:6125eeaa-3720-4cc7-b376-1b8818e8ab18",
+ "@id": "urn:fad5fe04-ff55-413d-ac3c-b845eb60abe7",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1035,7 +1035,7 @@
}
},
{
- "@id": "urn:f150c860-a320-4b6a-bffb-3296f4a0d6df",
+ "@id": "urn:69000e1a-e90e-4fe9-9148-a4e7bab105bc",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1043,34 +1043,34 @@
}
},
{
- "@id": "urn:0b33d168-0899-4fa2-b3aa-87ae050f04f7",
+ "@id": "urn:56d76a74-54b9-4c18-94ef-0e7ffee7589d",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:618fc7f8-1c11-4b09-85db-22ba7d0e74a6",
+ "GeneratedBy": "urn:28cb7508-1b38-4619-b8bb-a2dc2b849553",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:33d18bc3-e882-4fba-bf30-f7b91218f422",
+ "@id": "urn:22332602-c1dd-46ac-8021-349e698a0939",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:00d0dd9b-49a6-4edb-942a-98bf60c00693",
+ "GeneratedBy": "urn:5c4586db-865a-4612-818d-aedbe8a7214c",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:8f306cc1-f996-42e7-9d77-2467d960872b",
+ "@id": "urn:357c4736-e0f2-4459-a14e-8796a5614330",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:b88a65a1-2916-49de-be5d-06517bcb7976",
+ "GeneratedBy": "urn:5c2f4a20-c576-4e9f-b873-ce856594d1eb",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:667100fe-1645-4dd0-9b7f-2c28142a449a",
+ "@id": "urn:c6797c80-a805-4854-ae91-70a8444c022d",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1078,34 +1078,34 @@
}
},
{
- "@id": "urn:e627c9be-9e10-4f74-aa24-583b88f495a7",
+ "@id": "urn:0651b820-6157-4a1d-a001-93201fb81bda",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:566bad3a-0d1d-4981-a676-8b044f761589",
+ "GeneratedBy": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:6861a623-9c0f-4e38-a22e-5c2ca462fefb",
+ "@id": "urn:14538410-322b-433e-89a1-fb485be42a81",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:ee3cd2fb-999e-4a2c-b4f7-13eadd9a792c",
+ "GeneratedBy": "urn:4305cc71-294c-407a-be2e-082e60ec59c2",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:56324442-e0d7-4e0a-a988-0b3618c3a03e",
+ "@id": "urn:c27daab7-7b46-4a97-aef8-e9def2558de6",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0793c7ec-0feb-4aa0-bfb0-f2c1a23e3df6",
+ "GeneratedBy": "urn:8387f2d4-1fd6-4431-b2d2-fb5c9be44109",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:64dd7975-86f9-4f68-af87-ef3e6a3149c4",
+ "@id": "urn:3c1ac51f-9d28-4ce9-a5ee-787dc723fe39",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1113,106 +1113,106 @@
}
},
{
- "@id": "urn:48eb8fc4-4dde-4276-913a-35e1c1dcd0e2",
+ "@id": "urn:6f283968-276a-4175-ab1d-ad170199c3f3",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:3c5556a5-3f9b-487c-8fb1-83537d211fe6",
+ "GeneratedBy": "urn:98f84370-938e-4751-9130-dacf85d9b5fd",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:1ee453c4-5765-48b9-8227-12962cdb6860",
+ "@id": "urn:25e399d4-7e91-428b-ad79-8f22dee7bb11",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:1b1ff05f-85fe-4337-80e1-7a9b9cde64fc",
+ "GeneratedBy": "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:5e64a756-8f63-4ddf-97fd-1852bbaa7597",
+ "@id": "urn:1bc7a644-c310-44ec-8396-52c25d33a2de",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:48d1fa50-189a-4908-baba-601a43a8f22d",
+ "GeneratedBy": "urn:14381320-683a-4404-9dcf-f73101d00876",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:3fe1918e-0921-403c-aff5-bd68b8f11bf4",
+ "@id": "urn:bd26eb50-469a-4def-8b96-63879625c1ac",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:7a33b535-f02d-40b4-9e48-b6e94aeee80b",
+ "GeneratedBy": "urn:2629ff4e-7046-4bbb-9ced-42483142f1ba",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4",
+ "@id": "urn:ccb1560a-9028-47f0-ab4c-966f54c83553",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "GeneratedBy": "urn:372bd721-7ab0-4667-b4b6-a5412ee5062f",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:ba4263cb-024a-40f0-8b09-48834d5a2245",
+ "@id": "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:ca984797-be7e-42b0-9135-ca32141717b4",
+ "GeneratedBy": "urn:4a53d31b-ba56-4ff3-9b15-e37074df2718",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b",
+ "@id": "urn:8e23621e-af1f-4f36-aa91-fe74af747392",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:fde13367-6de1-4a55-9b52-eba74f0cd730",
+ "GeneratedBy": "urn:24a2e1fd-6f79-48cf-a9b4-0b3c50c00ef7",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:76678dac-6e11-45b4-8d18-36c4356ac96d",
+ "@id": "urn:32ec3ee6-1e9d-47e1-90db-591150f53238",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:2bafc123-f535-4eb0-9d99-98ffd606e387",
+ "GeneratedBy": "urn:14ddd282-4294-4c2e-a111-1bc95e4f5a39",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:2a0541ac-72b1-43f5-929b-fbbb9aae72ee",
+ "@id": "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:868a5cd1-12a1-444b-be3a-5bc2304b75a4",
+ "GeneratedBy": "urn:2461ed0f-a5f5-47b8-96f4-be8d20fc72ec",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:a9cc3337-7dfa-4f97-820f-bf23f4eb4e64",
+ "@id": "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:68e68da7-bcca-452f-b6f2-f83c35290e9e",
+ "GeneratedBy": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:128376a3-ab26-44cf-833c-902f376bae52",
+ "@id": "urn:11f223e3-299f-4f87-b5c6-b2cd5e69c374",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:8ff96632-d4d4-4fff-9a73-a76e6a9c355e",
+ "GeneratedBy": "urn:ba3fdc68-178d-4cf7-ad77-704f1b52cedd",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:0874b92d-50eb-4f06-aa11-1b4c1a3d7f25",
+ "@id": "urn:75142b97-c286-40c1-a0df-a19fee33956c",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1220,25 +1220,25 @@
}
},
{
- "@id": "urn:d9762ba0-28f1-4f2b-8d48-d26a5b51e993",
+ "@id": "urn:d59db5b5-4ab3-4475-bb6e-9e3510819631",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:bcd3b45f-f612-4860-9677-33435a987f2d",
+ "GeneratedBy": "urn:4fbd6045-cae5-4f0a-8b65-857ef927274f",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:2627df04-74d6-48a9-8477-97f0d80b5479",
+ "@id": "urn:636d3259-22bf-4dd3-a14a-b564569cac0d",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:c8d4dbf8-7fd9-4758-a617-722459e3fa10",
+ "GeneratedBy": "urn:fe68686f-5fe0-4994-a9b1-200e446ff6b9",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:3264d870-df93-44d9-b00d-1e80a6a58e24",
+ "@id": "urn:954dc233-a400-4356-98f9-d818f2b94a91",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1246,16 +1246,16 @@
}
},
{
- "@id": "urn:14f993bf-a7b7-4eb8-b904-564e770d919b",
+ "@id": "urn:6a2d483a-c551-4640-840d-afcc913d7b0c",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:71f4a784-5e42-413d-a991-c4aa0bda779d",
+ "GeneratedBy": "urn:132f8ed1-de07-49fe-bbcd-0e7d8bf4dc50",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:eee94271-3a18-4576-818c-4513e34e6363",
+ "@id": "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1263,22 +1263,22 @@
}
},
{
- "@id": "urn:a571a087-7a6a-4a92-bc68-41edb558da5c",
+ "@id": "urn:63092bb5-c00b-4806-ada8-4e675ca40481",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:a9593a39-5119-468e-96b2-5047fbc8492a"
+ "GeneratedBy": "urn:d09a9e6e-3b93-45ac-bc47-55d3f9553c11"
},
{
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{
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@@ -1286,13 +1286,13 @@
}
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{
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{
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@@ -1300,16 +1300,16 @@
}
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{
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{
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@@ -1317,16 +1317,16 @@
}
},
{
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@@ -1334,16 +1334,16 @@
}
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{
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{
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"digest": {
@@ -1351,25 +1351,25 @@
}
},
{
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- "GeneratedBy": "urn:62e03cb0-08ac-4ca1-9da2-ddec7b358f8d",
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{
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"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:62e03cb0-08ac-4ca1-9da2-ddec7b358f8d",
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"digest": {
@@ -1377,16 +1377,16 @@
}
},
{
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- "GeneratedBy": "urn:824f0992-a9ac-41bc-adc9-0af7ddf3a550",
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@@ -1394,25 +1394,25 @@
}
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{
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"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
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}
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{
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"AtLocation": "rendered_thresh_zstat1.png",
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{
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"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1420,46 +1420,46 @@
}
},
{
- "@id": "urn:df2b2d64-5c23-4874-ac1f-c16898f176c1",
+ "@id": "urn:a73f4c88-b010-423c-a66f-891d32b30cc8",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:6fd69f94-a903-4b36-8c44-b3836dc86b5e",
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}
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{
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"Label": "rendered_thresh_zfstat1",
"AtLocation": "rendered_thresh_zfstat1",
- "GeneratedBy": "urn:9709374e-08e8-47ef-a9cb-97210fd1eace",
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}
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{
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+ "@id": "urn:1b5ca7ef-1b1c-417d-9180-6a48d5f2fcb6",
"Label": "rendered_thresh_zfstat1.png",
"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:bf8771f2-a6ca-4308-a241-70cae05127e9",
+ "GeneratedBy": "urn:7b8a0aed-a199-45c6-9984-691a3b9342b0",
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}
},
{
- "@id": "urn:768b07e6-4c61-4e15-be15-27eb66dc108a",
+ "@id": "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:90bf0411-4781-4d6a-8402-b213e171d6a0",
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{
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+ "@id": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:0b19922d-9343-4d11-af8f-23b968d3fe61",
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diff --git a/examples/from_parsers/fsl/fsl_con_f_report_log.png b/examples/from_parsers/fsl/fsl_con_f_report_log.png
index 1fb484ecb..904373469 100644
Binary files a/examples/from_parsers/fsl/fsl_con_f_report_log.png and b/examples/from_parsers/fsl/fsl_con_f_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
index 085adf954..925107bbe 100644
--- a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "@id": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,688 +13,688 @@
],
"Activities": [
{
- "@id": "urn:2535402f-72cd-4bfd-89de-7e06823f466c",
+ "@id": "urn:b30a0c58-4263-4d7f-be30-876f71d4d2d0",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
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"Used": [
- "urn:0e6510cb-25ea-4024-9d79-6f39922fecd0"
+ "urn:717e6e9d-b97e-467c-aab3-ae4f15459b31"
]
},
{
- "@id": "urn:aae6b639-27bb-41b0-8cff-5b0f280e5ede",
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"Label": "fslroi",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:19ae0996-972d-4935-aa1d-00a3c81c8532"
+ "urn:d27d94c1-784a-4d97-94ff-b674103f64e8"
]
},
{
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+ "@id": "urn:92706503-83a5-42fd-b68e-7dba8a30c693",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
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- "urn:a7caba33-8e03-4df1-99c4-144388c1051a"
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]
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"Label": "Make directory",
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+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
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"Label": "epi_reg",
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"Label": "pngappend",
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- "urn:919b203e-22f8-4529-8a7c-0fd91cd96f88",
- "urn:a48732b4-acbc-4106-a1f7-459dcca22dd6",
- "urn:b92c80cd-35e5-4ed5-936a-1ec1f0154003",
- "urn:ba25215a-afad-45cb-8cb6-d4877a6c890e",
- "urn:bfecc9ae-1ef2-40a5-941a-89224c16e5b8",
- "urn:c5185326-5632-487d-9bad-382da355c44c",
- "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2",
- "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329",
- "urn:ff77f2b9-2a9c-4ab1-aa4a-2d6dbd63d7ad"
+ "urn:1807e023-7810-4c8a-ba7e-62ac784fe919",
+ "urn:312d6e00-b598-48e6-a211-aa787cc0f427",
+ "urn:34578183-176c-415f-b749-50fa24842adb",
+ "urn:5cef23cf-7cd9-4210-990e-6e91f48dbd73",
+ "urn:7acc757f-48c5-4675-a39b-3733beca8099",
+ "urn:98e35494-b413-4218-b09a-4736ca2f5580",
+ "urn:ab106e53-c496-4951-ad6d-145f6d4d938a",
+ "urn:aca5ea51-558c-4d26-b3e4-687a77410260",
+ "urn:b87ce270-a7b7-4db0-b9ea-1be043aad9f5",
+ "urn:ba3146d8-e52f-45f1-a1a4-a2af80050930",
+ "urn:c4baf3df-0ef1-46a1-837c-11aa62fc7a4e",
+ "urn:ed9cf935-b21a-42ec-a454-ee7dd58818f4"
]
},
{
- "@id": "urn:0de59090-a792-4965-b076-2ca69af34713",
+ "@id": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9",
"Label": "slicer",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:69086f35-26e1-4854-a167-a3329fe52c8b",
- "urn:d2c7cb89-4ee1-4f92-bda2-ed418db17cd5"
+ "urn:70f2b950-1da8-47bd-9a74-7baa69660fbe",
+ "urn:9b7413de-84c5-4192-89bf-80266e1ab5ee"
]
},
{
- "@id": "urn:cc487d82-3708-49ac-acd2-0bdbc3427711",
+ "@id": "urn:869adb8d-9320-4314-abe1-6b6d044a5c59",
"Label": "pngappend",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:05a732ed-44d0-4002-98ac-cec09f8f0b8d",
- "urn:28408038-4814-4994-93eb-6ec6c5e5217b",
- "urn:67d4bff9-65dc-4160-b555-72d89dbb6005",
- "urn:919b203e-22f8-4529-8a7c-0fd91cd96f88",
- "urn:a48732b4-acbc-4106-a1f7-459dcca22dd6",
- "urn:b92c80cd-35e5-4ed5-936a-1ec1f0154003",
- "urn:ba25215a-afad-45cb-8cb6-d4877a6c890e",
- "urn:bfecc9ae-1ef2-40a5-941a-89224c16e5b8",
- "urn:c5185326-5632-487d-9bad-382da355c44c",
- "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2",
- "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329",
- "urn:ff77f2b9-2a9c-4ab1-aa4a-2d6dbd63d7ad"
+ "urn:1807e023-7810-4c8a-ba7e-62ac784fe919",
+ "urn:312d6e00-b598-48e6-a211-aa787cc0f427",
+ "urn:34578183-176c-415f-b749-50fa24842adb",
+ "urn:5cef23cf-7cd9-4210-990e-6e91f48dbd73",
+ "urn:7acc757f-48c5-4675-a39b-3733beca8099",
+ "urn:98e35494-b413-4218-b09a-4736ca2f5580",
+ "urn:ab106e53-c496-4951-ad6d-145f6d4d938a",
+ "urn:aca5ea51-558c-4d26-b3e4-687a77410260",
+ "urn:b87ce270-a7b7-4db0-b9ea-1be043aad9f5",
+ "urn:ba3146d8-e52f-45f1-a1a4-a2af80050930",
+ "urn:c4baf3df-0ef1-46a1-837c-11aa62fc7a4e",
+ "urn:ed9cf935-b21a-42ec-a454-ee7dd58818f4"
]
},
{
- "@id": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "@id": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
"Label": "pngappend",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:75834617-a647-4b05-a66f-eed728dab266",
- "urn:b75866fd-6330-46da-ace3-0f92ce0575fe"
+ "urn:54127544-1b9f-4572-8ddf-9901871049e4",
+ "urn:74ad9995-210a-4a09-96c1-021ac291fc78"
]
},
{
- "@id": "urn:5150ea63-253e-4632-8e1c-e6d6f66d3f9b",
+ "@id": "urn:0708ea50-1d83-48c9-be2e-3871dfeb2b0a",
"Label": "rm",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:75834617-a647-4b05-a66f-eed728dab266",
- "urn:e2af0880-2a04-4a00-96a3-c41d53591247"
+ "urn:74ad9995-210a-4a09-96c1-021ac291fc78",
+ "urn:c3f9594d-ed7f-4c6d-b18c-c38b41dafd7f"
]
},
{
- "@id": "urn:c12def47-7729-4f52-94a9-db975e35d749",
+ "@id": "urn:842c7ba0-0064-4d8d-8f99-6361ff2599d4",
"Label": "rm",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:b75866fd-6330-46da-ace3-0f92ce0575fe"
+ "urn:54127544-1b9f-4572-8ddf-9901871049e4"
]
},
{
- "@id": "urn:65fc8f58-1648-4e1c-9bbc-86b738e26f72",
+ "@id": "urn:7977ef19-0ce9-4505-9a7b-b235b81e2024",
"Label": "mcflirt",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:19ae0996-972d-4935-aa1d-00a3c81c8532"
+ "urn:d27d94c1-784a-4d97-94ff-b674103f64e8"
]
},
{
- "@id": "urn:5cc39977-3988-4a79-94ae-15acef78badd",
+ "@id": "urn:5c7cbc9b-48c8-44b8-8f20-4487d457e76b",
"Label": "Make directory",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:811288a2-49a2-4a25-a88d-b9428fcb266e",
+ "@id": "urn:ac43406f-3117-41a6-b7af-c087a2a0ab63",
"Label": "mv",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:2b88e9cd-f0ae-44d5-b8f5-aac0f7d43b5b",
- "urn:2d3597e6-3bc3-4588-ad30-2b66d5d8c409",
- "urn:4110db24-024a-4682-b347-ed6128ea0917",
- "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c",
- "urn:f4a25276-5185-4794-a1d8-5096e20c0aa4",
- "urn:f5d7521b-b160-4096-8ba1-a7560ca00126"
+ "urn:03dc0426-616f-474d-baa7-d076a27da8f9",
+ "urn:3ebb9f9c-0f46-4208-9d6b-8e296d89ad87",
+ "urn:6aaedc63-f21c-4f7b-81ae-55afae124789",
+ "urn:768bdff7-fc79-48ed-b4be-76ffa67c22a7",
+ "urn:bfcf713f-14cd-4468-8f5c-7cf48df3c5b4",
+ "urn:ffee68b2-1ae4-4e18-b7c4-8b3ea7e3669d"
]
},
{
- "@id": "urn:4b629c6e-ec58-44b8-bf63-76521ab37ad1",
+ "@id": "urn:682174ce-71d8-497c-a179-f0b800788bb7",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c"
+ "urn:6aaedc63-f21c-4f7b-81ae-55afae124789"
]
},
{
- "@id": "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c",
+ "@id": "urn:5fc905ed-edca-44b6-ae43-65c143fb6ce5",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:b0246264-c0ee-4a84-afb9-bff6a8ca208c"
+ "urn:6aaedc63-f21c-4f7b-81ae-55afae124789"
]
},
{
- "@id": "urn:9ad2b4b3-af7c-4e12-aaff-39f1e5dd7553",
+ "@id": "urn:77da241f-f67f-473f-b2ba-3e092fcb2693",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:3c565e3e-f7b2-4c8c-82c7-06c46a42c8a9"
+ "urn:38ea2ea2-f085-4e72-9a11-8b81a426d4da"
]
},
{
- "@id": "urn:6ea2ff65-dfd0-42ff-ad83-bde0185582ab",
+ "@id": "urn:69ff2bf5-eb0b-4ec3-b409-c7915a8763fd",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5"
+ "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
]
},
{
- "@id": "urn:869b5598-910e-461c-8ce4-0a128e36966b",
+ "@id": "urn:57727fd5-7503-4003-9938-26f02c545627",
"Label": "bet2",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:7e86c053-51ee-4584-8815-4172d57aba3b"
+ "urn:1dbc03de-284a-4cbb-834e-9ec6a25791a0"
]
},
{
- "@id": "urn:d2a1f2c6-2d34-4efb-ac64-79df521d2eb9",
+ "@id": "urn:ea284690-ee72-45dd-9e8d-4c28ba50d808",
"Label": "immv",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:fa49893e-f5f8-4125-a711-ab61e8b086ad"
+ "urn:9c3526b4-b784-4300-968c-fc5b10e380a8"
]
},
{
- "@id": "urn:85977f2f-13db-440b-870c-874941174d02",
+ "@id": "urn:d5916783-9b2c-4299-b00f-0c402f2b5de0",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665",
- "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
]
},
{
- "@id": "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
+ "@id": "urn:c00db8db-eb32-474f-9295-5d4577ab7c7d",
"Label": "fslstats",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:749935d9-e8c4-461b-821b-65c0dc026333"
+ "urn:9365d298-c58e-4d85-89eb-b035a0a2db37"
]
},
{
- "@id": "urn:6a5caeb8-337c-469c-8880-3f3cf4ec8db4",
+ "@id": "urn:b1993396-80d7-421e-9034-9c4e853fc3af",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:749935d9-e8c4-461b-821b-65c0dc026333"
+ "urn:9365d298-c58e-4d85-89eb-b035a0a2db37"
]
},
{
- "@id": "urn:4016ae63-3771-450d-8fcf-47420bed83fa",
+ "@id": "urn:73c58698-91b1-4c9c-acbe-4e8dfa0baf93",
"Label": "fslstats",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5"
+ "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
]
},
{
- "@id": "urn:39568419-2c2e-4da0-8197-ccd1295f5f91",
+ "@id": "urn:9c0f6952-8770-4a4e-b180-052debb7b271",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819"
]
},
{
- "@id": "urn:fb111b45-6a50-416e-9ebc-47853b4ae1e8",
+ "@id": "urn:c3352e3a-ea37-483e-b2b1-280dca36a952",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
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- "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "urn:c2684b63-598f-4f5e-b259-31d0868f9fbd"
]
},
{
- "@id": "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
+ "@id": "urn:91fa6de6-3f29-454c-844f-7ac0acea8093",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8"
+ "urn:4c2f5457-5e29-4350-a2e1-dac8ecfa35c9"
]
},
{
- "@id": "urn:35156813-da64-4e25-a9be-f174a0d4fe62",
+ "@id": "urn:3dea5b32-a6d3-4561-93c2-9c2bd9440596",
"Label": "susan",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8"
+ "urn:4c2f5457-5e29-4350-a2e1-dac8ecfa35c9"
]
},
{
- "@id": "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20",
+ "@id": "urn:c942e5a2-3cba-4471-9a8d-83cfb7806b93",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4",
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665"
+ "urn:7bcd13f8-15cf-4d96-ad31-3adc7d5d4ac5",
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819"
]
},
{
- "@id": "urn:a4f27e7d-029b-48ed-b095-09e6c129877d",
+ "@id": "urn:42fd9295-622f-45a3-989a-5d0236370afe",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4"
+ "urn:7bcd13f8-15cf-4d96-ad31-3adc7d5d4ac5"
]
},
{
- "@id": "urn:7e77794f-c84b-4ec9-8330-ff8e325e3c25",
+ "@id": "urn:0ff95592-e05d-4465-84d2-4755ce6e3121",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:86a3d035-808a-4af8-a397-5761b4ce25b2"
+ "urn:a7f4c949-e33a-47c0-936e-17a33bbe797b"
]
},
{
- "@id": "urn:62e3812e-a3e8-4836-8119-a98496a70101",
+ "@id": "urn:8c8d4609-f20f-49da-ac41-b1fdfab6067c",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:7921758c-6274-495a-9ddb-602ba1b1b33d",
- "urn:86a3d035-808a-4af8-a397-5761b4ce25b2"
+ "urn:3db3351e-810d-4ab8-beca-d7de5a696f13",
+ "urn:a7f4c949-e33a-47c0-936e-17a33bbe797b"
]
},
{
- "@id": "urn:2d69372f-2ec8-4e73-8214-ca95009895aa",
+ "@id": "urn:223988f1-fdfc-4dfa-b192-f52e6e3df12f",
"Label": "imrm",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:7921758c-6274-495a-9ddb-602ba1b1b33d"
+ "urn:3db3351e-810d-4ab8-beca-d7de5a696f13"
]
},
{
- "@id": "urn:6a63c416-cfed-47a4-8f47-eea9d7eb01dd",
+ "@id": "urn:b7d85a37-7161-4b8b-8d00-a9248190fda3",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:23e90369-5cf2-465e-a4b0-c4ac55508925"
+ "urn:2b0afdd2-8abd-4f81-8748-cecd12c9987f"
]
},
{
- "@id": "urn:dad480ac-f312-4758-89c9-2c6765d6393a",
+ "@id": "urn:c122b76b-49dd-4080-9464-c17425a84159",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca"
+ "urn:90f4ce46-a2df-4096-90c7-3df6f3bed73f"
]
},
{
- "@id": "urn:0657b059-0285-4d8a-8fae-2fb268511c34",
+ "@id": "urn:a53f3efb-78d9-4ff0-b2c3-4ac3e36ff6ef",
"Label": "rm",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:bed01f22-b1b7-4c60-939d-4caa877b5cf6"
+ "urn:18a72054-7748-48b3-915b-e2258a624a59"
]
},
{
- "@id": "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
+ "@id": "urn:33f294ce-d765-47e4-b535-f1020bad14d8",
"Label": "Make directory",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:4db91689-fc53-437a-a4d4-465f1df3c016",
+ "@id": "urn:2a627ccb-2b5e-4427-8fef-388a1db6a555",
"Label": "fslFixText",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:ff211113-f43c-49ad-acba-57fd339badeb"
+ "urn:487c72a9-6acb-41f0-b6c3-b7ab2043a5b4"
]
},
{
- "@id": "urn:2e82d6a1-9e2a-446b-b508-0e5df37dbdfb",
+ "@id": "urn:7a17faa4-3ab2-4c80-9222-973582ab9023",
"Label": "Make directory",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:d13633e4-0e1f-4847-aa4b-872c2aaee8dc",
+ "@id": "urn:d7d53e37-2e1e-421a-bf26-c23e78eac0fe",
"Label": "fslFixText",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:49eefed4-4311-4ede-80a1-8ed5501adc77"
+ "urn:ce8b87ba-2004-4ada-a824-b801b408e7dd"
]
},
{
- "@id": "urn:32e9944d-72b1-4e01-8c59-14a8ffb09a0f",
+ "@id": "urn:14296cb6-f8ed-4556-a51f-d2fbc11b01b7",
"Label": "film_gls",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
- "@id": "urn:fd74433b-972f-43cf-a1b4-dfc0eda30f74",
+ "@id": "urn:f92855c4-a077-4204-9bfc-18f441b7ad0d",
"Label": "smoothest",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:3c3330f9-e4c8-4073-b802-98d8d99c58e4",
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "urn:ee1865c2-68cc-4fd3-8767-5b9488363617"
]
},
{
- "@id": "urn:2fc29d78-7b54-4548-b14f-ab9bc8df945d",
+ "@id": "urn:e4b557f4-93fa-4d8c-8650-78fd658a67b5",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "urn:9f4bb0cf-d032-467e-ba07-b8a64af8e023"
]
},
{
- "@id": "urn:f599026a-b8c6-4a3a-84ec-c35bfb1b8d22",
+ "@id": "urn:d01f6cb7-895c-4263-9c4f-66641a6521d4",
"Label": "echo",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:a86c86a4-3f9b-4369-8af5-f4c00a630aa8",
+ "@id": "urn:6bf1c686-4bf2-4b26-8333-472d5735d202",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665",
- "urn:d3dcadd3-c0fd-43b7-bcc1-dd468be525fd"
+ "urn:835ac5af-9eea-4ef7-9bdc-ea0fa543a819",
+ "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78"
]
},
{
- "@id": "urn:554ce204-f078-481e-a639-ef2963c04838",
+ "@id": "urn:8f10d30f-de71-4768-a788-1ab96c863c20",
"Label": "echo",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:0ba6cdcc-8a3d-4d06-b346-1e6354434c52",
+ "@id": "urn:696bea66-9b1b-47a7-9d50-4fc276f012d7",
"Label": "ptoz",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:53901983-6ef5-4277-8aab-db76acd0368b",
+ "@id": "urn:38c05196-6be2-4e4e-a4f1-0ec7328be2dd",
"Label": "cluster",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:6eedb142-3682-4af6-8349-57f2966acfc8",
- "urn:798b2a2d-2a07-4e9f-8617-e8c0b625ab40"
+ "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
+ "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f"
]
},
{
- "@id": "urn:1eeee773-a0f8-46a9-a05c-64cd0ada78df",
+ "@id": "urn:b8097281-e20e-4997-a059-1965f255d018",
"Label": "cluster2html",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:53c5588d-218d-4c33-abee-1c225e695bbf"
+ "urn:94c531f1-e0a2-45a2-955c-3c5e0fc00c59"
]
},
{
- "@id": "urn:1da9dbfa-c3ce-4e04-bd20-9f529928201b",
+ "@id": "urn:b64e7dcb-f9fd-480c-b8d1-f72de36ef22a",
"Label": "ptoz",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:f92ff9b2-56a1-4b1a-b115-f1c87cfd741f",
+ "@id": "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8",
"Label": "cluster",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:87cc6247-bc0d-422b-8b7e-d96348b86c74",
- "urn:9cbbee48-65ca-4a99-9a9d-1a91678dc392"
+ "urn:3fd0f707-15fa-407a-9224-edfda6528cb1",
+ "urn:7ec5b7a4-7374-4686-b27c-81a58c3b3e98"
]
},
{
- "@id": "urn:5bad2097-52c6-41d1-87eb-7b2041df9627",
+ "@id": "urn:4f7fe1b2-ce65-4d83-98cd-a2992b80e685",
"Label": "cluster2html",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:1f3989e8-ea60-4cbc-9444-3a3b6e170b93"
+ "urn:1f446a54-dba5-425b-95ef-552dba8677b7"
]
},
{
- "@id": "urn:750ac308-6b79-4101-84ee-eb728049f005",
+ "@id": "urn:951b9cd2-26a6-42d7-8125-f162f3a38fee",
"Label": "Make directory",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "mkdir -p conmask",
"Used": []
},
{
- "@id": "urn:dff39876-ad27-4e98-8d9a-30be0fc479ef",
+ "@id": "urn:b8d7c546-8d76-4977-902e-54a5f98165f9",
"Label": "fslmaths",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths thresh_zstat1 -mas thresh_zstat2 conmask/thresh_zstat1",
"Used": [
- "urn:6eedb142-3682-4af6-8349-57f2966acfc8",
- "urn:9cbbee48-65ca-4a99-9a9d-1a91678dc392"
+ "urn:7ec5b7a4-7374-4686-b27c-81a58c3b3e98",
+ "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f"
]
},
{
- "@id": "urn:07f41d41-3ca8-4a79-942b-64ea67ee5549",
+ "@id": "urn:ed8e6d73-f02f-417f-86a2-619df64156ac",
"Label": "mv",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/bin/mv -f conmask/* .",
"Used": [
- "urn:a49716a7-0b9c-4f99-8d39-e86d9e708e16"
+ "urn:5b10beae-c90a-4bd3-801e-3bba870ee006"
]
},
{
- "@id": "urn:f48d0ca0-9a14-4be3-90fd-991b09fcf53a",
+ "@id": "urn:d2b88a58-b171-48dd-9b24-909c0df5133d",
"Label": "rmdir",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "rmdir conmask",
"Used": [
- "urn:44ef785d-33ad-462c-8cbf-cde5037a61e5"
+ "urn:9aad2ff0-103d-4539-a7e1-72733b6c8cef"
]
},
{
- "@id": "urn:adabfb46-4b41-4613-aef9-b498df5e5fd6",
+ "@id": "urn:9a03f285-dfcd-410d-bb99-8b0ebbe3ef20",
"Label": "ptoz",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:ab1d786e-77c3-4a9b-8038-0202a1531374",
+ "@id": "urn:cda76e9d-1eab-41a7-bee3-e5b36b858062",
"Label": "cluster",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
+ "AssociatedWith": "urn:fe757dd9-4588-4498-813e-a29905e30b56",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
"Used": [
- "urn:6eedb142-3682-4af6-8349-57f2966acfc8",
- "urn:798b2a2d-2a07-4e9f-8617-e8c0b625ab40"
+ "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
+ "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f"
]
},
{
- "@id": "urn:e176cdc5-3382-40d6-a1af-d703e1ebf257",
+ "@id": "urn:85d40ec9-6104-4d35-a712-f30b1e91c0bc",
"Label": "cluster2html",
- "AssociatedWith": "urn:7cfe2168-dbba-4477-b70f-3defaf2c32de",
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},
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@@ -702,25 +702,25 @@
}
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@@ -728,7 +728,7 @@
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@@ -736,7 +736,7 @@
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@@ -776,13 +776,13 @@
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@@ -790,16 +790,16 @@
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@@ -807,250 +807,250 @@
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{
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"AtLocation": "example_func2highres1.png",
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{
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"AtLocation": "slb.png",
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{
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"AtLocation": "slc.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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{
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"AtLocation": "sld.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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{
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{
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"AtLocation": "slf.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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{
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"AtLocation": "slg.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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{
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- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
+ "GeneratedBy": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9",
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{
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"AtLocation": "slj.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
+ "GeneratedBy": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9",
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{
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"AtLocation": "slk.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
+ "GeneratedBy": "urn:bd299897-9eaf-4062-a392-2c4c2e29f7a9",
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{
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"AtLocation": "sll.png",
- "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
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{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:cc487d82-3708-49ac-acd2-0bdbc3427711",
+ "GeneratedBy": "urn:869adb8d-9320-4314-abe1-6b6d044a5c59",
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{
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "GeneratedBy": "urn:881e6701-d5f6-4e1d-8b08-b0f422bfc7f7",
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{
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"AtLocation": "sl?.png",
"digest": {
@@ -1058,25 +1058,25 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:65fc8f58-1648-4e1c-9bbc-86b738e26f72",
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{
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"AtLocation": "mc",
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+ "GeneratedBy": "urn:5c7cbc9b-48c8-44b8-8f20-4487d457e76b",
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{
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"AtLocation": "prefiltered_func_data_mcf.mat",
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@@ -1084,7 +1084,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1092,7 +1092,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1100,7 +1100,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
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@@ -1108,7 +1108,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_rel.rms",
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@@ -1116,7 +1116,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1124,34 +1124,34 @@
}
},
{
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"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:811288a2-49a2-4a25-a88d-b9428fcb266e",
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{
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- "GeneratedBy": "urn:4b629c6e-ec58-44b8-bf63-76521ab37ad1",
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{
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- "GeneratedBy": "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c",
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{
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@@ -1159,34 +1159,34 @@
}
},
{
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- "GeneratedBy": "urn:9ad2b4b3-af7c-4e12-aaff-39f1e5dd7553",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:6ea2ff65-dfd0-42ff-ad83-bde0185582ab",
+ "GeneratedBy": "urn:69ff2bf5-eb0b-4ec3-b409-c7915a8763fd",
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{
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- "GeneratedBy": "urn:869b5598-910e-461c-8ce4-0a128e36966b",
+ "GeneratedBy": "urn:57727fd5-7503-4003-9938-26f02c545627",
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{
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"digest": {
@@ -1194,106 +1194,106 @@
}
},
{
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- "GeneratedBy": "urn:d2a1f2c6-2d34-4efb-ac64-79df521d2eb9",
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{
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:85977f2f-13db-440b-870c-874941174d02",
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{
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{
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{
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"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:fb111b45-6a50-416e-9ebc-47853b4ae1e8",
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{
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"AtLocation": "mean_func",
- "GeneratedBy": "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
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{
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"AtLocation": "prefiltered_func_data_smooth",
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- "@id": "urn:21d8d15a-17bd-4d18-9034-2ae2bdba5013",
+ "@id": "urn:46953106-4e01-4407-a4a6-3f757a89965b",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20",
+ "GeneratedBy": "urn:c942e5a2-3cba-4471-9a8d-83cfb7806b93",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:86a3d035-808a-4af8-a397-5761b4ce25b2",
+ "@id": "urn:a7f4c949-e33a-47c0-936e-17a33bbe797b",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:a4f27e7d-029b-48ed-b095-09e6c129877d",
+ "GeneratedBy": "urn:42fd9295-622f-45a3-989a-5d0236370afe",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:7921758c-6274-495a-9ddb-602ba1b1b33d",
+ "@id": "urn:3db3351e-810d-4ab8-beca-d7de5a696f13",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:7e77794f-c84b-4ec9-8330-ff8e325e3c25",
+ "GeneratedBy": "urn:0ff95592-e05d-4465-84d2-4755ce6e3121",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:8e7762a4-60d2-4b68-a52a-b1cdecaa5a5b",
+ "@id": "urn:5bed2526-c418-4531-8f5c-210a4c2044b2",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:62e3812e-a3e8-4836-8119-a98496a70101",
+ "GeneratedBy": "urn:8c8d4609-f20f-49da-ac41-b1fdfab6067c",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:23e90369-5cf2-465e-a4b0-c4ac55508925",
+ "@id": "urn:2b0afdd2-8abd-4f81-8748-cecd12c9987f",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1301,25 +1301,25 @@
}
},
{
- "@id": "urn:ae14ed40-d28f-491f-ad7f-f9364a2daeca",
+ "@id": "urn:90f4ce46-a2df-4096-90c7-3df6f3bed73f",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:6a63c416-cfed-47a4-8f47-eea9d7eb01dd",
+ "GeneratedBy": "urn:b7d85a37-7161-4b8b-8d00-a9248190fda3",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:c5da5c16-852c-4a75-a6e6-f70fcc9bc766",
+ "@id": "urn:cd65ffe8-9cc1-4916-a8ec-12d359d7c0ad",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:dad480ac-f312-4758-89c9-2c6765d6393a",
+ "GeneratedBy": "urn:c122b76b-49dd-4080-9464-c17425a84159",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:bed01f22-b1b7-4c60-939d-4caa877b5cf6",
+ "@id": "urn:18a72054-7748-48b3-915b-e2258a624a59",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1327,16 +1327,16 @@
}
},
{
- "@id": "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
+ "@id": "urn:ab6f0993-5b04-419b-b373-e7d235e9e740",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
+ "GeneratedBy": "urn:33f294ce-d765-47e4-b535-f1020bad14d8",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:ff211113-f43c-49ad-acba-57fd339badeb",
+ "@id": "urn:487c72a9-6acb-41f0-b6c3-b7ab2043a5b4",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1344,22 +1344,22 @@
}
},
{
- "@id": "urn:7ccada4d-6e81-49f3-83c6-d266594f0c20",
+ "@id": "urn:f0832953-3f73-48a7-8fe2-1b48270b2cd4",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:4db91689-fc53-437a-a4d4-465f1df3c016"
+ "GeneratedBy": "urn:2a627ccb-2b5e-4427-8fef-388a1db6a555"
},
{
- "@id": "urn:c3457a35-c5f9-45de-931c-89a71bb169f0",
+ "@id": "urn:744a70cd-015b-4826-9ba4-98cdeb78c2f7",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:2e82d6a1-9e2a-446b-b508-0e5df37dbdfb",
+ "GeneratedBy": "urn:7a17faa4-3ab2-4c80-9222-973582ab9023",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:49eefed4-4311-4ede-80a1-8ed5501adc77",
+ "@id": "urn:ce8b87ba-2004-4ada-a824-b801b408e7dd",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1367,13 +1367,13 @@
}
},
{
- "@id": "urn:9c331ad8-b671-4cd6-9d35-d2c9da897c4b",
+ "@id": "urn:c096c03f-c432-46db-905d-5012d624a850",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:d13633e4-0e1f-4847-aa4b-872c2aaee8dc"
+ "GeneratedBy": "urn:d7d53e37-2e1e-421a-bf26-c23e78eac0fe"
},
{
- "@id": "urn:3c3330f9-e4c8-4073-b802-98d8d99c58e4",
+ "@id": "urn:ee1865c2-68cc-4fd3-8767-5b9488363617",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1381,16 +1381,16 @@
}
},
{
- "@id": "urn:fdc26ec5-1cc2-4ccd-b9a1-399b018d25cc",
+ "@id": "urn:1d965db1-c424-4236-9d86-cd4a7939aad7",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:fd74433b-972f-43cf-a1b4-dfc0eda30f74",
+ "GeneratedBy": "urn:f92855c4-a077-4204-9bfc-18f441b7ad0d",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
+ "@id": "urn:9f4bb0cf-d032-467e-ba07-b8a64af8e023",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1398,16 +1398,16 @@
}
},
{
- "@id": "urn:6eedb142-3682-4af6-8349-57f2966acfc8",
+ "@id": "urn:ccc86f3b-621d-42b8-9fa0-b8df15f2fc1f",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:2fc29d78-7b54-4548-b14f-ab9bc8df945d",
+ "GeneratedBy": "urn:e4b557f4-93fa-4d8c-8650-78fd658a67b5",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:d3dcadd3-c0fd-43b7-bcc1-dd468be525fd",
+ "@id": "urn:a1ae76b6-98c6-405b-aadb-5898c973ad78",
"Label": "zstat2",
"AtLocation": "stats/zstat2",
"digest": {
@@ -1415,16 +1415,16 @@
}
},
{
- "@id": "urn:9cbbee48-65ca-4a99-9a9d-1a91678dc392",
+ "@id": "urn:7ec5b7a4-7374-4686-b27c-81a58c3b3e98",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:a86c86a4-3f9b-4369-8af5-f4c00a630aa8",
+ "GeneratedBy": "urn:6bf1c686-4bf2-4b26-8333-472d5735d202",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:798b2a2d-2a07-4e9f-8617-e8c0b625ab40",
+ "@id": "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1432,25 +1432,25 @@
}
},
{
- "@id": "urn:bb9634f9-be32-4008-9ba3-ffea4e168cba",
+ "@id": "urn:e4549dc8-e7dc-4d2d-a4fc-5aef29e6af69",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:53901983-6ef5-4277-8aab-db76acd0368b",
+ "GeneratedBy": "urn:38c05196-6be2-4e4e-a4f1-0ec7328be2dd",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:3a82b429-cfef-4b92-af9f-7d68efd3692d",
+ "@id": "urn:dda7883b-7b5a-4449-bac3-ffcbe0ef3bf2",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:53901983-6ef5-4277-8aab-db76acd0368b",
+ "GeneratedBy": "urn:38c05196-6be2-4e4e-a4f1-0ec7328be2dd",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:53c5588d-218d-4c33-abee-1c225e695bbf",
+ "@id": "urn:94c531f1-e0a2-45a2-955c-3c5e0fc00c59",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1458,7 +1458,7 @@
}
},
{
- "@id": "urn:87cc6247-bc0d-422b-8b7e-d96348b86c74",
+ "@id": "urn:3fd0f707-15fa-407a-9224-edfda6528cb1",
"Label": "cope2",
"AtLocation": "stats/cope2",
"digest": {
@@ -1466,25 +1466,25 @@
}
},
{
- "@id": "urn:1a04bdf8-5441-4f18-a241-1b3ecf3a0a09",
+ "@id": "urn:f7465d5c-46f7-490e-a5a2-08d59b567b0d",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:f92ff9b2-56a1-4b1a-b115-f1c87cfd741f",
+ "GeneratedBy": "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:fcd11beb-5c6d-48b9-ae12-6e40be7ec4e6",
+ "@id": "urn:33c0adb5-01c5-4303-a15c-09d7f72fe426",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:f92ff9b2-56a1-4b1a-b115-f1c87cfd741f",
+ "GeneratedBy": "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8",
"digest": {
"sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
}
},
{
- "@id": "urn:1f3989e8-ea60-4cbc-9444-3a3b6e170b93",
+ "@id": "urn:1f446a54-dba5-425b-95ef-552dba8677b7",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1492,87 +1492,87 @@
}
},
{
- "@id": "urn:44ef785d-33ad-462c-8cbf-cde5037a61e5",
+ "@id": "urn:9aad2ff0-103d-4539-a7e1-72733b6c8cef",
"Label": "conmask",
"AtLocation": "conmask",
- "GeneratedBy": "urn:750ac308-6b79-4101-84ee-eb728049f005",
+ "GeneratedBy": "urn:951b9cd2-26a6-42d7-8125-f162f3a38fee",
"digest": {
"sha256": "f555349cd698b294f93ff993006671506ca822960218ca0076bb984de8105368"
}
},
{
- "@id": "urn:28aa1a15-b895-4244-b676-5f4c7a10b638",
+ "@id": "urn:f4f108d9-ad44-4f62-bef2-0214e3e76d69",
"Label": "thresh_zstat1",
"AtLocation": "conmask/thresh_zstat1",
- "GeneratedBy": "urn:dff39876-ad27-4e98-8d9a-30be0fc479ef"
+ "GeneratedBy": "urn:b8d7c546-8d76-4977-902e-54a5f98165f9"
},
{
- "@id": "urn:a49716a7-0b9c-4f99-8d39-e86d9e708e16",
+ "@id": "urn:5b10beae-c90a-4bd3-801e-3bba870ee006",
"Label": "*",
"AtLocation": "conmask/*"
},
{
- "@id": "urn:6aaf2f10-d644-48e2-83c2-dfde7dc9ee02",
+ "@id": "urn:deab5f4e-3598-41de-a361-d573731a55b5",
"Label": ".",
"AtLocation": ".",
- "GeneratedBy": "urn:07f41d41-3ca8-4a79-942b-64ea67ee5549"
+ "GeneratedBy": "urn:ed8e6d73-f02f-417f-86a2-619df64156ac"
},
{
- "@id": "urn:c0623cbc-3022-46fa-a837-1ac4e08f23d6",
+ "@id": "urn:1a741297-35d4-4b05-886b-1d1e8c91bf2e",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:ab1d786e-77c3-4a9b-8038-0202a1531374",
+ "GeneratedBy": "urn:cda76e9d-1eab-41a7-bee3-e5b36b858062",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:c50f4c0e-829c-4018-8716-66b3a0398a8b",
+ "@id": "urn:b5ed0dcb-6f8b-4f0b-972e-0d08e249d112",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:ab1d786e-77c3-4a9b-8038-0202a1531374",
+ "GeneratedBy": "urn:cda76e9d-1eab-41a7-bee3-e5b36b858062",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:00bc09c4-e285-462f-b5df-8454180948a3",
+ "@id": "urn:99b48746-909d-452d-bf6b-24a0e1ebf9c5",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:7b9573eb-6f4b-428c-a624-a39ae72d7ba3",
+ "GeneratedBy": "urn:2e0e52f8-04a3-4102-b205-304afb4b5f2e",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:0c3feed0-413f-4eab-9696-66fca2ed9942",
+ "@id": "urn:b2fe76ce-e994-4c27-95fb-efa9e1b13e2a",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:7b9573eb-6f4b-428c-a624-a39ae72d7ba3",
+ "GeneratedBy": "urn:2e0e52f8-04a3-4102-b205-304afb4b5f2e",
"digest": {
"sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
}
},
{
- "@id": "urn:952cfaa3-f29a-4dbc-8c74-1a7ebdf25b15",
+ "@id": "urn:08f0a212-4e7f-4c0f-972e-7e64312cdf16",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:9e7ed5bc-3c0b-48bc-8ce5-59a7516f3758",
+ "GeneratedBy": "urn:795e07b1-1d9b-4dab-a710-0d6826630aca",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:ddc16ce1-81df-4141-b0a5-d37af7954d92",
+ "@id": "urn:83cb5338-7333-4019-a2bf-e413de151931",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:1f495cc0-2caf-4f57-9ea2-ab897f49ba3b",
+ "GeneratedBy": "urn:fdec7cf7-b051-44d5-a381-e3b0ebab89f3",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:6bfab610-89eb-4c16-ba6b-1b1b030f8292",
+ "@id": "urn:ca9d036e-8e6c-430a-9cdb-c8333b595eeb",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1580,46 +1580,46 @@
}
},
{
- "@id": "urn:c92d9e2c-6ecb-46aa-8a8f-10ad148eaee9",
+ "@id": "urn:3f4c9f31-a464-4c8c-8391-72d97a89b53c",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:4d55ae09-a747-4397-a177-d909c1abdec2",
+ "GeneratedBy": "urn:0fe8ebe4-db43-4829-83ac-469fc72abfdc",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:80f3d3b7-d1b6-4ea1-8cc5-9b5eaf2b067f",
+ "@id": "urn:b361905e-407f-4981-8e58-3208f23a069a",
"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:a649d3a2-43b7-49c1-a75c-fd246df97d53",
+ "GeneratedBy": "urn:127a38fe-34a4-4248-9396-9b5106b4bca0",
"digest": {
"sha256": "b988cb8ba2b862b6fa88f223fcd3279c70e2ea217477bd1ec664c023be079cad"
}
},
{
- "@id": "urn:0e527626-b2bd-4931-85eb-daf1ae844ea5",
+ "@id": "urn:fdfa03a0-afb7-4faf-ac92-c3820dcd9366",
"Label": "rendered_thresh_zstat2.png",
"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:361bb30a-f4e4-47bc-958d-75674d9c59a8",
+ "GeneratedBy": "urn:9ae838f4-3473-4c09-af74-fad420e11482",
"digest": {
"sha256": "0d60298d9eb509148075cbac8a22e6a95de919f17a069624fb42f86c29e1e199"
}
},
{
- "@id": "urn:8ad65810-e0b3-4254-8473-17ac44058252",
+ "@id": "urn:8ddecffb-ef11-4fc1-87c4-ab560a8c9f96",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:753c9b01-3b08-43d7-9a2a-55787d643953",
+ "GeneratedBy": "urn:ba57b40b-bdc1-4b20-baa6-a0a500e6d912",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7",
+ "@id": "urn:4495f152-217c-4c22-8568-7fa88bb8598d",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:52486c9c-cd8f-4e19-a5f5-4243aafa1285",
+ "GeneratedBy": "urn:b396ec48-bd2b-4ab4-9f0b-81683e0d3dbb",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png
index e8984f168..937bcf220 100644
Binary files a/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png and b/examples/from_parsers/fsl/fsl_contrast_mask_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.jsonld b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
index 885aefe13..5d973c20f 100644
--- a/examples/from_parsers/fsl/fsl_default_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_default_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "@id": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,540 +13,540 @@
],
"Activities": [
{
- "@id": "urn:8b7ebf9b-55a0-4a1d-b503-719151eebc50",
+ "@id": "urn:dd7dba6e-c651-4e36-82aa-19b93d86be8b",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:cc8f8d80-4f02-496d-9a4a-e0e2bfbe3189"
+ "urn:2bafc123-f535-4eb0-9d99-98ffd606e387"
]
},
{
- "@id": "urn:74cebf5a-7236-4402-8dc4-8d5936bcc43c",
+ "@id": "urn:a0e060d4-45b1-40c4-85c6-7e89e9ead411",
"Label": "fslroi",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:0924054c-0c39-4d36-b059-e742e85e493d"
+ "urn:9ac084f8-a2a9-4829-8788-56f98d0a15ac"
]
},
{
- "@id": "urn:e9a73030-0006-4ef8-95e3-5834de3078f3",
+ "@id": "urn:b2cf8224-5803-41f9-8444-1a022f60fda2",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
- "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01",
- "urn:fadd4862-4c4b-4a39-ba35-666f29181e2c"
+ "urn:2a0541ac-72b1-43f5-929b-fbbb9aae72ee",
+ "urn:5c5526d3-9ff7-428e-91db-935ee6ff422f",
+ "urn:68e68da7-bcca-452f-b6f2-f83c35290e9e"
]
},
{
- "@id": "urn:3e26d898-d64e-4301-8def-9765c710bcdf",
+ "@id": "urn:8ff96632-d4d4-4fff-9a73-a76e6a9c355e",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_voxelwise_p0001.feat/reg",
"Used": []
},
{
- "@id": "urn:1e662f78-13a4-474a-9645-9ee637aa9e4b",
+ "@id": "urn:926d02b6-a8ff-4d5b-b823-8b030b3526b2",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9"
+ "urn:68e68da7-bcca-452f-b6f2-f83c35290e9e"
]
},
{
- "@id": "urn:26a00968-1740-4b01-8330-41148ecff2f1",
+ "@id": "urn:1dc3fde5-282a-415a-bdae-7d2dbcda22f7",
"Label": "fslmaths",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:e9aec74c-9fea-437a-8d93-0ae9789f2d8a"
+ "urn:bcd3b45f-f612-4860-9677-33435a987f2d"
]
},
{
- "@id": "urn:42bc175e-636a-4d3f-8a84-ab0cec178f89",
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"Label": "epi_reg",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:cb078c97-7316-4480-a77e-abf7f6853c4e",
+ "@id": "urn:c8d4dbf8-7fd9-4758-a617-722459e3fa10",
"Label": "convert_xfm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:5f05c7a5-2284-4cdf-b443-eaacdd73c3dc"
+ "urn:a300eddf-c764-4425-9145-adeb4ae34f9e"
]
},
{
- "@id": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
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"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53"
+ "urn:3264d870-df93-44d9-b00d-1e80a6a58e24",
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]
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{
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+ "@id": "urn:2a58dcdd-eba2-4f92-bfc6-3b35b9284e38",
"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
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- "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e"
+ "urn:14f993bf-a7b7-4eb8-b904-564e770d919b",
+ "urn:351aa42f-fff6-4ad9-b528-7d19cf588dd6",
+ "urn:3bf09c53-a4f0-4561-b21b-40b1c6fceaae",
+ "urn:5cd4aaac-de35-4a6f-91b9-7698cb28da7e",
+ "urn:72ca6d99-b763-4a26-a7b5-27932336af26",
+ "urn:8811bbe0-dc52-4f36-854a-1115c78a7353",
+ "urn:a571a087-7a6a-4a92-bc68-41edb558da5c",
+ "urn:a9593a39-5119-468e-96b2-5047fbc8492a",
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+ "urn:ee6840ba-f606-4ad9-9e69-5ff2713e44b9",
+ "urn:eee94271-3a18-4576-818c-4513e34e6363",
+ "urn:f6d47919-1922-4bae-9e81-5647fe98c029"
]
},
{
- "@id": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "@id": "urn:f16cb397-77ab-427b-bd4e-8f8416d08687",
"Label": "slicer",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
- "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53"
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]
},
{
- "@id": "urn:fc548620-4d3b-4aaf-a4d6-39a1641f8bcb",
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"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
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- "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e"
+ "urn:14f993bf-a7b7-4eb8-b904-564e770d919b",
+ "urn:351aa42f-fff6-4ad9-b528-7d19cf588dd6",
+ "urn:3bf09c53-a4f0-4561-b21b-40b1c6fceaae",
+ "urn:5cd4aaac-de35-4a6f-91b9-7698cb28da7e",
+ "urn:72ca6d99-b763-4a26-a7b5-27932336af26",
+ "urn:8811bbe0-dc52-4f36-854a-1115c78a7353",
+ "urn:a571a087-7a6a-4a92-bc68-41edb558da5c",
+ "urn:a9593a39-5119-468e-96b2-5047fbc8492a",
+ "urn:b58a4b95-7e2c-42ca-8cf1-12c9a3e329fa",
+ "urn:ee6840ba-f606-4ad9-9e69-5ff2713e44b9",
+ "urn:eee94271-3a18-4576-818c-4513e34e6363",
+ "urn:f6d47919-1922-4bae-9e81-5647fe98c029"
]
},
{
- "@id": "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "@id": "urn:90bf0411-4781-4d6a-8402-b213e171d6a0",
"Label": "pngappend",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:9fbead39-7891-43e5-8dc9-12d985617f2c",
- "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4"
+ "urn:62e03cb0-08ac-4ca1-9da2-ddec7b358f8d",
+ "urn:b190365e-a81a-49de-8516-a4ec5f695a35"
]
},
{
- "@id": "urn:6b72f628-1ec4-4a98-ae8a-929cba33bab5",
+ "@id": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
"Label": "rm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:9fbead39-7891-43e5-8dc9-12d985617f2c",
- "urn:ea755f41-a00d-4582-be8c-86b8d98cf377"
+ "urn:b190365e-a81a-49de-8516-a4ec5f695a35",
+ "urn:c4b41eb0-6e4c-466e-907d-9ae326422bdb"
]
},
{
- "@id": "urn:84e58995-014d-4089-bad8-578e23399b07",
+ "@id": "urn:cd76fc5a-b376-4723-bac8-111eaaa24083",
"Label": "rm",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4"
+ "urn:62e03cb0-08ac-4ca1-9da2-ddec7b358f8d"
]
},
{
- "@id": "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "@id": "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
"Label": "mcflirt",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:0924054c-0c39-4d36-b059-e742e85e493d"
+ "urn:9ac084f8-a2a9-4829-8788-56f98d0a15ac"
]
},
{
- "@id": "urn:7556cc7a-14ba-46ba-a8f2-ba3d98f37993",
+ "@id": "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
"Label": "Make directory",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:5dc549f4-647c-486e-8759-782021b9509f",
+ "@id": "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
"Label": "mv",
- "AssociatedWith": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:1de485b9-a047-4a69-b2bf-8d71b7de8903",
- "urn:470281e3-3e60-4466-ae7f-99338ead202e",
- "urn:5a7b2004-f5c6-4f5b-ace8-adb7207782e0",
- "urn:5d2b1b83-5fd8-4230-8e74-13743ba69bb6",
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]
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]
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]
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"Label": "fsl_tsplot",
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"Label": "bet2",
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"Label": "immv",
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"Label": "fslmaths",
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- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
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]
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"Label": "fslstats",
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]
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
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]
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"Label": "fslstats",
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]
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{
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"Label": "fslmaths",
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]
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{
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"Label": "fslmaths",
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- "urn:c00ec312-9c80-4217-b67b-1cf38581bceb"
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]
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{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
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]
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"Label": "susan",
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]
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{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:a08509a8-7e5c-425e-b284-91fba26756e9"
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"Label": "fslmaths",
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]
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
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]
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"Label": "fslmaths",
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- "urn:839d773c-d1ea-428c-980b-5c45cbd39a55"
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]
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{
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"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
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]
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{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
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]
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"Label": "fslmaths",
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+ "urn:beae7e86-fb11-4df3-84b4-4666debc7e5f"
]
},
{
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"Label": "rm",
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+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/bin/rm -rf prefiltered_func_data*",
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]
},
{
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"Label": "Make directory",
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+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Label": "fslFixText",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
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]
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{
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"Label": "Make directory",
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"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Label": "fslFixText",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
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+ "urn:a96a152e-7be7-475f-9d8a-a44d41b5a899"
]
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{
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"Label": "film_gls",
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"Used": []
},
{
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"Label": "smoothest",
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+ "AssociatedWith": "urn:98b37057-a7c5-41c7-a584-2b9af6c287bb",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
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- "urn:c2986c0c-ed72-4122-9a88-1a28862e6651"
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]
},
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]
},
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"Used": []
},
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]
},
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]
},
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]
},
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]
},
{
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+ "@id": "urn:a7f17246-55db-4911-bfc2-1c25c8cbd171",
"Label": "Make directory",
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"Command": "mkdir -p tsplot",
"Used": []
},
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}
],
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"digest": {
@@ -554,25 +554,25 @@
}
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@@ -580,7 +580,7 @@
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@@ -588,7 +588,7 @@
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@@ -596,31 +596,31 @@
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@@ -628,13 +628,13 @@
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@@ -642,16 +642,16 @@
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@@ -659,250 +659,250 @@
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{
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"AtLocation": "example_func2highres1.png",
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{
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"AtLocation": "sla.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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},
{
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"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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{
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"AtLocation": "slc.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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{
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"AtLocation": "sld.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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}
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"AtLocation": "sle.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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}
},
{
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"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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}
},
{
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"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:f16cb397-77ab-427b-bd4e-8f8416d08687",
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}
},
{
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"AtLocation": "slh.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:f16cb397-77ab-427b-bd4e-8f8416d08687",
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{
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"AtLocation": "sli.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:f16cb397-77ab-427b-bd4e-8f8416d08687",
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},
{
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"AtLocation": "slj.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
+ "GeneratedBy": "urn:f16cb397-77ab-427b-bd4e-8f8416d08687",
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}
},
{
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"AtLocation": "slk.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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}
},
{
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"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
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},
{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:fc548620-4d3b-4aaf-a4d6-39a1641f8bcb",
+ "GeneratedBy": "urn:131dc7aa-56e6-499c-9250-668ed5c15c90",
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}
},
{
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+ "@id": "urn:ca79b157-4377-4949-9689-0d2ab409a269",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "GeneratedBy": "urn:90bf0411-4781-4d6a-8402-b213e171d6a0",
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},
{
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+ "@id": "urn:c4b41eb0-6e4c-466e-907d-9ae326422bdb",
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"AtLocation": "sl?.png",
"digest": {
@@ -910,25 +910,25 @@
}
},
{
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+ "@id": "urn:3e6964e1-0ce4-4cae-b165-83f556a2a6e4",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "GeneratedBy": "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
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},
{
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"AtLocation": "mc",
- "GeneratedBy": "urn:7556cc7a-14ba-46ba-a8f2-ba3d98f37993",
+ "GeneratedBy": "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
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}
},
{
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+ "@id": "urn:11447d06-8a2a-4344-baaa-cf78666297e9",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -936,7 +936,7 @@
}
},
{
- "@id": "urn:470281e3-3e60-4466-ae7f-99338ead202e",
+ "@id": "urn:e743a0bb-478d-4238-aedf-b1620721c88b",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -944,7 +944,7 @@
}
},
{
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+ "@id": "urn:322ef859-6275-4576-b46c-c4b1de5333f5",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -952,7 +952,7 @@
}
},
{
- "@id": "urn:5a7b2004-f5c6-4f5b-ace8-adb7207782e0",
+ "@id": "urn:a65b8d80-0bd7-4490-b8d2-6dbe12682ca9",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -960,7 +960,7 @@
}
},
{
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+ "@id": "urn:6670247b-4942-4a7a-a1fa-31c4d3f24695",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -968,7 +968,7 @@
}
},
{
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+ "@id": "urn:9ab1f065-b1b1-4d54-a405-59ef938a5da1",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -976,34 +976,34 @@
}
},
{
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"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:5dc549f4-647c-486e-8759-782021b9509f",
+ "GeneratedBy": "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
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},
{
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- "GeneratedBy": "urn:cbfc8ec2-5355-4a4f-aaf8-dc161b588f7d",
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}
},
{
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"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:252514db-a544-4986-996e-fdaf40afdb46",
+ "GeneratedBy": "urn:9d1898a7-03e2-445f-8756-faeb5bec2948",
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}
},
{
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"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1011,34 +1011,34 @@
}
},
{
- "@id": "urn:0f469813-3e5f-475c-a372-f4c2eccfb6a5",
+ "@id": "urn:3c8f1e80-b4dc-4d12-b22c-ac616848f9ae",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:765995cc-ff2c-4b3d-ab06-620255e297ff",
+ "GeneratedBy": "urn:f68ab65b-7eba-43ac-9558-ac93d8a9627f",
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},
{
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"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a07b6f8c-7c19-4e7e-b155-24fb0168516e",
+ "GeneratedBy": "urn:01916163-39ab-406b-a4ad-fe365cf6bf5e",
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},
{
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- "GeneratedBy": "urn:93dba0ab-ccea-44d9-8dc3-a8e853cd4d31",
+ "GeneratedBy": "urn:0f4ce3cb-edbe-49d3-954c-6b5cc6ffdab8",
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}
},
{
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+ "@id": "urn:a5fc0d33-b76e-4555-a307-ff6b719128b6",
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"digest": {
@@ -1046,106 +1046,106 @@
}
},
{
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"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:68476387-e9e1-4562-bd05-044521173b60",
+ "GeneratedBy": "urn:7cbb179d-b703-4f73-8e1f-296962f7bdf8",
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}
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{
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:7eef4a4b-730b-4fea-b783-9403cf46b7fa",
+ "GeneratedBy": "urn:1f493787-989c-4c06-97df-d5dde83c5dcf",
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{
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- "GeneratedBy": "urn:525029ed-c19f-49c3-ba6d-2d971b656318",
+ "GeneratedBy": "urn:82533282-c050-4033-8227-7a8e5d1dcc98",
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}
},
{
- "@id": "urn:9bfa1c28-4a98-4831-a854-82969c939da3",
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"Label": "mask",
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- "GeneratedBy": "urn:bd112a10-b4d7-4dc4-af3c-b22efb773c55",
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}
},
{
- "@id": "urn:95fcf1df-0d61-4ca6-9267-40abe42fb652",
+ "@id": "urn:055168ca-a31a-46a5-9856-c4d65f4ff571",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94",
+ "GeneratedBy": "urn:94eca642-e7a4-4516-bb04-d3ec7205f2f0",
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}
},
{
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+ "@id": "urn:23b3a8fd-1d9d-4840-b592-ff7a5854e10b",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a63366cb-4305-471f-9c59-3eb80e99629e",
+ "GeneratedBy": "urn:5ac2aa06-d1d0-4302-9070-1a4f8ee7298d",
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{
- "@id": "urn:a08509a8-7e5c-425e-b284-91fba26756e9",
+ "@id": "urn:af12b69b-fe39-4e11-90eb-ebe03f5f448a",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:f0df4582-6ede-4262-af8a-21feda9b538b",
+ "GeneratedBy": "urn:7fd9b3c1-a451-4a03-8201-3e8beeab3afe",
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{
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"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:c96b85ef-9bad-41dc-a413-025a5563094d",
+ "GeneratedBy": "urn:eabecb28-a594-4a8b-a24d-2b23bac3fb4b",
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}
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{
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"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:133cc17d-bdb0-4a73-a87d-102c3a843276",
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"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
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+ "@id": "urn:0557adb8-317b-43b3-9a7c-cc92bc076ae4",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7",
+ "GeneratedBy": "urn:fa13ccbc-6608-4043-95b5-766380e790af",
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}
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{
- "@id": "urn:25f83831-8237-4bcf-a95d-c1c43b678e9a",
+ "@id": "urn:8cc3c85c-f86e-4cbf-a49d-309ec01af2ec",
"Label": "15.0",
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}
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{
- "@id": "urn:9b63ff00-e57d-492c-9a6a-22e0bc8d0efd",
+ "@id": "urn:f1adcdf3-1142-44e9-91b5-d5e17469c02e",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1153,25 +1153,25 @@
}
},
{
- "@id": "urn:8c44dd51-35e1-4b89-8524-f882421e5782",
+ "@id": "urn:beae7e86-fb11-4df3-84b4-4666debc7e5f",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:64c5f41e-349c-42dd-a27f-95f04499e42a",
+ "GeneratedBy": "urn:565d6945-cf43-4637-91dd-959ef59fd94f",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:9b37749a-3351-487a-8ae2-eb5aca1a5d50",
+ "@id": "urn:2b244cf4-5e67-41c2-bf50-4eab48c53424",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:07f1d615-da56-4401-a194-3f2c26ee1978",
+ "GeneratedBy": "urn:a593e27f-7e1a-44ef-85cc-4712ba305740",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:6c3d4bab-9cb1-46cf-a0be-a4a89caec3cb",
+ "@id": "urn:23a6da3c-5123-4785-9953-2811110cbadd",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,16 +1179,16 @@
}
},
{
- "@id": "urn:87e6336f-0546-4d51-8158-72b17abf6e90",
+ "@id": "urn:dbc11716-e865-4e0f-9e6b-70c3603b6f2c",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:d0e0899e-adea-40d8-9ab3-eec5b6976039",
+ "GeneratedBy": "urn:0aaa9b00-90b6-4f7c-bef2-5e46efd3abe5",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "@id": "urn:1ea5f0a6-5c3a-4f1c-a8b2-2471344253bc",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1196,22 +1196,22 @@
}
},
{
- "@id": "urn:38268715-5065-43de-85de-fcdd8865fc95",
+ "@id": "urn:6552d457-a0a9-4e38-8b97-5b3f3c6e4d0e",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:83cd1459-54f5-4567-bf38-85450c050b8a"
+ "GeneratedBy": "urn:f330816b-b82a-4d29-83cd-78e2d6e6a680"
},
{
- "@id": "urn:db065346-363d-4ba1-826a-e17bbdd3fcaf",
+ "@id": "urn:1fd2dd12-ffa7-44e4-811e-45bfdb10fdff",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:771a00ec-f716-4c32-b8e0-1d6bc6bd887b",
+ "GeneratedBy": "urn:16abfbc5-89b6-4a8d-bcb3-5216a6cca934",
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"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:51ef0d6d-7762-419d-9632-8d9387a31422",
+ "@id": "urn:a96a152e-7be7-475f-9d8a-a44d41b5a899",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1219,13 +1219,13 @@
}
},
{
- "@id": "urn:9a55a587-c9e7-4bc3-bb33-5994676d9f7b",
+ "@id": "urn:e654e524-4ecb-49e1-844a-6cfd6bf2cda9",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:e8c59636-f0da-46b6-812b-0911a423417e"
+ "GeneratedBy": "urn:87b39aea-7485-4ccb-be46-cf814c21fc7b"
},
{
- "@id": "urn:c2986c0c-ed72-4122-9a88-1a28862e6651",
+ "@id": "urn:e3e660d5-d5a7-48fc-98fe-18d4e59a04e0",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1233,16 +1233,16 @@
}
},
{
- "@id": "urn:467b9693-0182-4117-a2ee-1578a9db65c6",
+ "@id": "urn:a68b66ec-2367-4d43-8664-e02dd673998a",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:7989ed26-c111-4c65-a7f2-c118f1201bff",
+ "GeneratedBy": "urn:a2e9a27e-e4fc-454e-a015-e4591a0003df",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:71cb60e0-66dd-4d10-b2e8-2c188def3d27",
+ "@id": "urn:74423947-e686-4ba8-9fbf-1df2c6f63d5b",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1250,16 +1250,16 @@
}
},
{
- "@id": "urn:3e7ea993-af25-4097-bcde-e19282d42de7",
+ "@id": "urn:14fea31e-6012-42ea-b435-728cb9bb44ae",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:0f339db7-b6d0-472c-86d9-935025f1e945",
+ "GeneratedBy": "urn:ea8a00b5-0155-4e66-b452-2ccbd7fd3940",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:a3bdc092-1cb5-4795-9796-f21fd99a495e",
+ "@id": "urn:095384b1-8649-42be-85d8-93f6790e8498",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1267,25 +1267,25 @@
}
},
{
- "@id": "urn:90161d09-6f0c-46e4-9d1c-a16798b445cf",
+ "@id": "urn:542d59dc-af4e-49b0-b3a0-9512a2ecf64d",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:b90ae67f-f83f-4488-b865-b9ae7fd73bd6",
+ "GeneratedBy": "urn:8713b1e0-13ad-450b-904d-babd44c29b53",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:ed331241-db7d-4bc0-8c44-35d1d4d65364",
+ "@id": "urn:614e1d98-68ea-4037-959c-218caac702b4",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:b90ae67f-f83f-4488-b865-b9ae7fd73bd6",
+ "GeneratedBy": "urn:8713b1e0-13ad-450b-904d-babd44c29b53",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:e97db26f-22a5-423d-ac55-e88ca7ffbfaf",
+ "@id": "urn:e4093739-43a7-4659-8500-2162b6e06ac1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1293,25 @@
}
},
{
- "@id": "urn:646c895a-c042-47ce-8c9e-f28f3cae2eee",
+ "@id": "urn:cd0c6bf0-a4e1-4661-91d7-3ac3a921f611",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55",
+ "GeneratedBy": "urn:212c4ad6-6acd-4cb2-8203-059fcc216375",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:ad95a8e0-1090-4d6a-97da-f496eb5bb94d",
+ "@id": "urn:7aca56e1-8ce5-4d71-8b92-30d76246e94d",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:21d25c7b-b33e-438b-8e59-6bf13beaa9de",
+ "GeneratedBy": "urn:073168b5-b593-4406-9b08-d95f08b1cd1e",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:11e0fa70-a9c1-4e01-b834-3fb6ff42fd18",
+ "@id": "urn:01dc9cfe-e1e5-4460-b7cc-8bffb7c50a91",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1319,28 @@
}
},
{
- "@id": "urn:6305398a-67f9-40b5-8456-ff711cd48892",
+ "@id": "urn:99294797-5ac2-4a26-ac54-35efb70dd070",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:0f4d6eea-0d6c-4fec-8a2d-9fefb6752db1",
+ "GeneratedBy": "urn:cd2192eb-05ca-4a36-b7f3-02f2de727f03",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:f4dc34ba-c07a-4a04-b16f-2778478dfb60",
+ "@id": "urn:66264a2d-510c-4b43-ba0b-f808d8aa1fbf",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:241de80c-b8e2-43b3-be20-f4200ac54a29",
+ "GeneratedBy": "urn:a7f17246-55db-4911-bfc2-1c25c8cbd171",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:9b09580c-b95c-4672-ac21-1789f9976135",
+ "@id": "urn:6fbdb553-8156-4158-aa41-c34fe4536a6f",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f",
+ "GeneratedBy": "urn:4e52c079-40a2-41a8-95a5-03cc45bf1bad",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_default_report_log.png b/examples/from_parsers/fsl/fsl_default_report_log.png
index eefd5eb7a..b1f4f542b 100644
Binary files a/examples/from_parsers/fsl/fsl_default_report_log.png and b/examples/from_parsers/fsl/fsl_default_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
index 25507bb5c..b026184b2 100644
--- a/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_full_examples001_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "@id": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,749 +13,749 @@
],
"Activities": [
{
- "@id": "urn:36a64250-989a-45ef-8809-cd162468e5f2",
+ "@id": "urn:7c54373f-c93e-4f5c-b2d9-d3a7b7ea47aa",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri prefiltered_func_data -odt float",
"Used": [
- "urn:76e24d10-75b5-4d38-a1ea-1dfea30ed114"
+ "urn:3f5fcc63-c232-47b9-9bfe-231b359c95b9"
]
},
{
- "@id": "urn:0c1f173a-a1e8-43ad-942f-d3231383ed70",
+ "@id": "urn:e648c12f-577e-426e-b264-ef77b5359fad",
"Label": "fslroi",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslroi prefiltered_func_data example_func 53 1",
"Used": [
- "urn:447b3e40-4c33-4a46-8121-5c9a3af866aa"
+ "urn:3a84825d-17a3-4434-a37e-373c79ae4e45"
]
},
{
- "@id": "urn:957b2a43-07df-4b2e-942d-783862b74031",
+ "@id": "urn:ff7ca2bc-829f-4438-bdcf-a712c5c42578",
"Label": "mcflirt",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs",
"Used": [
- "urn:447b3e40-4c33-4a46-8121-5c9a3af866aa"
+ "urn:3a84825d-17a3-4434-a37e-373c79ae4e45"
]
},
{
- "@id": "urn:f55c118c-56ab-4383-a123-3704c2418a98",
+ "@id": "urn:aae4ed70-8823-4964-83b4-5d2f17e7fcc3",
"Label": "Make directory",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:1e0b939a-7f03-4ce5-94d3-ec2db95d67b5",
+ "@id": "urn:394e603e-0619-459e-a1c1-6dffeac3be20",
"Label": "mv",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
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- "urn:886a634a-92ae-4b6a-a202-50de6c793825",
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- "urn:958a9af3-d67a-49c5-be0f-f910d982040b",
- "urn:e987b7b3-5351-425a-80bd-1c18f436aa05"
+ "urn:029ac7ce-e0ca-4637-8d00-caec11c22c76",
+ "urn:1c4d8379-a962-4530-b203-961ea5164edd",
+ "urn:2a83909e-befd-42a8-bfd8-2c3310b0f853",
+ "urn:2eabf927-c80e-4338-b26a-0d07283fc38a",
+ "urn:703d1215-6aca-48fc-b9b0-5ae629fcaade",
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]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
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+ "urn:2a83909e-befd-42a8-bfd8-2c3310b0f853"
]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
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]
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{
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+ "@id": "urn:6f845091-280e-49cb-9947-2af6d2e7b4d3",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:97719e5d-4229-4ff2-8310-05340e8ce878"
+ "urn:aa3780c6-2017-4f4c-ae10-2b0ec098f095"
]
},
{
- "@id": "urn:9b687564-6599-4fc2-a127-ba19d5e56934",
+ "@id": "urn:446e55f7-85e1-46c5-93b0-3352c67424e9",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109"
]
},
{
- "@id": "urn:0ca14c7d-bdca-4c21-8942-3567d6212845",
+ "@id": "urn:6ef4ad96-4836-4a98-a268-4a7432f14d2e",
"Label": "bet2",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:c82e7fa3-80eb-4169-978d-93ec72026c55"
+ "urn:5901a2ea-b788-4e6d-ba09-54cf00c5d378"
]
},
{
- "@id": "urn:3f293e77-c0ee-4d38-8aad-1c5aa4760477",
+ "@id": "urn:a5bb8cf2-12e7-4eec-95de-1d20dceb808b",
"Label": "immv",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/immv mask_mask mask",
"Used": [
- "urn:c774d4f0-4ad3-44d8-b9c5-7775c0dc9776"
+ "urn:3e01c911-337e-4cb1-9895-651a60dd23c8"
]
},
{
- "@id": "urn:ad20686e-7a8c-4964-a10e-799a1c8761c9",
+ "@id": "urn:775c1fd8-bd01-4511-a0a0-ccbb75a6b43c",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109"
]
},
{
- "@id": "urn:7b98fe35-6185-46c1-b6ab-218cd580fb53",
+ "@id": "urn:798791af-c988-414c-b76e-7d4b43099a24",
"Label": "fslstats",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8"
+ "urn:9a6b936f-0fad-4390-bf3e-71423676502a"
]
},
{
- "@id": "urn:cc89346d-5c53-4652-84d4-847a29ab7c7c",
+ "@id": "urn:13e5912f-05c3-476e-8f43-f0b19c8158e6",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_bet -thr 978.24375 -Tmin -bin mask -odt char",
"Used": [
- "urn:ca644e16-bc8f-4cb8-a310-fb2005b8f3d8"
+ "urn:9a6b936f-0fad-4390-bf3e-71423676502a"
]
},
{
- "@id": "urn:2c4629c9-90fd-4777-a252-2d2d739ff1ee",
+ "@id": "urn:78ac9ac3-ab64-48ed-9595-5a8da7c4a7cc",
"Label": "fslstats",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109"
]
},
{
- "@id": "urn:5b90ef67-d464-423c-9769-46fed7afde85",
+ "@id": "urn:3bc61e8b-94a4-47fe-bbcd-8af24b2a709b",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e"
]
},
{
- "@id": "urn:b850c3bb-c708-4927-a081-f0f6462076a0",
+ "@id": "urn:518d211c-544f-47e0-935d-d420c3a17f4d",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109"
]
},
{
- "@id": "urn:0ea248cd-0b5c-47e6-86ab-b81edcdad19f",
+ "@id": "urn:0ac84f61-aaa5-4bd2-aab9-06b005e382ee",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:73706964-2ab5-4dbc-8f4a-edc7d81fe7eb"
+ "urn:a43093fa-48c6-4d94-9392-d68edb15a82b"
]
},
{
- "@id": "urn:fe9f2e68-5450-4466-b842-ccc9dd39f6f7",
+ "@id": "urn:449d68ef-002c-4c72-890e-200c2ca7deae",
"Label": "susan",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/susan prefiltered_func_data_thresh 5646.963501 2.97239915074 3 1 1 mean_func 5646.963501 prefiltered_func_data_smooth",
"Used": [
- "urn:73706964-2ab5-4dbc-8f4a-edc7d81fe7eb"
+ "urn:a43093fa-48c6-4d94-9392-d68edb15a82b"
]
},
{
- "@id": "urn:61509192-5cb3-441a-8c1d-ad52d092302a",
+ "@id": "urn:4350385e-083c-468c-b204-ff7ce3734c0e",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:32f9bfaf-ad74-42f3-9703-e946cb2ec370",
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "urn:b8da4d90-84a0-4f64-9a74-fcfc3fad2a0d"
]
},
{
- "@id": "urn:8ae31d5e-a3ad-42bd-ad51-5124acc6a71f",
+ "@id": "urn:17db490b-6935-4543-9638-2df1ae98971d",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_smooth -mul 1.32814741917 prefiltered_func_data_intnorm",
"Used": [
- "urn:32f9bfaf-ad74-42f3-9703-e946cb2ec370"
+ "urn:b8da4d90-84a0-4f64-9a74-fcfc3fad2a0d"
]
},
{
- "@id": "urn:ee2408cc-c449-4e10-93d3-7c11e0a58e0f",
+ "@id": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_intnorm -bptf 227.142867456 -1 prefiltered_func_data_tempfilt",
"Used": [
- "urn:431edd12-cde6-4811-9006-d6fed017d3c5"
+ "urn:0fb7b5bf-2160-4aae-bd8f-2d8a4d8a81bb"
]
},
{
- "@id": "urn:e70dd1e8-a92b-4729-967d-c0dbcba46a21",
+ "@id": "urn:7e64c091-d21a-455a-9ce9-820676099fa1",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:c7594a11-495b-4a28-a309-548106b04b0e"
+ "urn:42705fbf-bd87-439a-89a0-6f4a24e459e3"
]
},
{
- "@id": "urn:9c0ba698-c0c5-4305-977c-d9e1c1862185",
+ "@id": "urn:886f9970-4f49-49db-a6af-44441c2d0b8e",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:a3e61de6-6e73-40e4-a5ba-7044349cfb1a"
+ "urn:c35adba0-7fc6-485a-9a6e-546aeb651594"
]
},
{
- "@id": "urn:b7120cae-1b38-4812-9aa4-8123b3e36f0c",
+ "@id": "urn:9d2da488-b04e-4aae-b586-c30db9190292",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:d4a98127-8091-4ed0-9db3-ec2724d0dbcd"
+ "urn:e5aab2e8-72a6-4fb6-9085-b63d22e335a2"
]
},
{
- "@id": "urn:9220cdcc-449f-4185-b7fd-f95b6f48368b",
+ "@id": "urn:a8f99aa2-3c57-4b7e-a166-10298ab6e2bd",
"Label": "Make directory",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:541e1237-85be-4540-a701-7021ec7b91a1",
+ "@id": "urn:85de85e6-c096-4520-be17-2ef38ee27ba4",
"Label": "cp",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_generation.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:7374f398-be8e-4534-9ce6-61d41763e8e6"
+ "urn:0b905e9b-9dfc-4c55-ae37-69d8382573bd"
]
},
{
- "@id": "urn:7e4155c0-c82a-4288-9c97-0d282d04ea98",
+ "@id": "urn:cf35e9bf-17a2-4078-9ef0-07b72bc70c29",
"Label": "Make directory",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:b0d9a9c0-05e2-46e5-aecc-eb834e7acba1",
+ "@id": "urn:a15c84dd-d081-4919-b897-d046a70498ec",
"Label": "cp",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/cp /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/word_shadowing.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:7962f1b9-fbcc-4216-999d-a029e8e92124"
+ "urn:4634275d-8f31-4429-bf23-59bfd3c12e74"
]
},
{
- "@id": "urn:8afafea1-903a-4e02-b736-1ce962120865",
+ "@id": "urn:6a309aaf-e36f-4234-aee9-c8be9fdc3ddb",
"Label": "film_gls",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/film_gls -rn stats -sa -ms 5 filtered_func_data design.mat 1000.0",
"Used": []
},
{
- "@id": "urn:09759f75-f271-429a-ae59-0a44f00dd289",
+ "@id": "urn:6cb41f2f-497b-4e78-b633-10737e39dea4",
"Label": "smoothest",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:7dedc9bb-8c86-4990-a6b8-648da3100168"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "urn:d9c02ef8-ae4f-49fe-9649-3b35f4674c1e"
]
},
{
- "@id": "urn:ce0142d3-44e4-4af5-8105-eef77e501933",
+ "@id": "urn:18e33185-877f-4a53-a606-a91ceab1b3ca",
"Label": "contrast_mgr",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/contrast_mgr stats design.con",
"Used": []
},
{
- "@id": "urn:5387229e-d088-4ba4-884e-34bc3ff43df0",
+ "@id": "urn:eec7ccce-0779-437f-8450-c4b6f536a7bc",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:3beb9088-e8a6-44f2-b869-189fa7e32181",
- "urn:77aa0a79-3eb4-491a-b989-2bf687713453"
+ "urn:55fdee03-e7de-4695-b54a-3b1f4f92149e",
+ "urn:5ecbb2f9-d628-4980-8bed-9166dcee801a"
]
},
{
- "@id": "urn:171aa06b-6403-4488-adb4-7f3e89d9caf0",
+ "@id": "urn:2a5ca020-0854-4c98-8388-e8f1d6e3fa9d",
"Label": "echo",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "echo 45203 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:7a3ae6ca-12a9-4b93-af1d-4e77a0ecd4ec",
+ "@id": "urn:623eb35c-21fa-4b31-8073-dfdba666871f",
"Label": "cluster",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z > cluster_zstat1.txt",
"Used": [
- "urn:3ca7ac59-c231-4f0c-87ae-b1e12cd7e06a",
- "urn:453f2339-e213-4b5e-ab94-4573425a181a"
+ "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620",
+ "urn:b144c679-bde6-4e53-9a44-652deac50c93"
]
},
{
- "@id": "urn:e0ccf79c-c0c8-4648-9c87-5d2049923838",
+ "@id": "urn:52cfe718-8d39-42bd-9e65-221b5e1969e8",
"Label": "cluster2html",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:b3ed8412-1e48-46e4-ad7c-4485f55efb2d"
+ "urn:030f431e-c8bd-4ad2-a374-1f115df2930e"
]
},
{
- "@id": "urn:c7f540ab-8cca-4a10-bb24-c709b962b774",
+ "@id": "urn:57c70746-bc5d-4d0f-ac6b-cf37f0e790d1",
"Label": "fslstats",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:453f2339-e213-4b5e-ab94-4573425a181a"
+ "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620"
]
},
{
- "@id": "urn:a3c105fb-3a60-46d9-8d40-3788d08530ea",
+ "@id": "urn:a5f0a28c-5544-4428-87a1-a296cda93f56",
"Label": "overlay",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/overlay 1 0 example_func -a thresh_zstat1 2.300331 5.793015 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:97ff91d4-1ec0-4cf2-b743-78a8a0aa4cdf",
+ "@id": "urn:591e78c6-f12c-49e6-b053-b365d9daf3b8",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:753d9758-36e4-406a-b40f-4d8ec0e5d9dc"
+ "urn:1dc5978a-3a2c-41fe-93da-da44031facdc"
]
},
{
- "@id": "urn:acbe48d2-2243-4d5d-87be-c86b1864707e",
+ "@id": "urn:0ae1180e-9758-449b-96a6-998f6c382716",
"Label": "cp",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/cp /usr/local/fsl/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:b6bd7923-5f95-4de9-b336-d38e1ef54915"
+ "urn:19f7f936-05fb-4194-a6d8-10d878641d10"
]
},
{
- "@id": "urn:58ff1f1c-76ec-4363-a1d2-038927e2825b",
+ "@id": "urn:48508920-4ce5-4213-a180-264259df2d8f",
"Label": "Make directory",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:b6e36cc4-2772-48cd-b50f-e50e29ac1c74",
+ "@id": "urn:7d6b4ad3-03f6-4196-a307-35cc3bd624d6",
"Label": "tsplot",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
},
{
- "@id": "urn:138bed53-625a-4df3-a2fb-fbde4dd85a40",
+ "@id": "urn:05e8ba57-1f57-44a5-bad6-794adef06065",
"Label": "cluster",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/cluster -i thresh_zstat1 -c stats/cope1 -t 2.3 -p 0.05 -d 0.384676 --volume=45203 -x reg/example_func2standard.mat --stdvol=reg/standard --mm --connectivity=26 --olmax=lmax_zstat1_std.txt --scalarname=Z > cluster_zstat1_std.txt",
"Used": [
- "urn:3ca7ac59-c231-4f0c-87ae-b1e12cd7e06a",
- "urn:453f2339-e213-4b5e-ab94-4573425a181a"
+ "urn:07c230b3-a6ca-4c45-9fb4-593e85fba620",
+ "urn:b144c679-bde6-4e53-9a44-652deac50c93"
]
},
{
- "@id": "urn:11a104fa-e66b-41e8-b818-75667e809a71",
+ "@id": "urn:7d4825ae-8174-4ca0-9365-17e45a88294e",
"Label": "cluster2html",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/cluster2html . cluster_zstat1 -std",
"Used": [
- "urn:b3ed8412-1e48-46e4-ad7c-4485f55efb2d"
+ "urn:030f431e-c8bd-4ad2-a374-1f115df2930e"
]
},
{
- "@id": "urn:18bc1e51-3fac-487f-b249-7bd9ce9b56fc",
+ "@id": "urn:f7c6cade-4218-4595-9786-416f1729ab69",
"Label": "Make directory",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/mkdir -p /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri+.feat/reg",
"Used": []
},
{
- "@id": "urn:6cc2dc97-7d0f-4575-aae6-5ea89fc778b7",
+ "@id": "urn:f419f0a0-b006-4fad-abe7-2d18c1268838",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths /Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/structural_brain highres",
"Used": [
- "urn:bf4a6373-4547-42e7-a6f6-db7f2f907ea5"
+ "urn:10dfb433-94b4-4ea4-b283-3fec0ed1cbd2"
]
},
{
- "@id": "urn:6ce3dbc9-b7ef-4e84-8cfa-fb2f54ada26d",
+ "@id": "urn:14281794-e920-4a57-9fc3-b130a5687c98",
"Label": "fslmaths",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/fslmaths /usr/local/fsl/data/standard/MNI152_T1_2mm_brain standard",
"Used": [
- "urn:454caa2e-6cdb-40f4-acf7-786cfbbda286"
+ "urn:a5e308d1-648c-48a2-80f6-91ea050a021c"
]
},
{
- "@id": "urn:56b37ee0-3fb0-4a62-820c-76bcdcb90b46",
+ "@id": "urn:9a7421be-512a-4690-b023-7d1996cf5544",
"Label": "flirt",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/flirt -in example_func -ref highres -out example_func2highres -omat example_func2highres.mat -cost corratio -dof 7 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
"Used": [
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b",
- "urn:c00eeda2-be42-487f-b6e2-28515f578f3e"
+ "urn:6ed8d342-b419-4019-bef6-278dea44193e",
+ "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9"
]
},
{
- "@id": "urn:216f85ed-b590-4747-8b5b-0ef17c869cbf",
+ "@id": "urn:ee9492d3-dd42-42d4-8ccd-d465757bf39e",
"Label": "convert_xfm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:0fe9750e-e253-4ce3-9501-6f9b5be5612c"
+ "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407"
]
},
{
- "@id": "urn:b4fd17d8-e6fa-4d22-baaa-acd338aa8ec8",
+ "@id": "urn:d0c4406f-db80-4b51-8651-292b0bd35f81",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:3e2d0b3c-a9d8-459a-a5b6-1c442573c6a9",
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b"
+ "urn:602573c9-fda2-46ea-9e8a-09d94381a855",
+ "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9"
]
},
{
- "@id": "urn:78c69982-04a2-404f-afba-2445db0955dc",
+ "@id": "urn:5bad2a8e-da77-4dab-8f6a-3821b93f7584",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:0814d606-b899-4bab-9a5f-6c31b6e97f7e",
+ "@id": "urn:76cbe384-e9c5-4aee-a9eb-7366d46724c1",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:3e2d0b3c-a9d8-459a-a5b6-1c442573c6a9",
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b"
+ "urn:602573c9-fda2-46ea-9e8a-09d94381a855",
+ "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9"
]
},
{
- "@id": "urn:9797bc52-7adb-412d-8bda-1583d063dfee",
+ "@id": "urn:6a92fc75-06fa-4645-ada0-51d2db7973ff",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:1bcf3fb2-1e79-4118-82a5-230693a38f9e",
+ "@id": "urn:b5098ff2-a4c4-41d9-9478-fb6768535e96",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:937b139f-5ca7-42f5-8f3d-ac6cfbb528d9",
- "urn:a5e01309-a083-4d4d-8aef-4a5e487731b8"
+ "urn:10021c12-ce10-4d57-857a-2ae8ef4cb9fc",
+ "urn:fb2fd256-c73b-4683-a7af-081528d7939c"
]
},
{
- "@id": "urn:fa4621bc-c290-4d99-a4f0-507a34817870",
+ "@id": "urn:dc701791-8a77-4bd3-824a-7020c444d4ad",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:42562745-8ff4-4e2d-8775-7ac339c7d569",
- "urn:937b139f-5ca7-42f5-8f3d-ac6cfbb528d9"
+ "urn:10021c12-ce10-4d57-857a-2ae8ef4cb9fc",
+ "urn:8f33c5d7-6ef2-4d67-bb97-4e9ba7523eb4"
]
},
{
- "@id": "urn:771ae86f-2170-4828-b748-e4319401099b",
+ "@id": "urn:6f970a8c-d670-4c0e-8b97-41839e3c3c90",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:a5e01309-a083-4d4d-8aef-4a5e487731b8"
+ "urn:fb2fd256-c73b-4683-a7af-081528d7939c"
]
},
{
- "@id": "urn:447495e3-84ca-460f-81ae-cda583bde9f9",
+ "@id": "urn:6f0bc278-4854-410a-8ce5-2c52d30c5e7b",
"Label": "flirt",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/flirt -in highres -ref standard -out highres2standard -omat highres2standard.mat -cost corratio -dof 12 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear",
"Used": [
- "urn:48d9754b-4a40-49db-a0de-65552667fd1b",
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e"
+ "urn:ef0a17e7-2410-459e-aa85-dd27e49780c9",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:26c85652-df8e-4d98-8ff4-7a8429f8f216",
+ "@id": "urn:26ec0d70-3f21-4bfe-be83-27f9b8eda5f9",
"Label": "convert_xfm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2highres.mat highres2standard.mat",
"Used": [
- "urn:9bb3b3c7-d9e7-4990-b618-54e62cdb8449"
+ "urn:24abf5de-fe14-4a83-8d3c-5e3a723811fc"
]
},
{
- "@id": "urn:660e76f5-e52e-4958-ab9a-ca2aa5d72ee0",
+ "@id": "urn:2efbc0e7-5b73-40dc-aab5-ba4b75054202",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer highres2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:92427393-98b5-4022-8061-336cc4b00dde",
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e"
+ "urn:a90f4fb2-fcc8-408a-93ec-a207e8f2a842",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d",
+ "@id": "urn:4b6329f7-79ad-4a55-aa01-952b8b7513db",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard1.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:1e702c29-b4e1-41fa-bc95-23dfe6921348",
+ "@id": "urn:763b7462-e409-4572-ab59-5401b92a5da6",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer standard highres2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:92427393-98b5-4022-8061-336cc4b00dde",
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e"
+ "urn:a90f4fb2-fcc8-408a-93ec-a207e8f2a842",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:757e1873-4676-46d2-a92f-5b67fb687b7c",
+ "@id": "urn:60e714fe-8ee1-42e7-a6da-d0bd9dde8c93",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png highres2standard2.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:18bcf888-7184-4614-8154-0e51dab9d2e7",
+ "@id": "urn:2ff88d43-bf8a-4d17-97fb-032d91ec1903",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend highres2standard1.png highres2standard2.png highres2standard.png",
"Used": [
- "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661",
- "urn:f0e04c2e-44e8-4aff-aab5-a7e1ee98098f"
+ "urn:9b581ae8-7368-4411-84c6-4d66165bd5c4",
+ "urn:f99457e7-83a1-4e36-9139-6343f87a9a6b"
]
},
{
- "@id": "urn:13bfb68d-6090-4f83-a70e-3f46774397ec",
+ "@id": "urn:ab16f273-2c0a-4821-ba88-1636745d121a",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm -f sl?.png highres2standard2.png",
"Used": [
- "urn:42562745-8ff4-4e2d-8775-7ac339c7d569",
- "urn:f0e04c2e-44e8-4aff-aab5-a7e1ee98098f"
+ "urn:8f33c5d7-6ef2-4d67-bb97-4e9ba7523eb4",
+ "urn:9b581ae8-7368-4411-84c6-4d66165bd5c4"
]
},
{
- "@id": "urn:a12f67fa-445a-4453-bfea-0530ee29ab2d",
+ "@id": "urn:335ec760-8131-4706-84e5-ec26bcbb76aa",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm highres2standard1.png",
"Used": [
- "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661"
+ "urn:f99457e7-83a1-4e36-9139-6343f87a9a6b"
]
},
{
- "@id": "urn:83c18660-6b2b-43ef-9001-34ec53eb6663",
+ "@id": "urn:61c386a1-698a-46a2-a770-18e5ec43fcf8",
"Label": "convert_xfm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/convert_xfm -omat example_func2standard.mat -concat highres2standard.mat example_func2highres.mat",
"Used": [
- "urn:0fe9750e-e253-4ce3-9501-6f9b5be5612c"
+ "urn:aee884d0-ebf7-4771-87a5-0ca4fe8a0407"
]
},
{
- "@id": "urn:2070ae2f-3560-47c0-ac79-34a688f24a9a",
+ "@id": "urn:47b36bbc-f1ff-4bbd-8c90-6f05275ec35f",
"Label": "flirt",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/flirt -ref standard -in example_func -out example_func2standard -applyxfm -init example_func2standard.mat -interp trilinear",
"Used": [
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e",
- "urn:c00eeda2-be42-487f-b6e2-28515f578f3e",
- "urn:c7199008-6f75-4762-a1e8-cf1323e12c40"
+ "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec",
+ "urn:6ed8d342-b419-4019-bef6-278dea44193e",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:1c51ee27-d1e8-4e43-a40f-6ccd1b31dc4d",
+ "@id": "urn:bcc8aaac-4310-4786-8364-ddfe40fd5712",
"Label": "convert_xfm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/convert_xfm -inverse -omat standard2example_func.mat example_func2standard.mat",
"Used": [
- "urn:c7199008-6f75-4762-a1e8-cf1323e12c40"
+ "urn:3a9ac2c0-6d83-46a5-9337-3e2a7dd912ec"
]
},
{
- "@id": "urn:78ed0f4d-6f99-449e-a8c8-4eefb0449abd",
+ "@id": "urn:e169e92d-af0e-44de-9e28-1903bc99ef94",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer example_func2standard standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e",
- "urn:cd9873c3-d9ba-4e4e-a33a-017011561abf"
+ "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:0d2d17a2-b566-4927-927c-9f4a9d8d2883",
+ "@id": "urn:d2e6341a-2c4e-4dfd-a507-10d4a06328cb",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard1.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "@id": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
"Label": "slicer",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/slicer standard example_func2standard -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:b6a5e321-c95b-4668-a67d-261166c3e79e",
- "urn:cd9873c3-d9ba-4e4e-a33a-017011561abf"
+ "urn:bd9ba12f-ca5a-4b94-b3ef-b1630faf29b2",
+ "urn:f8d879cd-b835-4036-a683-af5dccf73a8e"
]
},
{
- "@id": "urn:059c5470-f710-433e-b7f0-16be8f4d6632",
+ "@id": "urn:1b7d2ad3-8d29-4aef-a8fa-f9fb4bbb9a40",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2standard2.png",
"Used": [
- "urn:1e49c15c-14eb-4d2a-91f1-2b6617511ba6",
- "urn:407a0dcc-199e-43d1-820c-6c4488d6b491",
- "urn:4a906933-51a2-44bc-b703-d09459da47ac",
- "urn:5538393a-0e9e-4399-a092-fabfef6b5282",
- "urn:7c1874c9-f93c-4559-9f77-77113ffc2a9f",
- "urn:7e0c56eb-958e-44b5-be14-a6d366612be8",
- "urn:be62d30a-74c7-4d75-8b5e-a9279b6f18b9",
- "urn:dcbb9a26-c93b-4b31-bcd1-59dacb0383d6",
- "urn:e5a7f06e-badf-4d72-ad52-7cadde4b7157",
- "urn:e98f18a4-0565-4a3c-82c0-2a43e2465c28",
- "urn:ed233bfd-1b60-4d80-9dce-035f0c183896",
- "urn:f1704fe7-f6ea-4663-9608-648f52503c52"
+ "urn:1fd805ed-6069-4b1c-b02f-478a21ca0f26",
+ "urn:27ffde96-4f34-45ef-902d-38cfe55597c7",
+ "urn:3199a455-85e5-4b30-94e5-bb3c78222246",
+ "urn:59f89e09-43f9-4f11-a93f-2fc0517e82f3",
+ "urn:6bdf816f-71a1-4910-bbe8-023bcc9f033f",
+ "urn:74469c27-c574-4f02-9288-00dcb5161c82",
+ "urn:758ad9e2-7feb-4de4-928e-1f722e1209d0",
+ "urn:8880cc2d-05aa-4bcd-894f-f104ec88d7ae",
+ "urn:9cfed3d2-3adb-4e38-8d3e-24dda4043257",
+ "urn:aae0a1f9-bf6f-45ac-88dc-8bb6df4ed04d",
+ "urn:ab4edefa-3c5c-4fc8-bdfc-207e67b483bb",
+ "urn:b97857bc-8e1c-448e-82f9-d862603dac3a"
]
},
{
- "@id": "urn:0e440f30-8029-41ae-b5c9-3fefd356c1bd",
+ "@id": "urn:38c17bbc-be12-48da-8ba9-ce5a9511513a",
"Label": "pngappend",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/usr/local/fsl/bin/pngappend example_func2standard1.png example_func2standard2.png example_func2standard.png",
"Used": [
- "urn:3d913eb5-ba20-4cc6-99d1-a6b7887c18c8",
- "urn:b1207d77-5b40-4bd8-b6a6-55ac3138df83"
+ "urn:592f88cc-114e-41ab-9d6a-e95cfddb13f4",
+ "urn:6fbf9fb5-0b22-40ee-9f75-d4453d47cfcf"
]
},
{
- "@id": "urn:cccc4f59-e637-443d-afc8-653b7d3c359d",
+ "@id": "urn:77c5d290-e89c-4ae3-b320-2f1c59a8606a",
"Label": "rm",
- "AssociatedWith": "urn:ed650386-5a53-4329-b53b-a0fd3776085b",
+ "AssociatedWith": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
"Command": "/bin/rm -f sl?.png example_func2standard2.png",
"Used": [
- "urn:42562745-8ff4-4e2d-8775-7ac339c7d569",
- "urn:b1207d77-5b40-4bd8-b6a6-55ac3138df83"
+ "urn:592f88cc-114e-41ab-9d6a-e95cfddb13f4",
+ "urn:8f33c5d7-6ef2-4d67-bb97-4e9ba7523eb4"
]
}
],
"Entities": [
{
- "@id": "urn:76e24d10-75b5-4d38-a1ea-1dfea30ed114",
+ "@id": "urn:3f5fcc63-c232-47b9-9bfe-231b359c95b9",
"Label": "fmri",
"AtLocation": "/Users/cmaumet/Data/fsl_practicals/fsl_course_data/fmri/fmri_fluency/fmri",
"digest": {
@@ -763,43 +763,43 @@
}
},
{
- "@id": "urn:447b3e40-4c33-4a46-8121-5c9a3af866aa",
+ "@id": "urn:3a84825d-17a3-4434-a37e-373c79ae4e45",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:36a64250-989a-45ef-8809-cd162468e5f2",
+ "GeneratedBy": "urn:7c54373f-c93e-4f5c-b2d9-d3a7b7ea47aa",
"digest": {
"sha256": "2bea6005bace2adbea3534588b8c1b0d1759aa1af85b703b7f5bd2959c961a29"
}
},
{
- "@id": "urn:c00eeda2-be42-487f-b6e2-28515f578f3e",
+ "@id": "urn:6ed8d342-b419-4019-bef6-278dea44193e",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:0c1f173a-a1e8-43ad-942f-d3231383ed70",
+ "GeneratedBy": "urn:e648c12f-577e-426e-b264-ef77b5359fad",
"digest": {
"sha256": "57841df382242a0e56f4fd1f340b30d4eb3bbd270342825da476367c640135e4"
}
},
{
- "@id": "urn:7772020d-ac05-4d0e-aa6b-ba7c6516fb74",
+ "@id": "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
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@@ -807,7 +807,7 @@
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@@ -815,7 +815,7 @@
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@@ -823,7 +823,7 @@
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@@ -831,7 +831,7 @@
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@@ -839,7 +839,7 @@
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@@ -847,34 +847,34 @@
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@@ -882,34 +882,34 @@
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@@ -917,97 +917,97 @@
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@@ -1015,25 +1015,25 @@
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@@ -1041,16 +1041,16 @@
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@@ -1058,22 +1058,22 @@
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@@ -1081,13 +1081,13 @@
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@@ -1095,16 +1095,16 @@
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@@ -1112,16 +1112,16 @@
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@@ -1129,25 +1129,25 @@
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@@ -1155,25 +1155,25 @@
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@@ -1181,61 +1181,61 @@
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@@ -1243,16 +1243,16 @@
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@@ -1260,286 +1260,286 @@
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@@ -1547,541 +1547,541 @@
}
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{
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{
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"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:78ed0f4d-6f99-449e-a8c8-4eefb0449abd",
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{
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"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:78ed0f4d-6f99-449e-a8c8-4eefb0449abd",
+ "GeneratedBy": "urn:e169e92d-af0e-44de-9e28-1903bc99ef94",
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},
{
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"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:78ed0f4d-6f99-449e-a8c8-4eefb0449abd",
+ "GeneratedBy": "urn:e169e92d-af0e-44de-9e28-1903bc99ef94",
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},
{
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+ "@id": "urn:6fbf9fb5-0b22-40ee-9f75-d4453d47cfcf",
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"AtLocation": "example_func2standard1.png",
- "GeneratedBy": "urn:0d2d17a2-b566-4927-927c-9f4a9d8d2883",
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}
},
{
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{
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{
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"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
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{
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"Label": "sld.png",
"AtLocation": "sld.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
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{
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- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
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{
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{
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"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
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{
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"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "GeneratedBy": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
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}
},
{
- "@id": "urn:f06ec3d0-2cd7-457d-b277-1b3d818c1cad",
+ "@id": "urn:36233805-7fb6-46b5-a36f-addd6b513571",
"Label": "sli.png",
"AtLocation": "sli.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "GeneratedBy": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
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}
},
{
- "@id": "urn:41da3ae7-d09c-401e-8d9f-c440dcdfc993",
+ "@id": "urn:43c4789a-f863-4b01-8b90-5bf445bb185f",
"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "GeneratedBy": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
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}
},
{
- "@id": "urn:5e886210-d28e-41de-9740-05d572c5593e",
+ "@id": "urn:cfdb95e1-7d60-4620-9040-f3583d5d7bca",
"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "GeneratedBy": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
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}
},
{
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+ "@id": "urn:50d48bd5-727e-4b5c-85d0-84a98ef98fa2",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:a5087b67-20a8-403c-a111-bdeb5a331f4b",
+ "GeneratedBy": "urn:d348588f-71a9-4495-ad5e-e635593fe986",
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}
},
{
- "@id": "urn:b1207d77-5b40-4bd8-b6a6-55ac3138df83",
+ "@id": "urn:592f88cc-114e-41ab-9d6a-e95cfddb13f4",
"Label": "example_func2standard2.png",
"AtLocation": "example_func2standard2.png",
- "GeneratedBy": "urn:059c5470-f710-433e-b7f0-16be8f4d6632",
+ "GeneratedBy": "urn:1b7d2ad3-8d29-4aef-a8fa-f9fb4bbb9a40",
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}
},
{
- "@id": "urn:d1a7cf1e-a9fe-46eb-b700-3db0ecdbd36e",
+ "@id": "urn:91ea8032-3aff-4df0-aa5c-1437dda477f2",
"Label": "example_func2standard.png",
"AtLocation": "example_func2standard.png",
- "GeneratedBy": "urn:0e440f30-8029-41ae-b5c9-3fefd356c1bd",
+ "GeneratedBy": "urn:38c17bbc-be12-48da-8ba9-ce5a9511513a",
"digest": {
"sha256": "695f0519df3c3ef4894dc5621ccc7d76b060494ed1497b1051ed31f46453be4a"
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diff --git a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png
index 8880dfd68..f6c0714e6 100644
Binary files a/examples/from_parsers/fsl/fsl_full_examples001_report_log.png and b/examples/from_parsers/fsl/fsl_full_examples001_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
index 1780d007a..79eaf7778 100644
--- a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "@id": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,1014 +13,1014 @@
],
"Activities": [
{
- "@id": "urn:aaa7b906-ee6a-4c9e-ad92-0f42cec51ab8",
+ "@id": "urn:39308342-7914-48eb-91d5-9ea9173ec4b1",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:6c939c93-038f-484b-8362-0d7ccb01dfa4"
+ "urn:5bdbbc48-a5da-48e9-8fc4-7ad28e5afa5c"
]
},
{
- "@id": "urn:c71afebf-facf-4f82-9a52-6ac3fc2d6384",
+ "@id": "urn:0fbfcad6-aac6-4a11-b707-c6889495087a",
"Label": "fslroi",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:a6a7d9c7-b476-48d8-b50d-0884eb184eb3"
+ "urn:550cc2b5-46c9-4929-b5ff-1fe49fb4ccba"
]
},
{
- "@id": "urn:ac9f2384-a0e0-4065-aa27-51ffe9369655",
+ "@id": "urn:af018c20-ff76-4d07-94f9-c469f5622002",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
"Used": [
- "urn:44e2aed7-c604-4e4d-8be6-5ac2defa313e",
- "urn:915a73a0-d2c9-476c-bb2b-55f6b431b745",
- "urn:a824a15d-3234-4f76-9f95-bb38ecf3ba84"
+ "urn:65b9fc59-6869-430a-999d-e71502d2b124",
+ "urn:7b92747e-b90b-492d-8e7e-c99795accc90",
+ "urn:8c989260-b8e4-4730-84f6-c9f317b5e801"
]
},
{
- "@id": "urn:d9f85d96-c33c-411a-8cfa-c8de426d250a",
+ "@id": "urn:877884bd-f37b-49d8-8854-b945da56459c",
"Label": "Make directory",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_gamma_basis.feat/reg",
"Used": []
},
{
- "@id": "urn:b8cb0ff5-5460-47f8-90c4-248b45cac8b7",
+ "@id": "urn:2f3eeebb-8a4d-4310-a504-9a07f32015ac",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:44e2aed7-c604-4e4d-8be6-5ac2defa313e"
+ "urn:8c989260-b8e4-4730-84f6-c9f317b5e801"
]
},
{
- "@id": "urn:6a233baf-1b6c-47eb-9adc-255967269d82",
+ "@id": "urn:7e6793d1-0414-4d9b-af8c-a9dd3f28798d",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:48aae18d-fcff-4f4d-bbd4-d8262dc89ce4"
+ "urn:3b4003ca-4008-441b-a571-22ee1c9d81a5"
]
},
{
- "@id": "urn:4f72060b-abb0-4451-8860-7302be4ce10c",
+ "@id": "urn:7cbbbda6-46f6-488b-a056-0d6322750ac8",
"Label": "epi_reg",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:48863a0d-1cea-4233-887c-2754a9ff4167",
+ "@id": "urn:6051bff2-78e1-4dcf-b920-720092259faa",
"Label": "convert_xfm",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:48a66e58-4e4c-451e-9433-857a97c1851c"
+ "urn:36ad2408-0778-45a6-875d-12bf7277cac0"
]
},
{
- "@id": "urn:0bf8d61a-569e-48a0-a2d0-a44e6e87a32f",
+ "@id": "urn:415d2eff-a2e6-4ce0-b03b-4590dc0b938f",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
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- "urn:b61b8e8c-4da7-4360-aaac-1b949f19e376"
+ "urn:c9f0d731-8984-47bd-aa5c-6b5afb7bfda4",
+ "urn:dbed9a86-280e-4ab0-a362-f8eac8382da6"
]
},
{
- "@id": "urn:f15d3f76-7e2d-4e64-a7a0-f05a7aabee92",
+ "@id": "urn:d8954007-4612-40b0-8ded-1060a7c2d47c",
"Label": "pngappend",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
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- "urn:19e29262-d365-463f-971e-ea6537b869f9",
- "urn:52bc166d-26d7-4569-93df-4e11d920e06e",
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- "urn:c7c2fc85-476d-4014-8b79-3edde2957456",
- "urn:d9b79bf0-3be3-414f-bc87-cea6e2b80f47"
+ "urn:083d8661-48cc-477b-8d5e-fa8106d0bfbc",
+ "urn:0df2b518-c426-40f8-afdf-be5a39b75735",
+ "urn:4cf18a5d-9510-4dcf-85c4-97b4ab57855f",
+ "urn:55c80a52-a73e-4790-9754-72f997c2a7c5",
+ "urn:71b058b4-2de9-4859-84b4-b860b34fd6ba",
+ "urn:77e12367-533f-4f74-b209-4e4c7a234c4e",
+ "urn:7aad8cde-f615-412f-8471-4c996f88ed9d",
+ "urn:9e9513d0-a33e-46aa-946c-56d1ed1d2b3c",
+ "urn:a76eb703-72e3-4454-ad06-13b0cfa15116",
+ "urn:b6d01152-e3cd-4131-83f8-5146de72e061",
+ "urn:bee9590c-02d3-4103-9e35-7a63dae85dc7",
+ "urn:e4884732-273d-40a3-ba49-baf3b9d8c03f"
]
},
{
- "@id": "urn:8275d440-30cc-4e5c-8c5a-b01e135fe60d",
+ "@id": "urn:f033c345-4c18-4394-8840-c59b67eb5768",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
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- "urn:b61b8e8c-4da7-4360-aaac-1b949f19e376"
+ "urn:c9f0d731-8984-47bd-aa5c-6b5afb7bfda4",
+ "urn:dbed9a86-280e-4ab0-a362-f8eac8382da6"
]
},
{
- "@id": "urn:ceee21da-5021-42e6-a2fb-7cdb8eb1c6b7",
+ "@id": "urn:a65fd1d4-ef92-4252-b635-1d83cdf8bb6e",
"Label": "pngappend",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
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- "urn:19e29262-d365-463f-971e-ea6537b869f9",
- "urn:52bc166d-26d7-4569-93df-4e11d920e06e",
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- "urn:c7c2fc85-476d-4014-8b79-3edde2957456",
- "urn:d9b79bf0-3be3-414f-bc87-cea6e2b80f47"
+ "urn:083d8661-48cc-477b-8d5e-fa8106d0bfbc",
+ "urn:0df2b518-c426-40f8-afdf-be5a39b75735",
+ "urn:4cf18a5d-9510-4dcf-85c4-97b4ab57855f",
+ "urn:55c80a52-a73e-4790-9754-72f997c2a7c5",
+ "urn:71b058b4-2de9-4859-84b4-b860b34fd6ba",
+ "urn:77e12367-533f-4f74-b209-4e4c7a234c4e",
+ "urn:7aad8cde-f615-412f-8471-4c996f88ed9d",
+ "urn:9e9513d0-a33e-46aa-946c-56d1ed1d2b3c",
+ "urn:a76eb703-72e3-4454-ad06-13b0cfa15116",
+ "urn:b6d01152-e3cd-4131-83f8-5146de72e061",
+ "urn:bee9590c-02d3-4103-9e35-7a63dae85dc7",
+ "urn:e4884732-273d-40a3-ba49-baf3b9d8c03f"
]
},
{
- "@id": "urn:7ecc666a-cc97-4a61-8503-bb525adfba6b",
+ "@id": "urn:3c5b5b1c-11b1-4891-8be9-96b21c82fdc1",
"Label": "pngappend",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
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- "urn:e979890c-b353-4ba7-b2af-7329f3b60492"
+ "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85",
+ "urn:f5913280-0bd6-4a37-8ccd-bebabdaff219"
]
},
{
- "@id": "urn:c2efd8eb-72e0-41e9-921d-fec41f42856b",
+ "@id": "urn:575e8845-cb64-412b-a3bd-03a8ca28dac8",
"Label": "rm",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:33ea97ed-7601-42c3-99f1-bdad2cd7a2fa",
- "urn:e979890c-b353-4ba7-b2af-7329f3b60492"
+ "urn:23118e41-8c41-4e4c-9e3e-3c36de30538d",
+ "urn:f5913280-0bd6-4a37-8ccd-bebabdaff219"
]
},
{
- "@id": "urn:b40ccf75-ad84-4a4b-9482-2c31e4498ef0",
+ "@id": "urn:539cc786-d245-4e96-896f-106908ebe083",
"Label": "rm",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:91373dd3-513c-4e6a-a1a1-b11ca3ab6fd7"
+ "urn:0e625d98-8e7d-44c5-ab39-67df63fe0f85"
]
},
{
- "@id": "urn:f86a6c6f-3ced-4686-8ed9-79c1377c287a",
+ "@id": "urn:28408038-4814-4994-93eb-6ec6c5e5217b",
"Label": "mcflirt",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:a6a7d9c7-b476-48d8-b50d-0884eb184eb3"
+ "urn:550cc2b5-46c9-4929-b5ff-1fe49fb4ccba"
]
},
{
- "@id": "urn:9d505fad-bfb4-4d42-9041-d332f14f09ef",
+ "@id": "urn:919b203e-22f8-4529-8a7c-0fd91cd96f88",
"Label": "Make directory",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:d3a3868e-57ab-4fe3-913d-8d47a0d4fa52",
+ "@id": "urn:a48732b4-acbc-4106-a1f7-459dcca22dd6",
"Label": "mv",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
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- "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6",
- "urn:fb597bf8-04ef-4d61-9c23-d1bf17b700e7"
+ "urn:05a732ed-44d0-4002-98ac-cec09f8f0b8d",
+ "urn:67d4bff9-65dc-4160-b555-72d89dbb6005",
+ "urn:b92c80cd-35e5-4ed5-936a-1ec1f0154003",
+ "urn:bfecc9ae-1ef2-40a5-941a-89224c16e5b8",
+ "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329",
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]
},
{
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+ "@id": "urn:560bd7e9-df84-4134-a5a2-ffec5be80914",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6"
+ "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329"
]
},
{
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+ "@id": "urn:0288624e-3fe7-438c-a66e-8b0cd95f65c1",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6"
+ "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329"
]
},
{
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+ "@id": "urn:da717efa-327f-4ffa-89d2-92f59a19a50e",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
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+ "urn:19f44ccc-9b2b-4751-bf58-45cb48c9c540"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:1cc5bae4-9c74-47a2-a561-1b5e122d3051"
+ "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2"
]
},
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+ "@id": "urn:0de59090-a792-4965-b076-2ca69af34713",
"Label": "bet2",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:b41c1cc8-933c-4a8b-85d4-3a9f80498340"
+ "urn:b75866fd-6330-46da-ace3-0f92ce0575fe"
]
},
{
- "@id": "urn:0aefca75-8457-4b37-9220-9065a676cc39",
+ "@id": "urn:c08a1124-280f-4d98-8f24-0d05490b60e6",
"Label": "immv",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:d9de738d-c015-4ac9-afaa-938f4e8d54d7"
+ "urn:f6b805b2-5c95-418c-9a87-0998cbca636e"
]
},
{
- "@id": "urn:7b40b911-8757-4a00-bae1-fb3d68382e7b",
+ "@id": "urn:e98e90db-2675-4f55-be10-6f87b559e7d6",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:1cc5bae4-9c74-47a2-a561-1b5e122d3051",
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c",
+ "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2"
]
},
{
- "@id": "urn:79075283-4939-47c4-887c-0149f7626940",
+ "@id": "urn:7f04c2a9-c969-462a-bdb3-6c6fce9f667f",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:bb968bcf-419b-4bf7-a6c7-5ac98405a73f"
+ "urn:d9cd83b8-9b2d-44a2-a1e6-fd0651cabf03"
]
},
{
- "@id": "urn:0cac31cc-159f-4927-b0dd-f1a7166d6614",
+ "@id": "urn:001e2ebb-0f2e-4dbe-a80b-ad351aa0bcbe",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:bb968bcf-419b-4bf7-a6c7-5ac98405a73f"
+ "urn:d9cd83b8-9b2d-44a2-a1e6-fd0651cabf03"
]
},
{
- "@id": "urn:80662ef4-c7c3-46e4-9b40-65e7a758bfe0",
+ "@id": "urn:cc487d82-3708-49ac-acd2-0bdbc3427711",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:1cc5bae4-9c74-47a2-a561-1b5e122d3051"
+ "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2"
]
},
{
- "@id": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc",
+ "@id": "urn:a9c53e38-6940-4b59-9eef-3b5922f9ca7a",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:c8f49f12-8b13-478c-80d8-2e5352fe372b",
+ "@id": "urn:6d73fda2-0c34-40d4-920f-9e2a8fdfd781",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c",
+ "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2"
]
},
{
- "@id": "urn:00952bcd-b9f3-4b91-8e31-bc58ddbf8082",
+ "@id": "urn:c05d71d0-695d-4142-bbdb-88f57fb53219",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a"
+ "urn:32553c0c-47d4-4e17-b213-aeb143c39f70"
]
},
{
- "@id": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "@id": "urn:538a39c8-734b-4575-9dd3-02305261fdd6",
"Label": "susan",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a"
+ "urn:32553c0c-47d4-4e17-b213-aeb143c39f70"
]
},
{
- "@id": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "@id": "urn:d446fbfc-2ff1-4066-8050-bcc12f44e46e",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731",
- "urn:ea295298-15e9-4553-a615-29f04d8138b1"
+ "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:24a199cf-30a1-4540-a7d5-9830fee1989a",
+ "@id": "urn:e2af0880-2a04-4a00-96a3-c41d53591247",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:ea295298-15e9-4553-a615-29f04d8138b1"
+ "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd"
]
},
{
- "@id": "urn:82749c15-7a83-4b5d-abb9-b74aae16fa81",
+ "@id": "urn:38704d9b-61c8-49cc-9b71-84de095523bf",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:10a59a9e-d688-4beb-904f-a9f05eb85774"
+ "urn:c12def47-7729-4f52-94a9-db975e35d749"
]
},
{
- "@id": "urn:72122e17-9b35-403d-b214-abe7be549e59",
+ "@id": "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:71f9e9f7-19e5-459e-94c6-05e44e3cc474"
+ "urn:853061ad-42a3-405c-8ea4-4cdf534495d6",
+ "urn:c12def47-7729-4f52-94a9-db975e35d749"
]
},
{
- "@id": "urn:dd1ab2f3-4b39-4b1d-a6b1-d963de21e821",
+ "@id": "urn:4110db24-024a-4682-b347-ed6128ea0917",
"Label": "imrm",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:71f9e9f7-19e5-459e-94c6-05e44e3cc474"
+ "urn:853061ad-42a3-405c-8ea4-4cdf534495d6"
]
},
{
- "@id": "urn:a1b863ef-5a4f-4406-b100-3dddd647ef1c",
+ "@id": "urn:f5d7521b-b160-4096-8ba1-a7560ca00126",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:d2a1e303-a574-44e4-84ac-85293d3844d3"
+ "urn:f4a25276-5185-4794-a1d8-5096e20c0aa4"
]
},
{
- "@id": "urn:9f31b8ab-69ee-49ec-82c4-c8359d7de3c8",
+ "@id": "urn:2d3597e6-3bc3-4588-ad30-2b66d5d8c409",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:38359f0d-0376-4cd9-b242-9c4b33dc6392"
+ "urn:2b88e9cd-f0ae-44d5-b8f5-aac0f7d43b5b"
]
},
{
- "@id": "urn:966d0316-18ca-464b-95d6-60b4db248956",
+ "@id": "urn:6a10282f-6a38-4a4e-b8d8-91e7875c4262",
"Label": "rm",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:d6b8b109-1b37-4302-ba5c-7de9ea37de91"
+ "urn:32aae5a8-0964-451f-bcb0-8d617608c133"
]
},
{
- "@id": "urn:165bae48-7dae-427e-b10a-d1e238d9a17a",
+ "@id": "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c",
"Label": "Make directory",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:28317228-ec2f-447f-8c78-e171c1cbb61d",
+ "@id": "urn:abb994eb-f289-446f-b568-e9ebdb638e9d",
"Label": "fslFixText",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:68cdaeb7-59fc-440a-9c6b-7f7df63da8f4"
+ "urn:9ad2b4b3-af7c-4e12-aaff-39f1e5dd7553"
]
},
{
- "@id": "urn:68079d2a-f99a-4365-a455-48bcf66b0699",
+ "@id": "urn:4324d607-6f82-4b26-9b3f-be7b6646d02c",
"Label": "Make directory",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:b5ab0ba4-4889-4f87-a5c8-817a91c4de71",
+ "@id": "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2",
"Label": "fslFixText",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:3cb24f05-3dce-4413-98ce-0b5f694af482"
+ "urn:7e86c053-51ee-4584-8815-4172d57aba3b"
]
},
{
- "@id": "urn:647f8a33-8bc6-49e6-a24b-f19e4afe80b5",
+ "@id": "urn:2f72377d-7460-4e27-902b-a8fd279f404c",
"Label": "film_gls",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
"Used": []
},
{
- "@id": "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe",
+ "@id": "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665",
"Label": "smoothest",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
"Used": [
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- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c",
+ "urn:fa49893e-f5f8-4125-a711-ab61e8b086ad"
]
},
{
- "@id": "urn:bacd31a3-804a-4288-ac9a-a0a655acb9ef",
+ "@id": "urn:85977f2f-13db-440b-870c-874941174d02",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
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- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:6971be6a-53d5-42ae-9a7d-62bfc15d7199",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:4e42c1fa-6371-4fdc-b15f-6334c00a93a5",
+ "@id": "urn:7923f169-1149-48d3-ab90-aa7b13f7438f",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
+ "@id": "urn:5ec01159-c502-4272-a8e7-af88f3165ef8",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
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- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:14839d0c-c9ad-4342-b8e3-8ad6ccfcbc28",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:beae24c7-c164-4607-a1dd-53aeaa3faa50",
+ "@id": "urn:4016ae63-3771-450d-8fcf-47420bed83fa",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:6f461622-bc47-4e79-b351-2948972c5391",
+ "@id": "urn:20bde1e7-dd88-4056-81dd-b02a9243bc96",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
"Used": [
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731",
- "urn:f130abec-a52a-40eb-b88c-c66c103f5f6c"
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c",
+ "urn:e571d0ba-5590-4c78-8061-3aaebe4095b6"
]
},
{
- "@id": "urn:92d36e57-fdf4-41be-ac3f-ff88ff2caa71",
+ "@id": "urn:fb111b45-6a50-416e-9ebc-47853b4ae1e8",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat3.vol",
"Used": []
},
{
- "@id": "urn:72309cbc-a1ff-4ece-b74d-7ab14d5329ec",
+ "@id": "urn:a1248b06-2827-402c-a459-bf581539c214",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat4 -mas mask thresh_zstat4",
"Used": [
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731",
- "urn:f0f4353c-7637-4227-92b0-58e0afa1d0b9"
+ "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:3d6b5432-45bd-4528-81c3-dcd551a5b5f8",
+ "@id": "urn:a82cf252-e6d0-4fe9-bb18-cdc396c69ef5",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat4.vol",
"Used": []
},
{
- "@id": "urn:c108b15e-d09b-48b6-99b8-a0aa3bcaa657",
+ "@id": "urn:1d532a3f-d2f2-4331-8a39-1f17fa9cb5c0",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat5 -mas mask thresh_zstat5",
"Used": [
- "urn:3c8bd9ea-f940-4527-8bf8-7e2f9a190099",
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:1cd32c4e-606d-489b-bd86-54e96d1803e3",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:68a18c08-3b1d-4a17-92bf-7211f35d75f9",
+ "@id": "urn:a5ad4a2f-8b9e-420f-a5de-b26f57462d20",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat5.vol",
"Used": []
},
{
- "@id": "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
+ "@id": "urn:4e6d3431-054c-48d3-b7c9-8bd56f26a529",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat6 -mas mask thresh_zstat6",
"Used": [
- "urn:31afdc2f-30f8-4682-a3d6-58f886590e75",
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:21d8d15a-17bd-4d18-9034-2ae2bdba5013",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:27c5e77b-c388-49ac-8e7c-da3fd292e0ae",
+ "@id": "urn:5d1480fb-2652-4b92-8dff-7ad31fd4f73a",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zstat6.vol",
"Used": []
},
{
- "@id": "urn:39d91d05-0337-4cde-8b33-86c43a213344",
+ "@id": "urn:86a3d035-808a-4af8-a397-5761b4ce25b2",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
"Used": [
- "urn:226bd3cb-3e0d-4c85-82cc-7baa47c0f26e",
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:0dca7183-5a09-4e87-9168-f1ce2eea29b3",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:27efb73c-c0cf-4c10-9047-b4ff9de6bad4",
+ "@id": "urn:62e3812e-a3e8-4836-8119-a98496a70101",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
- "@id": "urn:83e679fa-bc45-496a-b380-e64dbf09045e",
+ "@id": "urn:a32dfe88-22f5-4e9b-b025-9892df2eb81a",
"Label": "fslmaths",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat2 -mas mask thresh_zfstat2",
"Used": [
- "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
- "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731"
+ "urn:8e7762a4-60d2-4b68-a52a-b1cdecaa5a5b",
+ "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c"
]
},
{
- "@id": "urn:32ca811a-225c-43e8-a31c-2546ee3ada58",
+ "@id": "urn:3daddd79-e238-4f90-a46e-a7ee2638e983",
"Label": "echo",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "echo 38352 > thresh_zfstat2.vol",
"Used": []
},
{
- "@id": "urn:9be18a5c-3e3e-47aa-bac9-211eae7b613e",
+ "@id": "urn:6a63c416-cfed-47a4-8f47-eea9d7eb01dd",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:4ae04bd2-f829-465d-967b-51490c165efc",
+ "@id": "urn:23e90369-5cf2-465e-a4b0-c4ac55508925",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:3790699d-27ec-4cd2-b718-ba21560d41e5",
- "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
+ "urn:749935d9-e8c4-461b-821b-65c0dc026333",
+ "urn:dad480ac-f312-4758-89c9-2c6765d6393a"
]
},
{
- "@id": "urn:536112dd-62ec-4f7c-bad8-95c16e582d83",
+ "@id": "urn:0657b059-0285-4d8a-8fae-2fb268511c34",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:0e2032e9-ee9a-41f0-bd5b-53089bd62c12"
+ "urn:bed01f22-b1b7-4c60-939d-4caa877b5cf6"
]
},
{
- "@id": "urn:53e45275-0dd2-4380-89b0-e06263477c86",
+ "@id": "urn:f63bd3cb-5e25-43e7-9b62-0a6b714b9fd0",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
+ "@id": "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:8ddb9164-7c2d-4c97-a86b-2b3ce2a96d47",
- "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df"
+ "urn:84f2ef39-b49d-4c49-8264-81af872b2cbc",
+ "urn:ff211113-f43c-49ad-acba-57fd339badeb"
]
},
{
- "@id": "urn:36bb8644-008c-45bd-8c8e-ce0fd687b486",
+ "@id": "urn:c3457a35-c5f9-45de-931c-89a71bb169f0",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:068a56ed-fa24-4ab2-9781-d333a439bf94"
+ "urn:d13633e4-0e1f-4847-aa4b-872c2aaee8dc"
]
},
{
- "@id": "urn:e15e0c07-ad7d-4cf8-8615-461337751f00",
+ "@id": "urn:49eefed4-4311-4ede-80a1-8ed5501adc77",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:acd4e7d2-df0c-48fb-aa83-679b3df6591c",
+ "@id": "urn:9c331ad8-b671-4cd6-9d35-d2c9da897c4b",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat3 -t 3.090232 --othresh=thresh_zstat3 -o cluster_mask_zstat3 --connectivity=26 --olmax=lmax_zstat3.txt --scalarname=Z --voxuncthresh -c stats/cope3 > cluster_zstat3.txt",
"Used": [
- "urn:8679d689-6609-4dd7-85a2-330a667c96e9",
- "urn:a6fb9f0f-15e6-4a8f-8544-b59c36ef72cb"
+ "urn:07004fc3-d47b-4f3a-bc7e-b1e7d2f03b6a",
+ "urn:fd74433b-972f-43cf-a1b4-dfc0eda30f74"
]
},
{
- "@id": "urn:e9c625c6-6f1f-4f30-a2ca-393e566b1ad8",
+ "@id": "urn:fdc26ec5-1cc2-4ccd-b9a1-399b018d25cc",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
"Used": [
- "urn:5d51bc01-580e-4fb9-a4b5-453ef634cd1a"
+ "urn:2fc29d78-7b54-4548-b14f-ab9bc8df945d"
]
},
{
- "@id": "urn:32bbae9d-fb30-4902-bf42-a34d51ac5989",
+ "@id": "urn:a9bf6b8f-0ab0-4e8d-be8d-2fd042339d25",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:f1197319-954d-477d-bb96-7dee72a45bd7",
+ "@id": "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat4 -t 3.090232 --othresh=thresh_zstat4 -o cluster_mask_zstat4 --connectivity=26 --olmax=lmax_zstat4.txt --scalarname=Z --voxuncthresh -c stats/cope4 > cluster_zstat4.txt",
"Used": [
- "urn:5a10086e-715a-46fb-a249-a2bb0dae791c",
- "urn:6af02df5-827e-4ddf-9b00-baecee725fcd"
+ "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
+ "urn:f599026a-b8c6-4a3a-84ec-c35bfb1b8d22"
]
},
{
- "@id": "urn:3a84825d-17a3-4434-a37e-373c79ae4e45",
+ "@id": "urn:d3dcadd3-c0fd-43b7-bcc1-dd468be525fd",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat4",
"Used": [
- "urn:e648c12f-577e-426e-b264-ef77b5359fad"
+ "urn:9cbbee48-65ca-4a99-9a9d-1a91678dc392"
]
},
{
- "@id": "urn:949d043a-545a-4b78-b266-8885d981bf99",
+ "@id": "urn:554ce204-f078-481e-a639-ef2963c04838",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:6ed8d342-b419-4019-bef6-278dea44193e",
+ "@id": "urn:0ba6cdcc-8a3d-4d06-b346-1e6354434c52",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat5 -t 3.090232 --othresh=thresh_zstat5 -o cluster_mask_zstat5 --connectivity=26 --olmax=lmax_zstat5.txt --scalarname=Z --voxuncthresh -c stats/cope5 > cluster_zstat5.txt",
"Used": [
- "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d",
- "urn:6c68e7db-4b96-4b16-b064-fbf79cad5a41"
+ "urn:38117d67-65a2-4205-a194-f063e257b0b1",
+ "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4"
]
},
{
- "@id": "urn:1e5abde0-a6bf-4444-81f8-23433fbd770a",
+ "@id": "urn:3a82b429-cfef-4b92-af9f-7d68efd3692d",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat5",
"Used": [
- "urn:394e603e-0619-459e-a1c1-6dffeac3be20"
+ "urn:1eeee773-a0f8-46a9-a05c-64cd0ada78df"
]
},
{
- "@id": "urn:703d1215-6aca-48fc-b9b0-5ae629fcaade",
+ "@id": "urn:53c5588d-218d-4c33-abee-1c225e695bbf",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:2a83909e-befd-42a8-bfd8-2c3310b0f853",
+ "@id": "urn:1da9dbfa-c3ce-4e04-bd20-9f529928201b",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat6 -t 3.090232 --othresh=thresh_zstat6 -o cluster_mask_zstat6 --connectivity=26 --olmax=lmax_zstat6.txt --scalarname=Z --voxuncthresh -c stats/cope6 > cluster_zstat6.txt",
"Used": [
- "urn:029ac7ce-e0ca-4637-8d00-caec11c22c76",
- "urn:13612015-a8d2-4871-b508-f4bb94ecc89b"
+ "urn:a4f27e7d-029b-48ed-b095-09e6c129877d",
+ "urn:f6592657-36ed-4171-a796-572995e39ac0"
]
},
{
- "@id": "urn:055e6616-8da2-44c5-aeb2-418931734dc0",
+ "@id": "urn:fcd11beb-5c6d-48b9-ae12-6e40be7ec4e6",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat6",
"Used": [
- "urn:6595ac2d-bf43-4a54-8cd9-f27e08178d8b"
+ "urn:5bad2097-52c6-41d1-87eb-7b2041df9627"
]
},
{
- "@id": "urn:f0febda5-28f8-4a7a-970e-4517c40e4ee5",
+ "@id": "urn:1f3989e8-ea60-4cbc-9444-3a3b6e170b93",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:9ec24ab3-4b92-46b9-9266-3c5e655db29c",
+ "@id": "urn:750ac308-6b79-4101-84ee-eb728049f005",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:8465e4d8-80f6-4f0f-b165-cb30f2704a4d"
+ "urn:7921758c-6274-495a-9ddb-602ba1b1b33d"
]
},
{
- "@id": "urn:f7d845ee-066a-455c-b70e-0a693a186017",
+ "@id": "urn:d8acd265-715c-4787-ac99-ecc8ed9c1a30",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:6f845091-280e-49cb-9947-2af6d2e7b4d3"
+ "urn:1989f88f-8d2d-48fb-ac53-233fd17be007"
]
},
{
- "@id": "urn:aa3780c6-2017-4f4c-ae10-2b0ec098f095",
+ "@id": "urn:28aa1a15-b895-4244-b676-5f4c7a10b638",
"Label": "ptoz",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:ec55145c-0b27-49f5-81ed-59dbe94ca102",
+ "@id": "urn:07f41d41-3ca8-4a79-942b-64ea67ee5549",
"Label": "cluster",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat2 -t 3.090232 --othresh=thresh_zfstat2 -o cluster_mask_zfstat2 --connectivity=26 --olmax=lmax_zfstat2.txt --scalarname=Z --voxuncthresh > cluster_zfstat2.txt",
"Used": [
- "urn:71bf85a6-3335-409a-a4bb-c2fa29231c14"
+ "urn:2d69372f-2ec8-4e73-8214-ca95009895aa"
]
},
{
- "@id": "urn:5901a2ea-b788-4e6d-ba09-54cf00c5d378",
+ "@id": "urn:f48d0ca0-9a14-4be3-90fd-991b09fcf53a",
"Label": "cluster2html",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat2",
"Used": [
- "urn:6ef4ad96-4836-4a98-a268-4a7432f14d2e"
+ "urn:6d1ba1f2-35ac-41f0-83b7-372b4b1093bf"
]
},
{
- "@id": "urn:18577179-bd3c-4dbb-b1eb-6a32757ed46f",
+ "@id": "urn:adabfb46-4b41-4613-aef9-b498df5e5fd6",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:3790699d-27ec-4cd2-b718-ba21560d41e5"
+ "urn:749935d9-e8c4-461b-821b-65c0dc026333"
]
},
{
- "@id": "urn:a5bb8cf2-12e7-4eec-95de-1d20dceb808b",
+ "@id": "urn:0994bdfc-8c4f-4872-89f1-8af5a3f902b6",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:8ddb9164-7c2d-4c97-a86b-2b3ce2a96d47"
+ "urn:84f2ef39-b49d-4c49-8264-81af872b2cbc"
]
},
{
- "@id": "urn:da2217a7-aee1-45a1-a872-1a94157cd6c3",
+ "@id": "urn:c0623cbc-3022-46fa-a837-1ac4e08f23d6",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:a6fb9f0f-15e6-4a8f-8544-b59c36ef72cb"
+ "urn:07004fc3-d47b-4f3a-bc7e-b1e7d2f03b6a"
]
},
{
- "@id": "urn:41c44de2-105b-4f51-a55d-9fb249a151ed",
+ "@id": "urn:e176cdc5-3382-40d6-a1af-d703e1ebf257",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat4 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:5a10086e-715a-46fb-a249-a2bb0dae791c"
+ "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb"
]
},
{
- "@id": "urn:9a6b936f-0fad-4390-bf3e-71423676502a",
+ "@id": "urn:7b9573eb-6f4b-428c-a624-a39ae72d7ba3",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat5 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d"
+ "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4"
]
},
{
- "@id": "urn:0ed10025-6c3b-498f-b8f7-145c6cf9829f",
+ "@id": "urn:9054a0f3-051b-4502-b73d-5c161e2b2d86",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat6 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:13612015-a8d2-4871-b508-f4bb94ecc89b"
+ "urn:a4f27e7d-029b-48ed-b095-09e6c129877d"
]
},
{
- "@id": "urn:018a0115-b414-4a52-8b4a-dcc8ddd77f1e",
+ "@id": "urn:0c3feed0-413f-4eab-9696-66fca2ed9942",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:8465e4d8-80f6-4f0f-b165-cb30f2704a4d"
+ "urn:7921758c-6274-495a-9ddb-602ba1b1b33d"
]
},
{
- "@id": "urn:78ac9ac3-ab64-48ed-9595-5a8da7c4a7cc",
+ "@id": "urn:7c7bf2d5-e7ab-4f62-aa37-76d4b7cad69d",
"Label": "fslstats",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:71bf85a6-3335-409a-a4bb-c2fa29231c14"
+ "urn:2d69372f-2ec8-4e73-8214-ca95009895aa"
]
},
{
- "@id": "urn:3bc61e8b-94a4-47fe-bbcd-8af24b2a709b",
+ "@id": "urn:e10a2fcb-4754-4170-aded-9b59f96dfc75",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090239 7.525257 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:087295b0-2f4b-4955-a595-429f14d9d263",
+ "@id": "urn:4bf36d8a-8717-485d-a782-efff67183308",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:fdcf607b-137a-4f04-807b-a47104dff267"
+ "urn:27b58ae0-82eb-423d-83c1-b8b2181da88d"
]
},
{
- "@id": "urn:9776a485-b8a2-4da8-b3d5-82c6db3edeb9",
+ "@id": "urn:1f495cc0-2caf-4f57-9ea2-ab897f49ba3b",
"Label": "cp",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:a43093fa-48c6-4d94-9392-d68edb15a82b"
+ "urn:0ee6edc0-db9c-4741-a232-708ca897be17"
]
},
{
- "@id": "urn:b661a5a3-de47-4bd5-9682-075e3dc7348f",
+ "@id": "urn:4d55ae09-a747-4397-a177-d909c1abdec2",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090239 7.525257 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:449d68ef-002c-4c72-890e-200c2ca7deae",
+ "@id": "urn:c92d9e2c-6ecb-46aa-8a8f-10ad148eaee9",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:3adea154-ab1b-43fd-9127-a12ecff84884"
+ "urn:6bfab610-89eb-4c16-ba6b-1b1b030f8292"
]
},
{
- "@id": "urn:4350385e-083c-468c-b204-ff7ce3734c0e",
+ "@id": "urn:361bb30a-f4e4-47bc-958d-75674d9c59a8",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat3 3.090239 7.525257 rendered_thresh_zstat3",
"Used": []
},
{
- "@id": "urn:29ed21f5-6774-4b24-a2d2-d14b61ce59b5",
+ "@id": "urn:0e527626-b2bd-4931-85eb-daf1ae844ea5",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat3 -A 750 rendered_thresh_zstat3.png",
"Used": [
- "urn:74597bc2-4728-4335-95bb-81025541b4ae"
+ "urn:893c5726-58fc-44e9-a077-2af27aa758a2"
]
},
{
- "@id": "urn:3ccfec6d-e2ec-4c67-b5b7-d49da48a2e61",
+ "@id": "urn:52486c9c-cd8f-4e19-a5f5-4243aafa1285",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat4 3.090239 7.525257 rendered_thresh_zstat4",
"Used": []
},
{
- "@id": "urn:bf062820-dfad-4ff5-a794-14bfe43fd48b",
+ "@id": "urn:e4db3a91-23a1-4bfc-8d9f-e44c398c6a2c",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat4 -A 750 rendered_thresh_zstat4.png",
"Used": [
- "urn:0fb7b5bf-2160-4aae-bd8f-2d8a4d8a81bb"
+ "urn:c55b4e40-acb8-4cb9-a44f-a885c97f4ea7"
]
},
{
- "@id": "urn:7e64c091-d21a-455a-9ce9-820676099fa1",
+ "@id": "urn:116e0cb2-5547-433d-9b0a-cd59c277c6b8",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat5 3.090239 7.525257 rendered_thresh_zstat5",
"Used": []
},
{
- "@id": "urn:c35adba0-7fc6-485a-9a6e-546aeb651594",
+ "@id": "urn:0ce32f62-4fc0-42c0-893b-b03f2e4ae488",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat5 -A 750 rendered_thresh_zstat5.png",
"Used": [
- "urn:42705fbf-bd87-439a-89a0-6f4a24e459e3"
+ "urn:6d1d8579-6a61-4011-b989-95c24e68e879"
]
},
{
- "@id": "urn:ee53297a-5ce2-4932-92b8-8550b3b89d1c",
+ "@id": "urn:5c92426e-803d-4eb0-81de-03f890ca7386",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat6 3.090239 7.525257 rendered_thresh_zstat6",
"Used": []
},
{
- "@id": "urn:e5aab2e8-72a6-4fb6-9085-b63d22e335a2",
+ "@id": "urn:0f0d8d27-624e-4177-a4ce-0e4655ee2e68",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat6 -A 750 rendered_thresh_zstat6.png",
"Used": [
- "urn:9d2da488-b04e-4aae-b586-c30db9190292"
+ "urn:42f5e934-e5d2-4707-ad09-4dd6a6b280fc"
]
},
{
- "@id": "urn:85de85e6-c096-4520-be17-2ef38ee27ba4",
+ "@id": "urn:1926242a-0d21-447f-99e9-e5dc8941f48c",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090239 7.525257 rendered_thresh_zfstat1",
"Used": []
},
{
- "@id": "urn:80894f34-5436-4a99-bd8c-cd28bd86ba6d",
+ "@id": "urn:fcf8088f-b2b9-4a81-a7e0-09c6db3b4aed",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
"Used": [
- "urn:0b905e9b-9dfc-4c55-ae37-69d8382573bd"
+ "urn:f6b2ac4c-0311-49b6-abf0-b0ea89ecab4c"
]
},
{
- "@id": "urn:a15c84dd-d081-4919-b897-d046a70498ec",
+ "@id": "urn:ebb97d70-b892-4949-9449-97c5864b16ae",
"Label": "overlay",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat2 3.090239 7.525257 rendered_thresh_zfstat2",
"Used": []
},
{
- "@id": "urn:7a795607-4194-4dc6-81cf-5d2b83bf47c1",
+ "@id": "urn:ca08e7e4-ce9d-43ff-994b-c2be02f6a9f7",
"Label": "slicer",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat2 -A 750 rendered_thresh_zfstat2.png",
"Used": [
- "urn:4634275d-8f31-4429-bf23-59bfd3c12e74"
+ "urn:d5506b4c-ab38-46d9-b17a-0e03a202eac8"
]
},
{
- "@id": "urn:38192dea-15e8-4bd3-b329-644b70132660",
+ "@id": "urn:3f6420f5-5f28-44a5-a547-f4a55c2d74a1",
"Label": "Make directory",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:acd749a0-2d7c-4376-98d0-74a4bf206371",
+ "@id": "urn:a899046d-1abd-4476-b24f-bb78675772cd",
"Label": "tsplot",
- "AssociatedWith": "urn:8063eb5f-7ced-4e8d-ab4b-70708b7b58cd",
+ "AssociatedWith": "urn:702737cb-6d07-4ec0-ab3a-7c31973394c1",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
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+ "GeneratedBy": "urn:f033c345-4c18-4394-8840-c59b67eb5768",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:e979890c-b353-4ba7-b2af-7329f3b60492",
+ "@id": "urn:f5913280-0bd6-4a37-8ccd-bebabdaff219",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:ceee21da-5021-42e6-a2fb-7cdb8eb1c6b7",
+ "GeneratedBy": "urn:a65fd1d4-ef92-4252-b635-1d83cdf8bb6e",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:88c55a65-128e-4b4b-94ba-19a350918ab6",
+ "@id": "urn:9b450b93-cbf6-4dfa-b2bc-7ddbce3cd232",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:7ecc666a-cc97-4a61-8503-bb525adfba6b",
+ "GeneratedBy": "urn:3c5b5b1c-11b1-4891-8be9-96b21c82fdc1",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:33ea97ed-7601-42c3-99f1-bdad2cd7a2fa",
+ "@id": "urn:23118e41-8c41-4e4c-9e3e-3c36de30538d",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -1384,25 +1384,25 @@
}
},
{
- "@id": "urn:1cc5bae4-9c74-47a2-a561-1b5e122d3051",
+ "@id": "urn:e7293b42-c5a8-4a4c-a0d5-9a29f7f215c2",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:f86a6c6f-3ced-4686-8ed9-79c1377c287a",
+ "GeneratedBy": "urn:28408038-4814-4994-93eb-6ec6c5e5217b",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:e22719b6-d4be-48ce-b94a-24c556ee69a8",
+ "@id": "urn:c5185326-5632-487d-9bad-382da355c44c",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:9d505fad-bfb4-4d42-9041-d332f14f09ef",
+ "GeneratedBy": "urn:919b203e-22f8-4529-8a7c-0fd91cd96f88",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:87b3d43b-7d89-4e8b-a598-0662190f537f",
+ "@id": "urn:b92c80cd-35e5-4ed5-936a-1ec1f0154003",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1410,7 +1410,7 @@
}
},
{
- "@id": "urn:f402aeb8-bdab-4572-9a90-d607a19d64e6",
+ "@id": "urn:ef3204e8-e1db-40ac-bf2b-fa7d12275329",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1418,7 +1418,7 @@
}
},
{
- "@id": "urn:087865c4-2517-4b7c-a084-f175c515884c",
+ "@id": "urn:05a732ed-44d0-4002-98ac-cec09f8f0b8d",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1426,7 +1426,7 @@
}
},
{
- "@id": "urn:29aba15c-e988-4938-8925-3e1516f516a3",
+ "@id": "urn:bfecc9ae-1ef2-40a5-941a-89224c16e5b8",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1434,7 +1434,7 @@
}
},
{
- "@id": "urn:fb597bf8-04ef-4d61-9c23-d1bf17b700e7",
+ "@id": "urn:67d4bff9-65dc-4160-b555-72d89dbb6005",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1442,7 +1442,7 @@
}
},
{
- "@id": "urn:87456180-00b3-4cc9-994f-62bb929164b8",
+ "@id": "urn:f0f6e742-8baf-4107-a547-640947bbf8a0",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1450,34 +1450,34 @@
}
},
{
- "@id": "urn:921aa6a9-365a-4981-8458-001d9ba50331",
+ "@id": "urn:763b1342-77ac-4c0b-a0c3-86f9a8076188",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:d3a3868e-57ab-4fe3-913d-8d47a0d4fa52",
+ "GeneratedBy": "urn:a48732b4-acbc-4106-a1f7-459dcca22dd6",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:9d464330-204c-4836-8e63-7577201ac4c2",
+ "@id": "urn:ce8afeee-0e8f-46ae-841d-b64bb7a018ab",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:c71305e5-49ab-4bec-9a88-4837edc1e558",
+ "GeneratedBy": "urn:560bd7e9-df84-4134-a5a2-ffec5be80914",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:117d50be-276e-44b9-a974-59a90cdc308c",
+ "@id": "urn:529ec39c-bfa2-4d42-9848-0d01fe2a5e55",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:b33646b2-646b-45ae-a449-43a0c28b1a6d",
+ "GeneratedBy": "urn:0288624e-3fe7-438c-a66e-8b0cd95f65c1",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:be8ba766-1555-453e-9644-52b7ea3e0b41",
+ "@id": "urn:19f44ccc-9b2b-4751-bf58-45cb48c9c540",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1485,34 +1485,34 @@
}
},
{
- "@id": "urn:f43ec009-6d83-4fde-8637-cfda36cba7c8",
+ "@id": "urn:c70dc9e0-dc50-4bfc-bbab-d88f9ebbe9f3",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:75bdbb93-ecf8-4707-b568-3acb8cd49ddc",
+ "GeneratedBy": "urn:da717efa-327f-4ffa-89d2-92f59a19a50e",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:b41c1cc8-933c-4a8b-85d4-3a9f80498340",
+ "@id": "urn:b75866fd-6330-46da-ace3-0f92ce0575fe",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:b9bd9710-5122-4098-9acf-8d228dce9a76",
+ "GeneratedBy": "urn:9ceeaf33-f1bf-42ea-953f-d6b7d6ae4452",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:e4aa0fb3-4756-47d6-9de6-77cec0ab9731",
+ "@id": "urn:cbfe29b0-9234-4b87-82c4-28b72f0df81c",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:3ca35147-dc66-46af-bd2a-ca466dc5c4f9",
+ "GeneratedBy": "urn:0de59090-a792-4965-b076-2ca69af34713",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:d9de738d-c015-4ac9-afaa-938f4e8d54d7",
+ "@id": "urn:f6b805b2-5c95-418c-9a87-0998cbca636e",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1520,106 +1520,106 @@
}
},
{
- "@id": "urn:0b1b7bde-9546-4772-abbe-3984f952f1ec",
+ "@id": "urn:0845cab6-e232-408e-b04b-bf8aefb3c349",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0aefca75-8457-4b37-9220-9065a676cc39",
+ "GeneratedBy": "urn:c08a1124-280f-4d98-8f24-0d05490b60e6",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:bb968bcf-419b-4bf7-a6c7-5ac98405a73f",
+ "@id": "urn:d9cd83b8-9b2d-44a2-a1e6-fd0651cabf03",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:7b40b911-8757-4a00-bae1-fb3d68382e7b",
+ "GeneratedBy": "urn:e98e90db-2675-4f55-be10-6f87b559e7d6",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:894cab31-3c91-43df-aa22-fcb41742d2e4",
+ "@id": "urn:25151d2d-9541-4702-910b-34e9337d6dc4",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:0cac31cc-159f-4927-b0dd-f1a7166d6614",
+ "GeneratedBy": "urn:001e2ebb-0f2e-4dbe-a80b-ad351aa0bcbe",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:6441239c-3ff4-45ce-a136-41bf8e6fd33a",
+ "@id": "urn:81d22aea-101a-4705-a80b-51377716f6ee",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:5e4c7270-4828-4ea5-9229-b98f490e9bbc",
+ "GeneratedBy": "urn:a9c53e38-6940-4b59-9eef-3b5922f9ca7a",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:75cc4aa9-4afb-4375-9045-4fc9c45c506a",
+ "@id": "urn:32553c0c-47d4-4e17-b213-aeb143c39f70",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:c8f49f12-8b13-478c-80d8-2e5352fe372b",
+ "GeneratedBy": "urn:6d73fda2-0c34-40d4-920f-9e2a8fdfd781",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:dba88ff1-79ae-4867-97c3-3685b147c297",
+ "@id": "urn:030ac5c4-f590-4652-abfb-c2415e30f6d0",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:00952bcd-b9f3-4b91-8e31-bc58ddbf8082",
+ "GeneratedBy": "urn:c05d71d0-695d-4142-bbdb-88f57fb53219",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:ea295298-15e9-4553-a615-29f04d8138b1",
+ "@id": "urn:7301e5d4-ee74-4643-b174-04dac2bc17bd",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a2872607-ec43-4a31-9ead-e326632837bf",
+ "GeneratedBy": "urn:538a39c8-734b-4575-9dd3-02305261fdd6",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:2c8bf5db-37af-4b00-92a0-d2310ccc0371",
+ "@id": "urn:5150ea63-253e-4632-8e1c-e6d6f66d3f9b",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:5929d021-c389-40b8-805a-044f09a71d42",
+ "GeneratedBy": "urn:d446fbfc-2ff1-4066-8050-bcc12f44e46e",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:10a59a9e-d688-4beb-904f-a9f05eb85774",
+ "@id": "urn:c12def47-7729-4f52-94a9-db975e35d749",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:24a199cf-30a1-4540-a7d5-9830fee1989a",
+ "GeneratedBy": "urn:e2af0880-2a04-4a00-96a3-c41d53591247",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:71f9e9f7-19e5-459e-94c6-05e44e3cc474",
+ "@id": "urn:853061ad-42a3-405c-8ea4-4cdf534495d6",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:82749c15-7a83-4b5d-abb9-b74aae16fa81",
+ "GeneratedBy": "urn:38704d9b-61c8-49cc-9b71-84de095523bf",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:1e5f5881-04e7-40df-85b6-db6338a8b9e1",
+ "@id": "urn:811288a2-49a2-4a25-a88d-b9428fcb266e",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:72122e17-9b35-403d-b214-abe7be549e59",
+ "GeneratedBy": "urn:b97ce5dd-8d4e-45b6-8bfb-c148e2c4eee5",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:d2a1e303-a574-44e4-84ac-85293d3844d3",
+ "@id": "urn:f4a25276-5185-4794-a1d8-5096e20c0aa4",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1627,25 +1627,25 @@
}
},
{
- "@id": "urn:38359f0d-0376-4cd9-b242-9c4b33dc6392",
+ "@id": "urn:2b88e9cd-f0ae-44d5-b8f5-aac0f7d43b5b",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:a1b863ef-5a4f-4406-b100-3dddd647ef1c",
+ "GeneratedBy": "urn:f5d7521b-b160-4096-8ba1-a7560ca00126",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:5abb2ca1-a8ca-400d-9fc6-4d55b714f708",
+ "@id": "urn:4b629c6e-ec58-44b8-bf63-76521ab37ad1",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:9f31b8ab-69ee-49ec-82c4-c8359d7de3c8",
+ "GeneratedBy": "urn:2d3597e6-3bc3-4588-ad30-2b66d5d8c409",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:d6b8b109-1b37-4302-ba5c-7de9ea37de91",
+ "@id": "urn:32aae5a8-0964-451f-bcb0-8d617608c133",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1653,16 +1653,16 @@
}
},
{
- "@id": "urn:6f8fe425-239f-4dfa-8b97-95d38d64b317",
+ "@id": "urn:22db26bd-486f-4dc5-980d-f943143a3734",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:165bae48-7dae-427e-b10a-d1e238d9a17a",
+ "GeneratedBy": "urn:c48eb7b9-b8c4-4983-b55e-e69acedcf06c",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:68cdaeb7-59fc-440a-9c6b-7f7df63da8f4",
+ "@id": "urn:9ad2b4b3-af7c-4e12-aaff-39f1e5dd7553",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1670,22 +1670,22 @@
}
},
{
- "@id": "urn:7af713f3-b8a5-4a79-95fd-8e6c5f25a64b",
+ "@id": "urn:3c565e3e-f7b2-4c8c-82c7-06c46a42c8a9",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:28317228-ec2f-447f-8c78-e171c1cbb61d"
+ "GeneratedBy": "urn:abb994eb-f289-446f-b568-e9ebdb638e9d"
},
{
- "@id": "urn:f3ec8a03-ff2c-4d67-af27-aebcebd30f5d",
+ "@id": "urn:6ea2ff65-dfd0-42ff-ad83-bde0185582ab",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:68079d2a-f99a-4365-a455-48bcf66b0699",
+ "GeneratedBy": "urn:4324d607-6f82-4b26-9b3f-be7b6646d02c",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:3cb24f05-3dce-4413-98ce-0b5f694af482",
+ "@id": "urn:7e86c053-51ee-4584-8815-4172d57aba3b",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1693,13 +1693,13 @@
}
},
{
- "@id": "urn:4728686d-9548-4cfa-b106-3de60ed831c1",
+ "@id": "urn:869b5598-910e-461c-8ce4-0a128e36966b",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:b5ab0ba4-4889-4f87-a5c8-817a91c4de71"
+ "GeneratedBy": "urn:da251042-e0c9-4a5d-aa0f-65586a9afef2"
},
{
- "@id": "urn:2fca9e42-28fe-4360-bfe7-d3f1e1490b0f",
+ "@id": "urn:fa49893e-f5f8-4125-a711-ab61e8b086ad",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1707,16 +1707,16 @@
}
},
{
- "@id": "urn:6d0835cf-78c8-4e50-931c-dc55ff948363",
+ "@id": "urn:7ef93785-2d16-4eb2-9651-a05fd8350c3a",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:c6a57e08-7b1d-4b28-aa5c-fc678f8a6bfe",
+ "GeneratedBy": "urn:7b48b2ff-cf50-4ebc-bf3e-89864d8e6665",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:9e567321-3457-41ae-bca6-51f4ab7a9e7f",
+ "@id": "urn:6971be6a-53d5-42ae-9a7d-62bfc15d7199",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1724,16 +1724,16 @@
}
},
{
- "@id": "urn:3790699d-27ec-4cd2-b718-ba21560d41e5",
+ "@id": "urn:749935d9-e8c4-461b-821b-65c0dc026333",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:bacd31a3-804a-4288-ac9a-a0a655acb9ef",
+ "GeneratedBy": "urn:85977f2f-13db-440b-870c-874941174d02",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:955d6933-0d82-4f2b-85c2-0958b8acfeda",
+ "@id": "urn:14839d0c-c9ad-4342-b8e3-8ad6ccfcbc28",
"Label": "zstat2",
"AtLocation": "stats/zstat2",
"digest": {
@@ -1741,16 +1741,16 @@
}
},
{
- "@id": "urn:8ddb9164-7c2d-4c97-a86b-2b3ce2a96d47",
+ "@id": "urn:84f2ef39-b49d-4c49-8264-81af872b2cbc",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:5fafa766-c98b-4270-a2d7-7245919ec15c",
+ "GeneratedBy": "urn:5ec01159-c502-4272-a8e7-af88f3165ef8",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:f130abec-a52a-40eb-b88c-c66c103f5f6c",
+ "@id": "urn:e571d0ba-5590-4c78-8061-3aaebe4095b6",
"Label": "zstat3",
"AtLocation": "stats/zstat3",
"digest": {
@@ -1758,16 +1758,16 @@
}
},
{
- "@id": "urn:a6fb9f0f-15e6-4a8f-8544-b59c36ef72cb",
+ "@id": "urn:07004fc3-d47b-4f3a-bc7e-b1e7d2f03b6a",
"Label": "thresh_zstat3",
"AtLocation": "thresh_zstat3",
- "GeneratedBy": "urn:6f461622-bc47-4e79-b351-2948972c5391",
+ "GeneratedBy": "urn:20bde1e7-dd88-4056-81dd-b02a9243bc96",
"digest": {
"sha256": "d0f88769369dc8215d7373817e8f9a48482b508bb9deb2ca29904069bb23f484"
}
},
{
- "@id": "urn:f0f4353c-7637-4227-92b0-58e0afa1d0b9",
+ "@id": "urn:4b53fd78-baf2-4ad9-b03b-f6950080ffc8",
"Label": "zstat4",
"AtLocation": "stats/zstat4",
"digest": {
@@ -1775,16 +1775,16 @@
}
},
{
- "@id": "urn:5a10086e-715a-46fb-a249-a2bb0dae791c",
+ "@id": "urn:e9d84da7-d15b-4a7a-8c90-240b2a88a4fb",
"Label": "thresh_zstat4",
"AtLocation": "thresh_zstat4",
- "GeneratedBy": "urn:72309cbc-a1ff-4ece-b74d-7ab14d5329ec",
+ "GeneratedBy": "urn:a1248b06-2827-402c-a459-bf581539c214",
"digest": {
"sha256": "7d0ee58ccf12389afd32deb44a620da2bd1f2ebfa70a72c43328055de692ff98"
}
},
{
- "@id": "urn:3c8bd9ea-f940-4527-8bf8-7e2f9a190099",
+ "@id": "urn:1cd32c4e-606d-489b-bd86-54e96d1803e3",
"Label": "zstat5",
"AtLocation": "stats/zstat5",
"digest": {
@@ -1792,16 +1792,16 @@
}
},
{
- "@id": "urn:43d395c3-1ccd-4588-ac63-d743e9d3d44d",
+ "@id": "urn:42b186e8-d358-4693-9d8c-cf46840ea4e4",
"Label": "thresh_zstat5",
"AtLocation": "thresh_zstat5",
- "GeneratedBy": "urn:c108b15e-d09b-48b6-99b8-a0aa3bcaa657",
+ "GeneratedBy": "urn:1d532a3f-d2f2-4331-8a39-1f17fa9cb5c0",
"digest": {
"sha256": "1f5c0f183460f4e90178ce2e1778cf74f2b9cbb163602d06d7b10023caef88c9"
}
},
{
- "@id": "urn:31afdc2f-30f8-4682-a3d6-58f886590e75",
+ "@id": "urn:21d8d15a-17bd-4d18-9034-2ae2bdba5013",
"Label": "zstat6",
"AtLocation": "stats/zstat6",
"digest": {
@@ -1809,16 +1809,16 @@
}
},
{
- "@id": "urn:13612015-a8d2-4871-b508-f4bb94ecc89b",
+ "@id": "urn:a4f27e7d-029b-48ed-b095-09e6c129877d",
"Label": "thresh_zstat6",
"AtLocation": "thresh_zstat6",
- "GeneratedBy": "urn:4dc65753-932f-49f4-b53e-3d8855fa336e",
+ "GeneratedBy": "urn:4e6d3431-054c-48d3-b7c9-8bd56f26a529",
"digest": {
"sha256": "9e3f489bd3068058a3f61a8aaaa0cc5b9ea4f4180ecff380d03a899d0cf3a976"
}
},
{
- "@id": "urn:226bd3cb-3e0d-4c85-82cc-7baa47c0f26e",
+ "@id": "urn:0dca7183-5a09-4e87-9168-f1ce2eea29b3",
"Label": "zfstat1",
"AtLocation": "stats/zfstat1",
"digest": {
@@ -1826,16 +1826,16 @@
}
},
{
- "@id": "urn:8465e4d8-80f6-4f0f-b165-cb30f2704a4d",
+ "@id": "urn:7921758c-6274-495a-9ddb-602ba1b1b33d",
"Label": "thresh_zfstat1",
"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:39d91d05-0337-4cde-8b33-86c43a213344",
+ "GeneratedBy": "urn:86a3d035-808a-4af8-a397-5761b4ce25b2",
"digest": {
"sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
}
},
{
- "@id": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
+ "@id": "urn:8e7762a4-60d2-4b68-a52a-b1cdecaa5a5b",
"Label": "zfstat2",
"AtLocation": "stats/zfstat2",
"digest": {
@@ -1843,16 +1843,16 @@
}
},
{
- "@id": "urn:71bf85a6-3335-409a-a4bb-c2fa29231c14",
+ "@id": "urn:2d69372f-2ec8-4e73-8214-ca95009895aa",
"Label": "thresh_zfstat2",
"AtLocation": "thresh_zfstat2",
- "GeneratedBy": "urn:83e679fa-bc45-496a-b380-e64dbf09045e",
+ "GeneratedBy": "urn:a32dfe88-22f5-4e9b-b025-9892df2eb81a",
"digest": {
"sha256": "c298297997e4640c4c2d803314ca8cee706d302781975cdc53946aa6ca0d69c1"
}
},
{
- "@id": "urn:73d43f31-95c3-4568-b492-5ca4371c4f13",
+ "@id": "urn:dad480ac-f312-4758-89c9-2c6765d6393a",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1860,25 +1860,25 @@
}
},
{
- "@id": "urn:9b12c597-55e3-4cc1-8d36-7229cbd4b64a",
+ "@id": "urn:a949df0d-6e4b-497e-be36-a43818510275",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:4ae04bd2-f829-465d-967b-51490c165efc",
+ "GeneratedBy": "urn:23e90369-5cf2-465e-a4b0-c4ac55508925",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:9d77733e-7a2d-451f-970e-c6292ca36386",
+ "@id": "urn:c5da5c16-852c-4a75-a6e6-f70fcc9bc766",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:4ae04bd2-f829-465d-967b-51490c165efc",
+ "GeneratedBy": "urn:23e90369-5cf2-465e-a4b0-c4ac55508925",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:0e2032e9-ee9a-41f0-bd5b-53089bd62c12",
+ "@id": "urn:bed01f22-b1b7-4c60-939d-4caa877b5cf6",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1886,7 +1886,7 @@
}
},
{
- "@id": "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df",
+ "@id": "urn:ff211113-f43c-49ad-acba-57fd339badeb",
"Label": "cope2",
"AtLocation": "stats/cope2",
"digest": {
@@ -1894,25 +1894,25 @@
}
},
{
- "@id": "urn:19e57842-9830-4d40-b483-414e17fe13b2",
+ "@id": "urn:7ccada4d-6e81-49f3-83c6-d266594f0c20",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
+ "GeneratedBy": "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
"digest": {
"sha256": "b88bb3cd4d809827a5c0a45cb4f6aac570cb25b7e056d5986d81d879548da121"
}
},
{
- "@id": "urn:ecb956c2-4afd-45b2-836a-a5deb9acec5b",
+ "@id": "urn:2e82d6a1-9e2a-446b-b508-0e5df37dbdfb",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
+ "GeneratedBy": "urn:cb038b70-f5e5-4619-a661-3b6f816e4043",
"digest": {
"sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
}
},
{
- "@id": "urn:068a56ed-fa24-4ab2-9781-d333a439bf94",
+ "@id": "urn:d13633e4-0e1f-4847-aa4b-872c2aaee8dc",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1920,7 +1920,7 @@
}
},
{
- "@id": "urn:8679d689-6609-4dd7-85a2-330a667c96e9",
+ "@id": "urn:fd74433b-972f-43cf-a1b4-dfc0eda30f74",
"Label": "cope3",
"AtLocation": "stats/cope3",
"digest": {
@@ -1928,25 +1928,25 @@
}
},
{
- "@id": "urn:5c190260-bee3-477a-956e-d0675ac7e19e",
+ "@id": "urn:73538065-1ce0-4b7e-b73a-e06e0bf72f6b",
"Label": "cluster_mask_zstat3",
"AtLocation": "cluster_mask_zstat3",
- "GeneratedBy": "urn:acd4e7d2-df0c-48fb-aa83-679b3df6591c",
+ "GeneratedBy": "urn:9c331ad8-b671-4cd6-9d35-d2c9da897c4b",
"digest": {
"sha256": "fac31b7cc91c4dbb519375fa9238cfde00689381b0783d7e3b623a937b9f51d0"
}
},
{
- "@id": "urn:9d964c85-58a1-40e2-8ea1-06c596be6661",
+ "@id": "urn:3c3330f9-e4c8-4073-b802-98d8d99c58e4",
"Label": "cope3",
"AtLocation": "stats/cope3",
- "GeneratedBy": "urn:acd4e7d2-df0c-48fb-aa83-679b3df6591c",
+ "GeneratedBy": "urn:9c331ad8-b671-4cd6-9d35-d2c9da897c4b",
"digest": {
"sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
}
},
{
- "@id": "urn:5d51bc01-580e-4fb9-a4b5-453ef634cd1a",
+ "@id": "urn:2fc29d78-7b54-4548-b14f-ab9bc8df945d",
"Label": "cluster_zstat3",
"AtLocation": "cluster_zstat3",
"digest": {
@@ -1954,7 +1954,7 @@
}
},
{
- "@id": "urn:6af02df5-827e-4ddf-9b00-baecee725fcd",
+ "@id": "urn:f599026a-b8c6-4a3a-84ec-c35bfb1b8d22",
"Label": "cope4",
"AtLocation": "stats/cope4",
"digest": {
@@ -1962,25 +1962,25 @@
}
},
{
- "@id": "urn:7c54373f-c93e-4f5c-b2d9-d3a7b7ea47aa",
+ "@id": "urn:a86c86a4-3f9b-4369-8af5-f4c00a630aa8",
"Label": "cluster_mask_zstat4",
"AtLocation": "cluster_mask_zstat4",
- "GeneratedBy": "urn:f1197319-954d-477d-bb96-7dee72a45bd7",
+ "GeneratedBy": "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
"digest": {
"sha256": "236c7040f9f44c5f102ed2cc3fad96a03bcdf369e764ef6bfea5b18d75e9abb5"
}
},
{
- "@id": "urn:3f5fcc63-c232-47b9-9bfe-231b359c95b9",
+ "@id": "urn:266b5cb2-05fc-4b42-911c-10ff37218065",
"Label": "cope4",
"AtLocation": "stats/cope4",
- "GeneratedBy": "urn:f1197319-954d-477d-bb96-7dee72a45bd7",
+ "GeneratedBy": "urn:45516259-81b3-4845-9a96-dcc09711ebd1",
"digest": {
"sha256": "b6f8f8cfc79a9728843c597031f0d708ffe70f4865e3ec6456482bcf5e988347"
}
},
{
- "@id": "urn:e648c12f-577e-426e-b264-ef77b5359fad",
+ "@id": "urn:9cbbee48-65ca-4a99-9a9d-1a91678dc392",
"Label": "cluster_zstat4",
"AtLocation": "cluster_zstat4",
"digest": {
@@ -1988,7 +1988,7 @@
}
},
{
- "@id": "urn:6c68e7db-4b96-4b16-b064-fbf79cad5a41",
+ "@id": "urn:38117d67-65a2-4205-a194-f063e257b0b1",
"Label": "cope5",
"AtLocation": "stats/cope5",
"digest": {
@@ -1996,25 +1996,25 @@
}
},
{
- "@id": "urn:a044d7d6-c80d-4b3f-873d-e0fae65af109",
+ "@id": "urn:798b2a2d-2a07-4e9f-8617-e8c0b625ab40",
"Label": "cluster_mask_zstat5",
"AtLocation": "cluster_mask_zstat5",
- "GeneratedBy": "urn:6ed8d342-b419-4019-bef6-278dea44193e",
+ "GeneratedBy": "urn:0ba6cdcc-8a3d-4d06-b346-1e6354434c52",
"digest": {
"sha256": "c017022e8f02a206ba703043a7cca57d23cbb1327fe198615792ef86a6d9e088"
}
},
{
- "@id": "urn:aae4ed70-8823-4964-83b4-5d2f17e7fcc3",
+ "@id": "urn:bb9634f9-be32-4008-9ba3-ffea4e168cba",
"Label": "cope5",
"AtLocation": "stats/cope5",
- "GeneratedBy": "urn:6ed8d342-b419-4019-bef6-278dea44193e",
+ "GeneratedBy": "urn:0ba6cdcc-8a3d-4d06-b346-1e6354434c52",
"digest": {
"sha256": "cce90c23c0b7646ad6ed60fe900a84c9a92a151e90e51a3c8d5bf609e48e7e37"
}
},
{
- "@id": "urn:394e603e-0619-459e-a1c1-6dffeac3be20",
+ "@id": "urn:1eeee773-a0f8-46a9-a05c-64cd0ada78df",
"Label": "cluster_zstat5",
"AtLocation": "cluster_zstat5",
"digest": {
@@ -2022,7 +2022,7 @@
}
},
{
- "@id": "urn:029ac7ce-e0ca-4637-8d00-caec11c22c76",
+ "@id": "urn:f6592657-36ed-4171-a796-572995e39ac0",
"Label": "cope6",
"AtLocation": "stats/cope6",
"digest": {
@@ -2030,25 +2030,25 @@
}
},
{
- "@id": "urn:2eabf927-c80e-4338-b26a-0d07283fc38a",
+ "@id": "urn:87cc6247-bc0d-422b-8b7e-d96348b86c74",
"Label": "cluster_mask_zstat6",
"AtLocation": "cluster_mask_zstat6",
- "GeneratedBy": "urn:2a83909e-befd-42a8-bfd8-2c3310b0f853",
+ "GeneratedBy": "urn:1da9dbfa-c3ce-4e04-bd20-9f529928201b",
"digest": {
"sha256": "b443499c0537a51d05605fa88d988683ccda5aedfeb1959b3a465864cfc16476"
}
},
{
- "@id": "urn:1c4d8379-a962-4530-b203-961ea5164edd",
+ "@id": "urn:1a04bdf8-5441-4f18-a241-1b3ecf3a0a09",
"Label": "cope6",
"AtLocation": "stats/cope6",
- "GeneratedBy": "urn:2a83909e-befd-42a8-bfd8-2c3310b0f853",
+ "GeneratedBy": "urn:1da9dbfa-c3ce-4e04-bd20-9f529928201b",
"digest": {
"sha256": "f45749b02e0f09e62c96d79da8d85078fec9357d695e8bc30eba2e0c0658fedb"
}
},
{
- "@id": "urn:6595ac2d-bf43-4a54-8cd9-f27e08178d8b",
+ "@id": "urn:5bad2097-52c6-41d1-87eb-7b2041df9627",
"Label": "cluster_zstat6",
"AtLocation": "cluster_zstat6",
"digest": {
@@ -2056,16 +2056,16 @@
}
},
{
- "@id": "urn:0db9f667-31ec-4cc1-b7d6-ddb0ea21f714",
+ "@id": "urn:dff39876-ad27-4e98-8d9a-30be0fc479ef",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:9ec24ab3-4b92-46b9-9266-3c5e655db29c",
+ "GeneratedBy": "urn:750ac308-6b79-4101-84ee-eb728049f005",
"digest": {
"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:6f845091-280e-49cb-9947-2af6d2e7b4d3",
+ "@id": "urn:1989f88f-8d2d-48fb-ac53-233fd17be007",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -2073,16 +2073,16 @@
}
},
{
- "@id": "urn:63f0031d-eb88-40a7-9545-42781f2da105",
+ "@id": "urn:6aaf2f10-d644-48e2-83c2-dfde7dc9ee02",
"Label": "cluster_mask_zfstat2",
"AtLocation": "cluster_mask_zfstat2",
- "GeneratedBy": "urn:ec55145c-0b27-49f5-81ed-59dbe94ca102",
+ "GeneratedBy": "urn:07f41d41-3ca8-4a79-942b-64ea67ee5549",
"digest": {
"sha256": "962ef7014f226d586c47fb23ebcde5968e55a03f06dae8514b358579d8457e7a"
}
},
{
- "@id": "urn:6ef4ad96-4836-4a98-a268-4a7432f14d2e",
+ "@id": "urn:6d1ba1f2-35ac-41f0-83b7-372b4b1093bf",
"Label": "cluster_zfstat2",
"AtLocation": "cluster_zfstat2",
"digest": {
@@ -2090,25 +2090,25 @@
}
},
{
- "@id": "urn:fdcf607b-137a-4f04-807b-a47104dff267",
+ "@id": "urn:27b58ae0-82eb-423d-83c1-b8b2181da88d",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:3bc61e8b-94a4-47fe-bbcd-8af24b2a709b",
+ "GeneratedBy": "urn:e10a2fcb-4754-4170-aded-9b59f96dfc75",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:ae232832-f515-4065-9319-c6c9a8f92921",
+ "@id": "urn:952cfaa3-f29a-4dbc-8c74-1a7ebdf25b15",
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diff --git a/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png b/examples/from_parsers/fsl/fsl_gamma_basis_report_log.png
index e9a5ee886..ca3075f01 100644
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diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
index 67a8725e3..a992ee954 100644
--- a/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_gaussian_report_log.jsonld
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- "urn:f0482e54-ccc8-49e0-aed4-703c4a8469ee",
- "urn:f52b1da6-54af-4ef5-b883-eef4570d66b1"
+ "urn:2b668af4-fe26-4fa7-b147-7a6123214e69",
+ "urn:4d974f57-b70e-4d4d-a845-906dc7319c45",
+ "urn:521d474c-ce81-4a45-bc60-cc7d7fdfb117",
+ "urn:59e90a02-6903-4b34-b581-656cc223956c",
+ "urn:66740f57-693a-4773-a79c-248ab7a34d24",
+ "urn:7b5de754-3451-4c33-96b1-ab7d2f389dda",
+ "urn:7f7c9933-2af8-4d36-bd84-1774cfe99bb6",
+ "urn:8774d01a-a6dd-4c0b-8182-170c0948c565",
+ "urn:c6e21f69-c865-4c72-8480-f4f6ada95937",
+ "urn:ee4d2236-e8f8-40a9-87da-519574228dc2",
+ "urn:ef52ae7f-9d76-4245-bd24-56a59d5a6dc3",
+ "urn:f3a7b92f-d4e3-4600-92d4-7ffd78ecf0ab"
]
},
{
- "@id": "urn:7c5b9650-7b6e-4d59-a889-e62a51997c2d",
+ "@id": "urn:a8472bb9-2ead-43f6-8616-18f9aae4d8e0",
"Label": "slicer",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:1297dbd7-23fe-4261-a4b7-62ac5775ae55",
- "urn:a0096f78-1a37-4831-9297-028f78e5f5bb"
+ "urn:8f3a6781-ee2f-445d-99bd-29309e221c13",
+ "urn:9b25a4c9-acc3-486d-b147-bfc7fcb1c086"
]
},
{
- "@id": "urn:2c2f9da6-1898-4f9a-b578-ed76c37eddd4",
+ "@id": "urn:a5c49bf0-371f-4eaf-8530-22d41303efbd",
"Label": "pngappend",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
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- "urn:f0482e54-ccc8-49e0-aed4-703c4a8469ee",
- "urn:f52b1da6-54af-4ef5-b883-eef4570d66b1"
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+ "urn:521d474c-ce81-4a45-bc60-cc7d7fdfb117",
+ "urn:59e90a02-6903-4b34-b581-656cc223956c",
+ "urn:66740f57-693a-4773-a79c-248ab7a34d24",
+ "urn:7b5de754-3451-4c33-96b1-ab7d2f389dda",
+ "urn:7f7c9933-2af8-4d36-bd84-1774cfe99bb6",
+ "urn:8774d01a-a6dd-4c0b-8182-170c0948c565",
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+ "urn:ee4d2236-e8f8-40a9-87da-519574228dc2",
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+ "urn:f3a7b92f-d4e3-4600-92d4-7ffd78ecf0ab"
]
},
{
- "@id": "urn:9afa03eb-c567-4dc5-be4b-5e5535fc712c",
+ "@id": "urn:5efcc7da-6ea6-4ad7-865b-000b7cafae19",
"Label": "pngappend",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
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- "urn:3b79334f-2482-4ea7-94d4-6e6090623211",
- "urn:fc4e83c4-c47d-46a0-b475-3bff18608a56"
+ "urn:03a5008d-7e31-4c29-aaf3-9f09303722a0",
+ "urn:b1267269-2d2e-4a09-a240-7a91144a3cd1"
]
},
{
- "@id": "urn:b42e214e-b817-49ea-b57e-688b5fe9413f",
+ "@id": "urn:0514ce80-6ce1-44f3-9482-53f6381f5b61",
"Label": "rm",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
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- "urn:b10d5108-8806-4746-a9d9-df7707480c86",
- "urn:fc4e83c4-c47d-46a0-b475-3bff18608a56"
+ "urn:658211ea-995c-4a62-9030-1fbf43b013cc",
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]
},
{
- "@id": "urn:36cdfedd-cdbc-4de1-84e8-ed8b0a881a96",
+ "@id": "urn:391cd034-fd83-462d-bba5-f6c952efe934",
"Label": "rm",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:3b79334f-2482-4ea7-94d4-6e6090623211"
+ "urn:03a5008d-7e31-4c29-aaf3-9f09303722a0"
]
},
{
- "@id": "urn:3a05e7d0-9801-405b-8bf1-1d8374bd2e13",
+ "@id": "urn:f7951e4e-be9b-4d7c-b9b1-209db014bb24",
"Label": "mcflirt",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:4082dae8-2701-4657-b4b2-bffea6e63154"
+ "urn:ed266509-aff9-46ad-a6e7-91929a3fc494"
]
},
{
- "@id": "urn:3e0f8be8-e09a-4de1-8898-42148d574f5a",
+ "@id": "urn:1c65e019-bff5-4652-9d67-24ad71333fd7",
"Label": "Make directory",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:fec24f26-05bc-46b1-a308-e387bad0083c",
+ "@id": "urn:7e3371bd-9b56-435d-b2af-b036ba2d16ea",
"Label": "mv",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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- "urn:e3a00e98-0b9c-486c-9d45-661ad0f29c5c"
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+ "urn:46d52892-c9a2-46ad-8f23-17546b04f64f",
+ "urn:b3975f6e-1985-46b7-80da-90f1e8cf8e62",
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]
},
{
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+ "@id": "urn:34acc4e6-eeea-4eeb-8ef6-2f617abe7a79",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:345fc00b-87bb-4394-992d-88b581c53a1e"
+ "urn:cfef7577-e215-4909-9add-3d091919ebc5"
]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:345fc00b-87bb-4394-992d-88b581c53a1e"
+ "urn:cfef7577-e215-4909-9add-3d091919ebc5"
]
},
{
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"Label": "fsl_tsplot",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
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+ "urn:0a8ced20-51bf-4c17-9698-3877f708ece6"
]
},
{
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+ "@id": "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3",
"Label": "bet2",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
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+ "urn:532d8402-2e20-4b27-bd4e-64574dbedc31"
]
},
{
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+ "@id": "urn:e242c59b-d93e-41c9-8735-d0be6238883a",
"Label": "immv",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:95bc5592-d6e4-4115-bd3d-370d21a66919"
+ "urn:d2ff1ab8-8bdb-47f4-bbb9-d8ddb4db7594"
]
},
{
- "@id": "urn:faa891cc-c004-44c1-9963-a6b67102e40f",
+ "@id": "urn:5efb5d23-6a8b-467e-8bed-0141cc4c6d0e",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:0a8ced20-51bf-4c17-9698-3877f708ece6",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
- "@id": "urn:6d405d1a-7fbd-4849-a1ee-23f4303f3b1f",
+ "@id": "urn:0f38703c-db4b-40a0-aec6-8c82cfea4b58",
"Label": "fslstats",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:6968d41e-97e9-4ec9-9933-6c069229bde1"
+ "urn:863ee7d1-4665-4b3d-819d-98ef254703bd"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
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+ "urn:863ee7d1-4665-4b3d-819d-98ef254703bd"
]
},
{
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+ "@id": "urn:eb06b57d-72f7-4db3-a83f-0b5375aaa208",
"Label": "fslstats",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:70dbec60-b908-498d-826f-65d7633bb261"
+ "urn:0a8ced20-51bf-4c17-9698-3877f708ece6"
]
},
{
- "@id": "urn:c2edea08-f4e8-4dc9-b627-453b1f7c9127",
+ "@id": "urn:f1669840-b2b3-444f-a7d7-833c7e46505d",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
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+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:0a8ced20-51bf-4c17-9698-3877f708ece6",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
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+ "urn:d26db05c-46bd-486f-ac18-7657421e4fc8"
]
},
{
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+ "@id": "urn:962cad7a-81dc-498c-9658-a367fc47be71",
"Label": "susan",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:e096c919-99a8-4bda-b143-6b221924d744"
+ "urn:d26db05c-46bd-486f-ac18-7657421e4fc8"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:3fb67843-9a96-48ae-b535-b18a05d6de44",
- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:460f0b95-3f6c-4c96-81a3-ddc96e1ec5d5",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
- "@id": "urn:4fd3e945-daaa-4e92-91ab-7e2849037ffa",
+ "@id": "urn:3811ee49-c3a4-46c2-b1e4-4ac6d4b99f8b",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:3fb67843-9a96-48ae-b535-b18a05d6de44"
+ "urn:460f0b95-3f6c-4c96-81a3-ddc96e1ec5d5"
]
},
{
- "@id": "urn:3b721c25-1fab-41a2-a931-79bbaf958ba1",
+ "@id": "urn:3e30763b-7c05-4a4a-92e0-ad2333589ebd",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:0f68c0d2-fae0-4d24-9eac-8fb527e05cca"
+ "urn:1565ab85-75cd-4a8f-8e85-fab31c94aaf1"
]
},
{
- "@id": "urn:9080e1ed-e597-485c-b563-6642ff91b475",
+ "@id": "urn:711029e7-1a0b-4010-b6df-ed04fa5e35c1",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:0f68c0d2-fae0-4d24-9eac-8fb527e05cca",
- "urn:16efefb5-f541-4233-82d6-1e9fe0e35bce"
+ "urn:1565ab85-75cd-4a8f-8e85-fab31c94aaf1",
+ "urn:7d0a4ae9-a2e7-48a7-b4df-e3e4596cb2bb"
]
},
{
- "@id": "urn:0ea02055-d0c6-4707-80d3-61cdeb1cb36c",
+ "@id": "urn:926ed1ec-af3b-452a-9b53-ca78b6f581bb",
"Label": "imrm",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:16efefb5-f541-4233-82d6-1e9fe0e35bce"
+ "urn:7d0a4ae9-a2e7-48a7-b4df-e3e4596cb2bb"
]
},
{
- "@id": "urn:4623a3e4-04d8-495c-9841-a8f1e6d88086",
+ "@id": "urn:ea8de012-dce4-4e09-b850-ed1d8f0a2896",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:a91c074f-a725-4f84-aa83-73630b62aadf"
+ "urn:3ee9492d-501c-49fa-8f15-d96306e9c0c6"
]
},
{
- "@id": "urn:a2aaea60-1d90-4ef3-926f-fec383eccbe1",
+ "@id": "urn:9b699ea3-8ad8-49af-83ff-7505506ab96c",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:0238939f-61b0-44a5-9e78-6dffb0b0b5e3"
+ "urn:cb548f71-12a7-43f4-a992-58f94d9d45df"
]
},
{
- "@id": "urn:98f15577-ff6b-46bc-9bf2-acb04558545b",
+ "@id": "urn:9298f076-ad34-43e2-aa3b-7864511f07e8",
"Label": "rm",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:c9306796-d6bc-4080-a91a-444981bbbf61"
+ "urn:5d1a543b-6df9-4541-ae83-2c723b8c6368"
]
},
{
- "@id": "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0",
+ "@id": "urn:c87eee96-f587-4647-b19b-c4e391998eff",
"Label": "Make directory",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:0c8f4df2-5718-4f96-b85b-1f9fb88c9ad1",
+ "@id": "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3",
"Label": "fslFixText",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:dc32a6ba-52b8-4331-8c20-c103684d9607"
+ "urn:78fdae39-e08e-4f0d-a442-3fe26d9438a2"
]
},
{
- "@id": "urn:23375a72-1ee5-4128-8d10-54fabae7b00c",
+ "@id": "urn:307b8e93-4018-4034-b02d-3b761ef5558a",
"Label": "Make directory",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:1ff46c81-17ab-417c-898c-5c967b8b6b74",
+ "@id": "urn:5dc94940-d8da-4daa-9934-dadf2166717d",
"Label": "fslFixText",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:70a63de5-2bb7-4f9d-b86b-0a8330de087f"
+ "urn:da0577c7-5820-4e87-9613-c32c52586f56"
]
},
{
- "@id": "urn:bab102ed-4797-4fa1-84b8-fa18fe447a52",
+ "@id": "urn:e8810ee0-cdb1-4e99-b6da-3277ccc23dd2",
"Label": "film_gls",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
- "@id": "urn:47a4a930-45a7-48f8-afc5-4e5281aa9e2c",
+ "@id": "urn:c065adcb-4f8a-4696-861b-6796936fc714",
"Label": "smoothest",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:78794883-5fae-4bcb-95e2-79995ba6442e",
- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:263e3610-fc97-46a1-a70f-f475bc13917d",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
- "@id": "urn:36155e48-6bd1-4f61-816c-dd5d0dbf062a",
+ "@id": "urn:b807382f-c648-42ed-85a4-e308b783d419",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:3f2ecad8-a8e5-493a-8abc-0ab3f1401d31",
- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:1145ef1c-602d-4806-bfa5-39cb20e1394f",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
- "@id": "urn:4a81a54c-f691-4024-8f90-299b7e38f7fc",
+ "@id": "urn:d75904a1-7cd3-4610-a894-e6c3c5d76011",
"Label": "echo",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:c8fa209f-5ecb-443c-9b74-ba12277d8e19",
+ "@id": "urn:961fc3ea-0194-4640-a8b7-8774f193fee2",
"Label": "fslmaths",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
"Used": [
- "urn:1daee25e-6e10-4a25-81f8-cf7861e3aaed",
- "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7"
+ "urn:18783c49-a892-4343-83e7-86b8183d3e83",
+ "urn:af1609a5-9d80-435a-8519-b5ba09d6da06"
]
},
{
- "@id": "urn:1f4c0713-f660-426f-90a7-8a053bb099f6",
+ "@id": "urn:435a68ac-72e9-4d77-8ee2-9eb12b1468c4",
"Label": "echo",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
- "@id": "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe",
+ "@id": "urn:551995e2-978b-482d-afd6-fe48b36f14c7",
"Label": "ptoz",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
+ "@id": "urn:158a8fa0-2415-4647-98be-add728d66819",
"Label": "cluster",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:086ca1fc-cef0-4bd7-9a98-1418e4dd7814",
- "urn:aec43d8a-1acf-483e-839f-a6b9d0413d1e"
+ "urn:2f900215-15bd-4a15-8c21-a8ab51007afb",
+ "urn:f9a25879-924c-40ca-beed-fd6bdae25812"
]
},
{
- "@id": "urn:c3f11886-2058-47ab-9ea0-93a32da106d8",
+ "@id": "urn:9eed7245-2062-4382-a312-e3700ce4e6ff",
"Label": "cluster2html",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43"
+ "urn:b2e2b66f-ee15-4e69-909e-63834dcb44d1"
]
},
{
- "@id": "urn:8b2c4ce3-6f47-46bc-b31b-3380285a85df",
+ "@id": "urn:31c406c9-e772-4346-bc0d-e20ecfc2a8a8",
"Label": "ptoz",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:4a346665-2f68-41f7-ad09-0c4d8f65ca4f",
+ "@id": "urn:d4ce1155-8e92-41de-ad87-a61a257d6e3f",
"Label": "cluster",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
"Used": [
- "urn:31d0fef0-41a4-4f4c-b800-6e08386d1bfd",
- "urn:da2f36c8-f656-4f6e-a4a8-8f2618a20752"
+ "urn:e057248b-dd5d-4c40-bd31-8505d330fb13",
+ "urn:e5e87ac3-64ba-45dd-b07c-87970adb1e87"
]
},
{
- "@id": "urn:f1bef987-0aa6-4482-a0af-4af6044db240",
+ "@id": "urn:b5870dff-e3fe-4ef7-a78c-3f71f29e7942",
"Label": "cluster2html",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:208eefab-d051-4765-bff4-67f1743005b2"
+ "urn:a906578f-aa09-42aa-aab9-8716786196b3"
]
},
{
- "@id": "urn:ea055e9f-2674-43d5-a9c6-1c5265d24cfa",
+ "@id": "urn:a5a99aec-f69e-4cea-b407-27243deea155",
"Label": "fslstats",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:086ca1fc-cef0-4bd7-9a98-1418e4dd7814"
+ "urn:f9a25879-924c-40ca-beed-fd6bdae25812"
]
},
{
- "@id": "urn:fa2f1c7b-7751-4b85-b51c-c0c7ff606a4e",
+ "@id": "urn:dd90df62-1518-4a69-b1cd-6b31c2c95e2f",
"Label": "fslstats",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:da2f36c8-f656-4f6e-a4a8-8f2618a20752"
+ "urn:e057248b-dd5d-4c40-bd31-8505d330fb13"
]
},
{
- "@id": "urn:a5942aa8-a74c-4c93-8ab1-1005a19f6693",
+ "@id": "urn:cd620add-4300-4d26-8e71-f9bd37cb0b8e",
"Label": "overlay",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090259 7.129133 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:792ea18a-543c-4720-bb39-266ed3d5a6f2",
+ "@id": "urn:96707788-783b-4a32-88cc-425b7e5cc0a2",
"Label": "slicer",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342"
+ "urn:6318eb1f-583c-409c-91e4-51a47494e702"
]
},
{
- "@id": "urn:2e21b4e4-5935-4855-8b93-dd5e88819342",
+ "@id": "urn:af85eb98-f60a-48ca-85fc-72ebed7a0c95",
"Label": "cp",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:b344a607-bd81-4876-9108-440c30497751"
+ "urn:6e133963-adde-4100-b5d9-8049067b311e"
]
},
{
- "@id": "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d",
+ "@id": "urn:18e2f45e-748e-4659-9dd3-fd58912f36ba",
"Label": "overlay",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090259 7.129133 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:33ed22a7-1c99-4461-8c48-648b04cd652a",
+ "@id": "urn:dfea9359-ff55-4f9f-80a3-b053d6b53085",
"Label": "slicer",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:c57808d3-5546-4118-b7fc-b778b5d26e99"
+ "urn:71d4b62d-e181-4b29-9cef-04ef856047a4"
]
},
{
- "@id": "urn:e1684662-ca16-489b-91c8-d1c156f0d690",
+ "@id": "urn:1662b1a2-1679-4d8d-b615-c41a992926ca",
"Label": "Make directory",
- "AssociatedWith": "urn:f951bad5-ca1f-40a5-ae00-27a60234ee51",
+ "AssociatedWith": "urn:71227f72-e774-4e17-ae09-07980d0ce996",
"Command": "mkdir -p tsplot",
"Used": []
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"sha256": "c540df2ed1d697609b08bd955a2ca31f3aeca3395c403edd9b036be63682eb64"
}
},
{
- "@id": "urn:260212da-3b7a-4a16-ba6c-820e5c061d98",
+ "@id": "urn:91b05bcc-7a2e-48cf-953c-a366b3419200",
"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:7c5b9650-7b6e-4d59-a889-e62a51997c2d",
+ "GeneratedBy": "urn:a8472bb9-2ead-43f6-8616-18f9aae4d8e0",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:fc4e83c4-c47d-46a0-b475-3bff18608a56",
+ "@id": "urn:b1267269-2d2e-4a09-a240-7a91144a3cd1",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:2c2f9da6-1898-4f9a-b578-ed76c37eddd4",
+ "GeneratedBy": "urn:a5c49bf0-371f-4eaf-8530-22d41303efbd",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:109585e9-fc1e-472d-a23c-92f69102aa1a",
+ "@id": "urn:253ea17d-16a9-4b4f-b9db-437c1d760ede",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:9afa03eb-c567-4dc5-be4b-5e5535fc712c",
+ "GeneratedBy": "urn:5efcc7da-6ea6-4ad7-865b-000b7cafae19",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:b10d5108-8806-4746-a9d9-df7707480c86",
+ "@id": "urn:658211ea-995c-4a62-9030-1fbf43b013cc",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -978,25 +978,25 @@
}
},
{
- "@id": "urn:70dbec60-b908-498d-826f-65d7633bb261",
+ "@id": "urn:0a8ced20-51bf-4c17-9698-3877f708ece6",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:3a05e7d0-9801-405b-8bf1-1d8374bd2e13",
+ "GeneratedBy": "urn:f7951e4e-be9b-4d7c-b9b1-209db014bb24",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d",
+ "@id": "urn:8101dccd-721c-473d-bce4-f9d73ef4f7c2",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:3e0f8be8-e09a-4de1-8898-42148d574f5a",
+ "GeneratedBy": "urn:1c65e019-bff5-4652-9d67-24ad71333fd7",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:7755f3ab-b260-4aaf-8e5d-afdb682dc989",
+ "@id": "urn:d4e33abf-38ab-40ee-b824-cb1c9e5d8c1c",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1004,7 +1004,7 @@
}
},
{
- "@id": "urn:345fc00b-87bb-4394-992d-88b581c53a1e",
+ "@id": "urn:cfef7577-e215-4909-9add-3d091919ebc5",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1012,7 +1012,7 @@
}
},
{
- "@id": "urn:e3a00e98-0b9c-486c-9d45-661ad0f29c5c",
+ "@id": "urn:df462c5e-a71d-4211-b18b-58f04504f189",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1020,7 +1020,7 @@
}
},
{
- "@id": "urn:0b064394-077e-4c5a-b3da-8fc4bb051868",
+ "@id": "urn:46d52892-c9a2-46ad-8f23-17546b04f64f",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1028,7 +1028,7 @@
}
},
{
- "@id": "urn:77b2e673-f6c4-4126-a0b2-14df6011123c",
+ "@id": "urn:095b5719-a730-49c9-bc74-ec5226812e96",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1036,7 +1036,7 @@
}
},
{
- "@id": "urn:da7c4a76-1cc5-4b5a-9b7a-aeee1f25a262",
+ "@id": "urn:b3975f6e-1985-46b7-80da-90f1e8cf8e62",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1044,34 +1044,34 @@
}
},
{
- "@id": "urn:0ed32843-e5ab-4481-afa1-03fc0a69ddc8",
+ "@id": "urn:ed74188c-0a4a-4b0a-a0a1-47234ed3304f",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:fec24f26-05bc-46b1-a308-e387bad0083c",
+ "GeneratedBy": "urn:7e3371bd-9b56-435d-b2af-b036ba2d16ea",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:97404bf1-deb1-4e37-b199-2280209c6e16",
+ "@id": "urn:b6a19b32-701a-42d0-9469-8b1da169301f",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:a5ae59a2-c246-483d-8555-2d6f0ad1dc75",
+ "GeneratedBy": "urn:34acc4e6-eeea-4eeb-8ef6-2f617abe7a79",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:0b61184a-cac9-40b6-81dc-6872a83e0af4",
+ "@id": "urn:8d3c0903-9944-4080-896f-b7cea95307e2",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:0d0e2d05-f309-4b04-a2a5-f10351b10b2c",
+ "GeneratedBy": "urn:94043e97-e422-407b-ac11-e740fdb6bf72",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:2783a287-676c-45f3-9447-710c44eeaaf1",
+ "@id": "urn:748557d0-dbf8-439f-9638-1d4963f93d52",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1079,34 +1079,34 @@
}
},
{
- "@id": "urn:c6d1eb8b-6f60-4d3c-88dd-dc6a63a8402c",
+ "@id": "urn:1f147a2f-28cb-40b8-a79a-a2a99e9adf77",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:93d0927d-619a-4809-a4aa-a47a9cf6c9f9",
+ "GeneratedBy": "urn:b649b7d7-7b32-4f2b-8ee0-dfbf074dff4e",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:bc402a7d-a8df-41e0-bf0f-30a4f6f4eb5d",
+ "@id": "urn:532d8402-2e20-4b27-bd4e-64574dbedc31",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:7f0c003b-cd9b-46bd-a0cb-e23e674efa0c",
+ "GeneratedBy": "urn:31e7bca8-5b2c-48d3-bb73-49fad30c957b",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:c71d2b44-1418-4682-a878-d1c3043c2ce7",
+ "@id": "urn:af1609a5-9d80-435a-8519-b5ba09d6da06",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:ee0a09e8-1dbc-43eb-99d6-fbae9704d1d7",
+ "GeneratedBy": "urn:7b15c0f3-de8f-4ab6-8390-16fee37cc8b3",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:95bc5592-d6e4-4115-bd3d-370d21a66919",
+ "@id": "urn:d2ff1ab8-8bdb-47f4-bbb9-d8ddb4db7594",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1114,106 +1114,106 @@
}
},
{
- "@id": "urn:7284b9e7-6c6e-4be4-a460-4c982404ecf9",
+ "@id": "urn:4e66afad-85bf-424d-aedf-ebb495b51d76",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:f6f8e17b-b0cb-4f0d-8a15-55d9885a63ee",
+ "GeneratedBy": "urn:e242c59b-d93e-41c9-8735-d0be6238883a",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:6968d41e-97e9-4ec9-9933-6c069229bde1",
+ "@id": "urn:863ee7d1-4665-4b3d-819d-98ef254703bd",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:faa891cc-c004-44c1-9963-a6b67102e40f",
+ "GeneratedBy": "urn:5efb5d23-6a8b-467e-8bed-0141cc4c6d0e",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:f21fb26e-c121-44f4-9518-59a3ba3cddfb",
+ "@id": "urn:dab0a08b-dacf-4844-a891-6ef77087c0aa",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:4624084d-96d7-4b18-b844-db1fe356c12d",
+ "GeneratedBy": "urn:054acb7b-ee66-486f-b423-9ea04a0fb2fb",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:e4050d28-ec12-473c-a20d-3ea94d62920f",
+ "@id": "urn:2210b633-7826-4cc6-b138-ccfc7f438608",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:c2edea08-f4e8-4dc9-b627-453b1f7c9127",
+ "GeneratedBy": "urn:f1669840-b2b3-444f-a7d7-833c7e46505d",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:e096c919-99a8-4bda-b143-6b221924d744",
+ "@id": "urn:d26db05c-46bd-486f-ac18-7657421e4fc8",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:b9764b4c-90f2-4ca6-8158-ea28ee9fff68",
+ "GeneratedBy": "urn:582ba438-47f5-434f-a321-cfe55992160a",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:4aeef158-d26c-4a7d-9ecd-51c007325113",
+ "@id": "urn:47831ace-48c1-422e-a87d-97ecf3810601",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:8bdae2ee-5aba-4cba-a854-3155f055fb73",
+ "GeneratedBy": "urn:4c69d19b-2099-4dda-8869-85976b9ba13c",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:3fb67843-9a96-48ae-b535-b18a05d6de44",
+ "@id": "urn:460f0b95-3f6c-4c96-81a3-ddc96e1ec5d5",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a9093ed2-7f77-49ac-aef1-ff6333feccdc",
+ "GeneratedBy": "urn:962cad7a-81dc-498c-9658-a367fc47be71",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:9a26f3e5-86c2-4593-81f3-cd533d64357d",
+ "@id": "urn:2686fab3-8dd5-45c0-813a-ba4f890534f7",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:af85f6f2-37a6-47f6-b706-5bb7237597f3",
+ "GeneratedBy": "urn:d9762aae-4f9c-4df0-8f73-a26f14726850",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:0f68c0d2-fae0-4d24-9eac-8fb527e05cca",
+ "@id": "urn:1565ab85-75cd-4a8f-8e85-fab31c94aaf1",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:4fd3e945-daaa-4e92-91ab-7e2849037ffa",
+ "GeneratedBy": "urn:3811ee49-c3a4-46c2-b1e4-4ac6d4b99f8b",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:16efefb5-f541-4233-82d6-1e9fe0e35bce",
+ "@id": "urn:7d0a4ae9-a2e7-48a7-b4df-e3e4596cb2bb",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:3b721c25-1fab-41a2-a931-79bbaf958ba1",
+ "GeneratedBy": "urn:3e30763b-7c05-4a4a-92e0-ad2333589ebd",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:712101dd-72bf-4522-84bd-2206e7600948",
+ "@id": "urn:7aa13188-2509-40a0-9f80-8816b8cc8f68",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:9080e1ed-e597-485c-b563-6642ff91b475",
+ "GeneratedBy": "urn:711029e7-1a0b-4010-b6df-ed04fa5e35c1",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:a91c074f-a725-4f84-aa83-73630b62aadf",
+ "@id": "urn:3ee9492d-501c-49fa-8f15-d96306e9c0c6",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1221,25 +1221,25 @@
}
},
{
- "@id": "urn:0238939f-61b0-44a5-9e78-6dffb0b0b5e3",
+ "@id": "urn:cb548f71-12a7-43f4-a992-58f94d9d45df",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:4623a3e4-04d8-495c-9841-a8f1e6d88086",
+ "GeneratedBy": "urn:ea8de012-dce4-4e09-b850-ed1d8f0a2896",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:d1d82229-9f97-4cbc-bec1-e900fc856882",
+ "@id": "urn:02f4afbd-27c0-4390-8a5b-d4efa5cc53eb",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a2aaea60-1d90-4ef3-926f-fec383eccbe1",
+ "GeneratedBy": "urn:9b699ea3-8ad8-49af-83ff-7505506ab96c",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:c9306796-d6bc-4080-a91a-444981bbbf61",
+ "@id": "urn:5d1a543b-6df9-4541-ae83-2c723b8c6368",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1247,16 +1247,16 @@
}
},
{
- "@id": "urn:4c5b85fe-32e6-4d2c-b34c-8a2fc87aec51",
+ "@id": "urn:dfac6fe0-1044-4cdf-a45d-fe1a9c249114",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0",
+ "GeneratedBy": "urn:c87eee96-f587-4647-b19b-c4e391998eff",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:dc32a6ba-52b8-4331-8c20-c103684d9607",
+ "@id": "urn:78fdae39-e08e-4f0d-a442-3fe26d9438a2",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1264,22 +1264,22 @@
}
},
{
- "@id": "urn:0e12140c-f0fa-4b1c-afdc-6b4072852687",
+ "@id": "urn:3c57f050-6e6c-4747-a278-14167f03b63f",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:0c8f4df2-5718-4f96-b85b-1f9fb88c9ad1"
+ "GeneratedBy": "urn:703bf55b-db97-472c-99ec-2a3a2e30d4c3"
},
{
- "@id": "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe",
+ "@id": "urn:73f3d293-8378-44e5-b97f-f0d210d07474",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:23375a72-1ee5-4128-8d10-54fabae7b00c",
+ "GeneratedBy": "urn:307b8e93-4018-4034-b02d-3b761ef5558a",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:70a63de5-2bb7-4f9d-b86b-0a8330de087f",
+ "@id": "urn:da0577c7-5820-4e87-9613-c32c52586f56",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1287,13 +1287,13 @@
}
},
{
- "@id": "urn:58233196-f676-4b22-b7b6-d2a803c73967",
+ "@id": "urn:367458e3-16bb-4dd1-ae1f-db628fdc3a0d",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:1ff46c81-17ab-417c-898c-5c967b8b6b74"
+ "GeneratedBy": "urn:5dc94940-d8da-4daa-9934-dadf2166717d"
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@@ -1318,16 +1318,16 @@
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@@ -1335,16 +1335,16 @@
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@@ -1352,25 +1352,25 @@
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@@ -1378,7 +1378,7 @@
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@@ -1386,25 +1386,25 @@
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@@ -1412,25 +1412,25 @@
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@@ -1438,46 +1438,46 @@
}
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diff --git a/examples/from_parsers/fsl/fsl_gaussian_report_log.png b/examples/from_parsers/fsl/fsl_gaussian_report_log.png
index 51361f947..28969a420 100644
Binary files a/examples/from_parsers/fsl/fsl_gaussian_report_log.png and b/examples/from_parsers/fsl/fsl_gaussian_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
index 91d029036..6e5cbf9c3 100644
--- a/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_btw_report_log.jsonld
@@ -4,7 +4,7 @@
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@@ -13,428 +13,428 @@
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"Used": []
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{
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"Used": []
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{
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"Label": "Make directory",
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"Command": "mkdir -p inputreg",
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"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
"Used": [
- "urn:02bf0272-90eb-449e-b7c2-12a1c3be169e",
- "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a"
+ "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
+ "urn:ba4eda0b-da8f-4557-9eee-a0238e0b407b"
]
},
{
- "@id": "urn:6f4cf849-a7eb-4c81-970f-47a667c23b32",
+ "@id": "urn:ec1b1898-9979-437d-8086-12211a8246ee",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
"Used": [
- "urn:78569eec-8f25-476a-af06-a67ddfefd121",
- "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a"
+ "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
+ "urn:a70196ed-9eb2-4d70-a7b1-e4a8ca0d7d22"
]
},
{
- "@id": "urn:8686801c-6354-4d39-80f7-52a85f1e1b00",
+ "@id": "urn:80b85a97-9a44-4363-bf4d-4571c48de600",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
"Used": [
- "urn:09ccab5e-c297-47cc-840d-dcb4a219870b",
- "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a"
+ "urn:3b428c80-be2a-4b11-8ee6-93612aaa80e6",
+ "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a"
]
},
{
- "@id": "urn:1732aee3-f835-45d5-9d6c-7b9bdbce72a5",
+ "@id": "urn:a10c794e-57a7-4a6f-8458-b2314ac9eeb7",
"Label": "overlay",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
"Used": []
},
{
- "@id": "urn:6add6bab-95e0-411c-be61-24f213edbb8c",
+ "@id": "urn:eb59440d-2791-4cca-bc1f-95613a35df61",
"Label": "slicer",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
- "urn:5eb19834-e313-4f3e-9e36-ada7e9e336ce"
+ "urn:882d78ff-a57f-4922-b1b6-f92337927d99"
]
},
{
- "@id": "urn:9f91de42-958b-4994-a2a1-cd5df69db358",
+ "@id": "urn:53169fdb-f990-4ee6-a17d-f6a53e7f67d9",
"Label": "cp",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:824606da-683f-4db1-8310-2850ded25d2f"
+ "urn:92573bd7-0dc6-4fc2-b0a1-b2ddef010a07"
]
},
{
- "@id": "urn:b454e49b-12d9-4aff-94c3-3fd59398132c",
+ "@id": "urn:baa47e1c-4dc8-4f43-a3e0-8197e323d309",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:f0a4f640-ad91-4683-ab30-e64c753264b1"
+ "urn:2368f219-d605-4d0c-ad67-c0703541b4c3"
]
},
{
- "@id": "urn:e90963c7-4df4-4e92-90a6-11df69e7316b",
+ "@id": "urn:a0ec00b1-b359-4e9e-b8db-0bdafe8871ab",
"Label": "fslmerge",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
"Used": []
},
{
- "@id": "urn:c7532fdd-ac39-43ff-acdd-62f316b3f815",
+ "@id": "urn:fb88b08f-d332-441d-a8a3-021f387930fb",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
"Used": [
- "urn:a30e7f05-30c9-4a93-831f-178beca06da5"
+ "urn:9c29ef12-a4eb-487a-b06c-8e85de3822a7"
]
},
{
- "@id": "urn:7889534a-66ae-4929-a22a-f26301659043",
+ "@id": "urn:96172092-ec47-43ee-ac02-50f2e3d7a303",
"Label": "fslmerge",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
"Used": []
},
{
- "@id": "urn:97899751-2ff9-4004-80b3-d252dd68e0c9",
+ "@id": "urn:e88da71c-ca92-450d-b036-3f57bec6a16a",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
"Used": [
- "urn:e917b63e-a583-43d1-b0a5-4b96417917d5",
- "urn:f0a4f640-ad91-4683-ab30-e64c753264b1"
+ "urn:2368f219-d605-4d0c-ad67-c0703541b4c3",
+ "urn:a7033b8a-6e10-4b48-a89c-7502b5a51730"
]
},
{
- "@id": "urn:96abea8f-96a7-4c19-9aec-d37b19881a27",
+ "@id": "urn:5d86a607-3005-48b0-bdf1-f80f1ffd0e59",
"Label": "printf",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "printf '1.01544485714 ' >> design.lcon",
"Used": []
},
{
- "@id": "urn:703a45c1-fcbe-4d35-adda-d89aca9c8e21",
+ "@id": "urn:6ad2c26d-6aab-4e86-bdf9-c83ad1cfe41b",
"Label": "fslmerge",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
"Used": []
},
{
- "@id": "urn:f81c36df-64ce-49ff-b928-c7ddf0b4c8c3",
+ "@id": "urn:180db3ed-c95d-4aa2-a55a-37a8e770cdcd",
"Label": "fslmaths",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
"Used": [
- "urn:125ed038-94b2-44ff-b08a-6b20a34563d1",
- "urn:f0a4f640-ad91-4683-ab30-e64c753264b1"
+ "urn:2368f219-d605-4d0c-ad67-c0703541b4c3",
+ "urn:93f188fc-1f90-49f6-b2a8-79198007a610"
]
},
{
- "@id": "urn:45354d21-9918-4d74-ab12-ab46e2456b13",
+ "@id": "urn:d0d06396-4c42-49c0-bd65-e7dc7f3e58e0",
"Label": "printf",
- "AssociatedWith": "urn:cd61fdbd-13e5-4d2a-a477-0490ac58a3e6",
+ "AssociatedWith": "urn:86648548-ef86-4c65-acb2-f66f919cd602",
"Command": "printf '1 ' >> design.lcon",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:0ee4fa58-9209-4ce1-8b1c-a38a4f26370c",
+ "@id": "urn:aa6e479e-739d-4039-8bea-d0c16c229162",
"Label": "bg_image",
"AtLocation": "bg_image",
"digest": {
@@ -442,25 +442,25 @@
}
},
{
- "@id": "urn:6a0124c1-72b2-49ce-9672-d4fbcca25c05",
+ "@id": "urn:4d9e2482-55d7-4b91-bbc7-09a94bcb01e2",
"Label": "bg_image",
"AtLocation": "bg_image",
- "GeneratedBy": "urn:e6ac63ff-c9dc-4262-a728-c238e58fe52a",
+ "GeneratedBy": "urn:de17c456-a14f-44bc-9ce1-63dc7817d3c6",
"digest": {
"sha256": "ee2ea46067dbf68f9438c2eca02baa42dc59c8f171830150d0621ae3e061d7d0"
}
},
{
- "@id": "urn:eb442016-d304-41a3-bc43-10b5afeb249c",
+ "@id": "urn:af40c8ba-fdd5-4c38-8e39-bbd8e2c54ca5",
"Label": "inputreg",
"AtLocation": "inputreg",
- "GeneratedBy": "urn:d0f77183-7ee9-4109-9528-436539caeb79",
+ "GeneratedBy": "urn:b286b508-ccb9-409b-aa7d-5629f06e613e",
"digest": {
"sha256": "d820f84544e66c638eb5c8e71e84a56b0a45e35a1b508ff270c8e01746985c3f"
}
},
{
- "@id": "urn:4c74efcc-3ca0-42dd-9513-41c6907b36f4",
+ "@id": "urn:717c4883-95a6-438b-a1e4-8cb4424a168c",
"Label": "mask",
"AtLocation": "../mask",
"digest": {
@@ -468,52 +468,52 @@
}
},
{
- "@id": "urn:09ccab5e-c297-47cc-840d-dcb4a219870b",
+ "@id": "urn:3b428c80-be2a-4b11-8ee6-93612aaa80e6",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:65996a2a-c60d-4c82-a7e9-1d7931c8a96c",
+ "GeneratedBy": "urn:ae890394-01bf-44f5-a3b2-d08ca303ddc6",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:33d5974c-41b2-41e1-b5e4-2f2a63eb1f54",
+ "@id": "urn:0588524e-1b30-4bda-89ea-90359ecc11e4",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:79a192b9-7d24-4e19-a5f7-1f2e64eae12d",
+ "GeneratedBy": "urn:cdf09df2-5840-4125-9b92-303ba836cdd7",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:caa87586-13ee-4b3b-81b8-2e25b51c127c",
+ "@id": "urn:d2fe0cae-b7d0-4df9-9cb1-c6858fbada4a",
"Label": "masksum_overlay",
"AtLocation": "masksum_overlay",
- "GeneratedBy": "urn:409ce7cf-7d59-4ed1-b811-729bbb018e10",
+ "GeneratedBy": "urn:17b70280-d407-407f-820c-85dbabbdcd62",
"digest": {
"sha256": "9f347d6ec7a789bf400954fc9f6576becdbfaae343b6e778e729bb02400c3e18"
}
},
{
- "@id": "urn:e9c63466-4b59-4de4-a718-cb7bbbba6b8c",
+ "@id": "urn:374840d1-759f-4a7e-babe-e91ec845f206",
"Label": "masksum_overlay.png",
"AtLocation": "masksum_overlay.png",
- "GeneratedBy": "urn:c8ad3c2e-e845-4477-970f-bc294a486166",
+ "GeneratedBy": "urn:02f1c791-5c7d-43a6-8e2f-f2536baa26d0",
"digest": {
"sha256": "cb87f6a075a6829b613c60ea6ed47ebd80fdb95356d0f783cf182255469425cb"
}
},
{
- "@id": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
+ "@id": "urn:7f284a13-dda9-4a1a-9fb1-c574b309533a",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:cf1cc1cc-9dc5-4b44-8bb2-dac4fb80d8f6",
+ "GeneratedBy": "urn:831bf263-33b5-4b62-aa16-89c91b9a5dc5",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:00c90417-9e57-48fe-b991-46dec5ed5a2d",
+ "@id": "urn:2fcd8594-4286-4cdf-9100-4477f5bdce8f",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
"digest": {
@@ -521,16 +521,16 @@
}
},
{
- "@id": "urn:81c04b1a-a3ec-4d42-b1f6-42b18c514646",
+ "@id": "urn:33c4a27f-28cd-4072-95b4-dc99b04d706c",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:232aa214-57d4-4533-bcb4-59ec9c7b9d91",
+ "GeneratedBy": "urn:2cb826db-6e4d-4c03-ae37-39e153fd415f",
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diff --git a/examples/from_parsers/fsl/fsl_group_btw_report_log.png b/examples/from_parsers/fsl/fsl_group_btw_report_log.png
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index 6ed4bb84b..57c32733b 100644
--- a/examples/from_parsers/fsl/fsl_group_ols_report_log.jsonld
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "featregapply",
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"Used": []
},
{
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"Label": "fslmerge",
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"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths bg_image -inm 1000 -Tmean bg_image -odt float",
"Used": [
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+ "urn:c7c86089-eaa4-4a18-8530-49a201b46d44"
]
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{
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"Label": "fslmerge",
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"Used": []
},
{
- "@id": "urn:ac189004-8387-4e75-bc93-a36cdff27e9f",
+ "@id": "urn:c1dbe336-6adc-43f6-beda-b35ac0809ea2",
"Label": "Make directory",
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+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "mkdir -p inputreg",
"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
"Used": [
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+ "urn:a1f58e1e-f61b-487b-8cce-219b0d8ca7c5"
]
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{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
"Used": [
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+ "urn:60ac6427-f2f9-4df8-b0a4-2e52279ea854"
]
},
{
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"Label": "overlay",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 -c ../bg_image -a masksum 0.9 28 masksum_overlay",
"Used": []
},
{
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"Label": "slicer",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer masksum_overlay -S 2 750 masksum_overlay.png",
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+ "urn:293853a7-2b50-43fc-9520-a57ca37b2b75"
]
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"Label": "fslmaths",
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]
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"Label": "fslmaths",
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- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
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"Label": "fslmaths",
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- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
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]
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"Label": "fslmaths",
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- "urn:c663425b-256d-4ff3-b4d9-a89d08feeac8"
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"Label": "fslmaths",
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- "urn:b8ae9b96-4a97-4a70-94ff-78d8eac99f4e"
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]
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"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mask -mul -1 -add 1 -mul 5 -add maskunique maskunique",
"Used": [
- "urn:3284254f-d765-4ec7-a503-877782162cff",
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
+ "urn:678905c1-d3f9-4079-8e8a-ebeff7b289ba",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:8dbbbca1-8bc2-4b0e-a357-1e05f5c0fc1f",
+ "@id": "urn:efc86a01-5f01-4b48-9380-fdb30ecd01b2",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mask -mul -1 -add 1 -mul 6 -add maskunique maskunique",
"Used": [
- "urn:0813e30b-9cdc-415d-b3cd-0645ea508097",
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
+ "urn:c7ebc85c-e88c-400a-8e89-237b22c196fe",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
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+ "@id": "urn:2865335c-14e3-4c09-91ec-1c2ce71c403a",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mask -mul -1 -add 1 -mul 7 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:edb1bdc5-b136-41ad-8df7-ac98335d54b7"
+ "urn:5ff1801c-9116-43a9-aa4a-c72b55bfef4e",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:e59dfce1-8b70-447a-a02c-691a728768dc",
+ "@id": "urn:a41cf029-3f2e-42b7-bdbf-e8d710365518",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mask -mul -1 -add 1 -mul 8 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:8a910438-5e5c-4222-b432-4df441bc68c3"
+ "urn:1407a659-fd7a-4484-8d8e-01defef6f7b1",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:cefc4a69-2580-432a-9712-462d38e98ed3",
+ "@id": "urn:14523d74-cb30-454d-aa4c-0d3ec2b47bb5",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mask -mul -1 -add 1 -mul 9 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:fb3d452a-38d7-4bd9-a880-ec07ab06e683"
+ "urn:bc442431-361a-4ce5-971c-cf8eddac2c4c",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:986f8c11-eedf-404b-bea2-fad45a7d6986",
+ "@id": "urn:ceeead2a-ad34-47d3-90e6-938a3309d894",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mask -mul -1 -add 1 -mul 10 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:77e850b5-6812-461e-93f0-580c0bd99f98"
+ "urn:65685219-a9c7-427e-9264-79afd22a5c76",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:5d9065a8-dd2c-4964-93a3-70a7eeeeb726",
+ "@id": "urn:fbc5b261-27ad-48b2-8d9d-f0abc6a2f421",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mask -mul -1 -add 1 -mul 11 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:d2bb0b98-8add-424a-a5df-c6d5ef27db61"
+ "urn:bc34e799-ee74-412a-bfec-b63b237f82cb",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:1d7d81e0-fb05-49a8-96f2-3f416d249dde",
+ "@id": "urn:96298bd4-56d1-49ad-8c03-cecf40d46075",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mask -mul -1 -add 1 -mul 12 -add maskunique maskunique",
"Used": [
- "urn:00018e45-1170-4456-abbd-a12eee652582",
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
+ "urn:1c76f216-0aa4-4f8e-85f7-bfbced813d7d",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:e2e35562-610f-4238-bbea-f339229b4f33",
+ "@id": "urn:c7f1f41c-a405-40c0-944e-f6749c09aa9b",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mask -mul -1 -add 1 -mul 13 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:dd4cd79c-c8c5-4f25-b7fd-0fe1731c5694"
+ "urn:a9909b0a-06e7-42d5-ae5b-699ba62cce5c",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:457d391d-f8af-4766-94cd-9b534bda02f2",
+ "@id": "urn:9a843d97-01d0-4bd0-87f5-e2fa80b1b1db",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mask -mul -1 -add 1 -mul 14 -add maskunique maskunique",
"Used": [
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b",
- "urn:8c63d766-0025-433f-8212-0ecaa555a1c2"
+ "urn:9df4f612-c16f-41e9-b391-85fa07806046",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:5bb8508a-eda5-4365-81fb-999ffd24853e",
+ "@id": "urn:6dcdf35f-a3f4-40f7-900a-3e1d4515f85c",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 13 -uthr 13 -bin -mul maskunique maskunique",
"Used": [
- "urn:4754665a-16eb-480f-bfcd-88b9d170d65a",
- "urn:67db15ca-b473-4920-934a-2c3c04e4217b"
+ "urn:60ac6427-f2f9-4df8-b0a4-2e52279ea854",
+ "urn:ed01e6fd-a6a0-4ff2-a6c0-ef61f178913f"
]
},
{
- "@id": "urn:4830f327-2309-4954-8099-23d6077d7c00",
+ "@id": "urn:15b051f7-2e68-47b4-8c46-1d2ca75e246f",
"Label": "overlay",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 0 0 ../bg_image -a maskunique 0.9 14 maskunique_overlay",
"Used": []
},
{
- "@id": "urn:375c91f6-f7c7-4879-8f95-2a01b4bf1ac9",
+ "@id": "urn:46008793-da4c-4675-95a2-9665da5c4eda",
"Label": "slicer",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
- "urn:c4c118f0-ce74-41f3-910b-79f9f4d747eb"
+ "urn:70371069-142c-4e78-b151-6ec28fa99fc4"
]
},
{
- "@id": "urn:5703fe98-7035-4267-bfc4-7fb711d4a477",
+ "@id": "urn:f1758c9e-2875-4d25-a759-8b459fd5f725",
"Label": "cp",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:99fdddd9-cb59-44fc-a275-ee3393b74160"
+ "urn:ea575ae5-8930-4141-a4c2-d8ef656487f6"
]
},
{
- "@id": "urn:f8b35d61-6b39-4d1e-b9e8-e8a0f7c1bf73",
+ "@id": "urn:9afb0d8c-87de-47ba-8300-b53136b969a7",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:606954f3-07c0-44bf-8837-500c331578fd"
+ "urn:6c751afa-da20-46ef-88be-683cd5a1c123"
]
},
{
- "@id": "urn:f95a770c-8509-4d92-9064-08ba635398ef",
+ "@id": "urn:8f5db629-7053-4922-b9f0-6bdf5a81ae52",
"Label": "fslmerge",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
"Used": []
},
{
- "@id": "urn:d3e40457-38d8-4822-829c-5c631ed80f9c",
+ "@id": "urn:4a912de4-b861-4bd1-82bb-5147dcb9be43",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
"Used": [
- "urn:d99020da-414e-4667-b1f4-695e3c5c3f4b"
+ "urn:34b6df30-bd5a-4398-9342-1874c1deb96d"
]
},
{
- "@id": "urn:a973b518-dde1-42af-b412-150d172947cb",
+ "@id": "urn:3cbb8f84-a9e2-44ca-8654-65448f05f932",
"Label": "fslmerge",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
"Used": []
},
{
- "@id": "urn:308fe337-072b-4704-8cdd-117d8eea1928",
+ "@id": "urn:b59ccf17-52ef-44e6-8967-572a84fccdb9",
"Label": "fslmaths",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
"Used": [
- "urn:606954f3-07c0-44bf-8837-500c331578fd",
- "urn:fea2ae1d-c64b-48ab-8876-37daa64c5c6f"
+ "urn:6c751afa-da20-46ef-88be-683cd5a1c123",
+ "urn:f92f1112-5e5e-475a-a057-1dffee538eca"
]
},
{
- "@id": "urn:130b200a-a004-4ac6-917b-fae4be88252d",
+ "@id": "urn:726b56ad-e50b-49f5-819b-0c8a8088d13f",
"Label": "printf",
- "AssociatedWith": "urn:c15521b1-b3dc-450a-9daa-37e51b591d75",
+ "AssociatedWith": "urn:5962072c-3aa9-4ad6-8cfc-4c74e34f8a37",
"Command": "printf '1.01544485714 ' >> design.lcon",
"Used": []
},
{
- "@id": "urn:b7d21574-2f03-409f-b7d5-363bb4297b36",
+ "@id": "urn:8ac247a6-00f0-4da1-88e5-7e74e5df7066",
"Label": "fslmerge",
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@@ -742,43 +742,43 @@
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@@ -786,16 +786,16 @@
}
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@@ -803,16 +803,16 @@
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@@ -820,16 +820,16 @@
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@@ -837,16 +837,16 @@
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@@ -854,10 +854,10 @@
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diff --git a/examples/from_parsers/fsl/fsl_group_ols_report_log.png b/examples/from_parsers/fsl/fsl_group_ols_report_log.png
index c4102da6f..b313d0f7c 100644
Binary files a/examples/from_parsers/fsl/fsl_group_ols_report_log.png and b/examples/from_parsers/fsl/fsl_group_ols_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
index 019e8ef6d..f986a2bc1 100644
--- a/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_group_wls_report_log.jsonld
@@ -4,7 +4,7 @@
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{
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@@ -13,428 +13,428 @@
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{
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},
{
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"Used": []
},
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"Used": []
},
{
- "@id": "urn:7eeace10-a018-45b9-b882-514a0a878de0",
+ "@id": "urn:db8f33dc-3bfa-470f-93dd-7d1d8d61e2a8",
"Label": "Make directory",
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+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "mkdir -p inputreg",
"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths ../mask -mul 14 -Tmean masksum -odt short",
"Used": [
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]
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths masksum -thr 14 -add masksum masksum",
"Used": [
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+ "urn:e6616dd8-25eb-4bfa-ac07-5b7a060ae105"
]
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{
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"Label": "overlay",
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"Used": []
},
{
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"Label": "slicer",
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+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
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]
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]
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"Label": "fslmaths",
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"Label": "fslmaths",
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]
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"Label": "fslmaths",
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"Label": "fslmaths",
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"Label": "fslmaths",
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{
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"Label": "fslmaths",
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"Label": "fslmaths",
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"Label": "fslmaths",
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{
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"Label": "fslmaths",
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"Label": "overlay",
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},
{
- "@id": "urn:9436c7f5-ce44-4311-8385-1d54351a4e9f",
+ "@id": "urn:5ae22539-5ee8-41d6-ac9b-8fc06f93b886",
"Label": "slicer",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer maskunique_overlay -S 2 750 maskunique_overlay.png",
"Used": [
- "urn:2dd4bdd9-81a3-4671-ae2b-3303e79bd597"
+ "urn:0d39f685-e244-438e-97a9-db23ff3af802"
]
},
{
- "@id": "urn:ce6d0fcd-9703-44df-9e5e-d126eaee7f4c",
+ "@id": "urn:574d3e7d-e246-4b11-965f-aa666574b423",
"Label": "cp",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:035f1ae5-a898-46bd-a450-430331b8b987"
+ "urn:3a5ec85b-4649-4e66-ae61-3226ead3490b"
]
},
{
- "@id": "urn:1f9cf81a-a168-4237-ba3c-30f95e1264eb",
+ "@id": "urn:22a3f6b3-48f6-4e6b-9396-de9d36478fb9",
"Label": "fslmaths",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -Tmin mask",
"Used": [
- "urn:e84ad552-4fd6-4f7a-b61f-af8268dbc4b7"
+ "urn:85de6a2e-faae-4cb2-b1be-233684dc4309"
]
},
{
- "@id": "urn:daeb538f-0c65-48b2-ab33-e130b3c24a79",
+ "@id": "urn:08f6f5f3-bd9b-44be-9d64-7caad9f19d62",
"Label": "fslmerge",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/mean_func /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/mean_func",
"Used": []
},
{
- "@id": "urn:52dc58df-35c5-4d53-999e-2377d2e2eddd",
+ "@id": "urn:26040560-8893-4c08-835e-2ae7ae40e431",
"Label": "fslmaths",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mean_func -Tmean mean_func",
"Used": [
- "urn:fb9f4b8d-e79b-4082-952e-839608db3b81"
+ "urn:60e316e3-5de9-4cf0-a078-e0e086a169c5"
]
},
{
- "@id": "urn:b0d684ca-f4e5-4906-a573-afa2b10fc2e3",
+ "@id": "urn:8a911323-f909-40de-950d-d0cd49e1e599",
"Label": "fslmerge",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/cope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/cope1",
"Used": []
},
{
- "@id": "urn:79ddf8b9-1b42-46e8-ae11-c94065e05fa1",
+ "@id": "urn:33552b33-dc97-4793-8385-2a87de22c0a4",
"Label": "fslmaths",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths cope1 -mas mask cope1",
"Used": [
- "urn:b263d905-07d9-4561-8e6f-3642c4753b72",
- "urn:e84ad552-4fd6-4f7a-b61f-af8268dbc4b7"
+ "urn:85de6a2e-faae-4cb2-b1be-233684dc4309",
+ "urn:88d6bd28-7a69-4044-b46a-836e2f61ccd3"
]
},
{
- "@id": "urn:cd4904d9-50f8-40f4-ba37-150beaa53fb0",
+ "@id": "urn:5a177f0b-f843-4725-9475-1b1e4ddf5e18",
"Label": "printf",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "printf '1.01544485714 ' >> design.lcon",
"Used": []
},
{
- "@id": "urn:522057cf-87c1-4b9f-bbd3-24f853426872",
+ "@id": "urn:35751964-58b2-4afc-897d-9dc411dff9b0",
"Label": "fslmerge",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmerge -t varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-05.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-06.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-07.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-08.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-09.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-10.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-11.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-12.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-13.feat/reg_standard/stats/varcope1 /home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-14.feat/reg_standard/stats/varcope1",
"Used": []
},
{
- "@id": "urn:785ab00d-b2b2-4d41-9517-5340e9a6b666",
+ "@id": "urn:1be6efab-9929-4b1e-8bbc-c165cd38270f",
"Label": "fslmaths",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths varcope1 -mas mask varcope1",
"Used": [
- "urn:dc6c04c1-ad18-4892-92a4-c031e29dca9d",
- "urn:e84ad552-4fd6-4f7a-b61f-af8268dbc4b7"
+ "urn:035c3970-5a13-491b-a04b-584ca86e8397",
+ "urn:85de6a2e-faae-4cb2-b1be-233684dc4309"
]
},
{
- "@id": "urn:9c7c6f27-48e0-4fea-9462-0562a157958e",
+ "@id": "urn:0935d3f6-d3b7-44a9-877c-9e3cc384b111",
"Label": "printf",
- "AssociatedWith": "urn:fa8d9523-1bbe-4d63-99df-ddfc0e3f8fd7",
+ "AssociatedWith": "urn:1a0347c5-1103-4187-9fe3-2e53100f089c",
"Command": "printf '1 ' >> design.lcon",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:82368305-14a5-444d-9f57-a96589e51937",
+ "@id": "urn:22a28170-7c0e-4430-b02f-0800d1ecf2a4",
"Label": "bg_image",
"AtLocation": "bg_image",
"digest": {
@@ -442,25 +442,25 @@
}
},
{
- "@id": "urn:afd3d158-c888-4146-81cc-da7a53e3cd8c",
+ "@id": "urn:0f9b9bf5-4213-468d-a35c-0b18e6ea023d",
"Label": "bg_image",
"AtLocation": "bg_image",
- "GeneratedBy": "urn:482a00bc-4f3f-4866-adff-1ca4914f0f9c",
+ "GeneratedBy": "urn:9e9057eb-e197-4c3e-b411-5cc092df19e5",
"digest": {
"sha256": "ee2ea46067dbf68f9438c2eca02baa42dc59c8f171830150d0621ae3e061d7d0"
}
},
{
- "@id": "urn:3a2f1b8e-942c-4178-8f58-491c55c796a7",
+ "@id": "urn:0807935a-9ab8-477e-8608-b44b647607cf",
"Label": "inputreg",
"AtLocation": "inputreg",
- "GeneratedBy": "urn:7eeace10-a018-45b9-b882-514a0a878de0",
+ "GeneratedBy": "urn:db8f33dc-3bfa-470f-93dd-7d1d8d61e2a8",
"digest": {
"sha256": "d820f84544e66c638eb5c8e71e84a56b0a45e35a1b508ff270c8e01746985c3f"
}
},
{
- "@id": "urn:bf820444-ae9b-4433-98a7-a11014b56ea1",
+ "@id": "urn:6a7c684d-98df-4535-be47-fcf9e2eda67d",
"Label": "mask",
"AtLocation": "../mask",
"digest": {
@@ -468,52 +468,52 @@
}
},
{
- "@id": "urn:d227a590-b746-4e62-a756-06959e2f290e",
+ "@id": "urn:e6616dd8-25eb-4bfa-ac07-5b7a060ae105",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:0840ffaf-344d-4b50-b9b5-1a4dd76fe080",
+ "GeneratedBy": "urn:91516a9b-26bb-4933-a4e1-563ee506a9b1",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:42579cc8-6d6b-44d4-bbb5-b30f3f880bfc",
+ "@id": "urn:d7435782-a021-4eae-a533-fbeccbabbf59",
"Label": "masksum",
"AtLocation": "masksum",
- "GeneratedBy": "urn:fa9c14f8-dc0e-4bf6-a4c1-efa702904c63",
+ "GeneratedBy": "urn:40828fc2-6694-4c66-98a2-66f47b52da95",
"digest": {
"sha256": "11b44d8f49c65d763a7e80d2a07bc61d6269bc71dc9ea9f77bfe5f7795d4a58c"
}
},
{
- "@id": "urn:df70a01a-6213-44d8-b679-676dd6bfb129",
+ "@id": "urn:07b4df38-c764-4ea2-90d2-4ec7525e4376",
"Label": "masksum_overlay",
"AtLocation": "masksum_overlay",
- "GeneratedBy": "urn:65ac2267-948b-4892-afd1-d931dd616401",
+ "GeneratedBy": "urn:47c2ec0e-da50-49f4-81fc-36c6e5a8251d",
"digest": {
"sha256": "9f347d6ec7a789bf400954fc9f6576becdbfaae343b6e778e729bb02400c3e18"
}
},
{
- "@id": "urn:d3bbe5ef-0da2-4c47-bf61-d804b9ebc44b",
+ "@id": "urn:01695c88-880b-4165-a6c4-0832f9174f62",
"Label": "masksum_overlay.png",
"AtLocation": "masksum_overlay.png",
- "GeneratedBy": "urn:db70a010-5f90-48af-8c31-6be63a2c5d14",
+ "GeneratedBy": "urn:324e098a-3bca-4dee-a253-bc65ca24c92a",
"digest": {
"sha256": "cb87f6a075a6829b613c60ea6ed47ebd80fdb95356d0f783cf182255469425cb"
}
},
{
- "@id": "urn:2f1d7d43-4b07-48b9-8496-eebbf76893b0",
+ "@id": "urn:8e1d5762-8fbd-4ff1-a41a-903dfe42bdbd",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:17be67dd-6c13-4769-b68a-36e4a40852c4",
+ "GeneratedBy": "urn:0b6603a3-dd8f-4854-9a7f-096e2cdbae56",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:9e154a04-adf5-4892-9856-fd8ce771786a",
+ "@id": "urn:fcc1f2b7-e347-48be-9bfa-66d805405da8",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-01.feat/reg_standard/mask",
"digest": {
@@ -521,16 +521,16 @@
}
},
{
- "@id": "urn:72200829-1d73-419e-aec9-c1447e92e941",
+ "@id": "urn:28044b83-5c10-442b-8893-0fcf7e0b9d91",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:208141cb-d264-4585-803c-add159a34691",
+ "GeneratedBy": "urn:e2378519-04e3-4715-84b2-6bc7ea8690bf",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:ad350bf9-e517-49d8-9019-361963775a0f",
+ "@id": "urn:c107ddf9-4793-48b4-b1db-74f660d9b4a5",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-02.feat/reg_standard/mask",
"digest": {
@@ -538,16 +538,16 @@
}
},
{
- "@id": "urn:78f3984b-919a-4bcb-8f8d-2868961736c1",
+ "@id": "urn:d5dd2de4-21d3-4f70-94c0-ebdac0c475c7",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:be55819c-21bc-4561-934b-edc05d5e660a",
+ "GeneratedBy": "urn:3540e9a9-468a-4af4-856c-88accf4a79c9",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:cf0b023c-b6b6-4cc3-b7eb-3708194092e5",
+ "@id": "urn:ba668017-e912-4946-b252-0bf10dffbfea",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-03.feat/reg_standard/mask",
"digest": {
@@ -555,16 +555,16 @@
}
},
{
- "@id": "urn:e7b0996d-40d0-4d73-b587-f8982e0c5c55",
+ "@id": "urn:11a19e58-b18a-4068-9317-2e48372cc90a",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:f3e2b286-a6e2-427e-b5fe-bc4389dea257",
+ "GeneratedBy": "urn:2f9bb8f0-6d78-4390-a502-3fcf6741b82c",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:78048600-5a41-4e61-a4cf-16d22e2bc63f",
+ "@id": "urn:afd5f1ae-2faf-4017-bf1b-0e6bf599fdf2",
"Label": "mask",
"AtLocation": "/home/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/LEVEL1/sub-04.feat/reg_standard/mask",
"digest": {
@@ -572,16 +572,16 @@
}
},
{
- "@id": "urn:a6f01e18-f324-4587-938f-b524db505088",
+ "@id": "urn:89b667c5-1f4a-49b9-bb49-dcab4ea6d9b9",
"Label": "maskunique",
"AtLocation": "maskunique",
- "GeneratedBy": "urn:3d1775e1-e6d1-44d4-9cc6-e7b2558fbaec",
+ "GeneratedBy": "urn:5d17d672-2c7c-4a90-aa51-7047bdba2a44",
"digest": {
"sha256": "b42669f6ae81e72b18aa1d23957a1f32022844786d867c099c24f0796227762a"
}
},
{
- "@id": "urn:2c0f03e8-19de-4de6-8318-65d031bacb43",
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diff --git a/examples/from_parsers/fsl/fsl_group_wls_report_log.png b/examples/from_parsers/fsl/fsl_group_wls_report_log.png
index 15b6aca89..51d5175aa 100644
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diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
index e6dff0097..27f093b5c 100644
--- a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.jsonld
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"Records": {
"Software": [
{
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:3fd0f707-15fa-407a-9224-edfda6528cb1"
+ "urn:3ef69f43-addd-4b3e-a08d-72e58ac1cc5e"
]
},
{
- "@id": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4",
+ "@id": "urn:c2e3c6f9-ef9b-4224-81c0-d12f2387a4ab",
"Label": "fslmaths",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:0e24554b-322d-4be9-87cd-9dd642325442"
+ "urn:6125b559-65da-4d84-91f6-f5e0bb74253d"
]
},
{
- "@id": "urn:ed8e6d73-f02f-417f-86a2-619df64156ac",
+ "@id": "urn:a47f7d54-cf4a-4bfe-af42-a419f102dd1b",
"Label": "epi_reg",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:5b10beae-c90a-4bd3-801e-3bba870ee006",
+ "@id": "urn:b8510365-9a63-4fce-a710-1fac7f827369",
"Label": "convert_xfm",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:deab5f4e-3598-41de-a361-d573731a55b5"
+ "urn:d16e1d03-91c1-44be-b2e2-01f8510acb7c"
]
},
{
- "@id": "urn:5b45b716-037e-42e9-a47c-f350030ae099",
+ "@id": "urn:c5509615-585c-4c3e-89d6-842233802aa1",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:9a03f285-dfcd-410d-bb99-8b0ebbe3ef20",
- "urn:b8d7c546-8d76-4977-902e-54a5f98165f9"
+ "urn:7f2241be-00ff-42bb-a0ff-019307d039e3",
+ "urn:e6fbf256-8d35-47ec-876b-0357ad3e8ea9"
]
},
{
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+ "@id": "urn:a526b97a-55a5-4dc9-b3f9-814e2a95b0fe",
"Label": "pngappend",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
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- "urn:bf004824-b637-4840-942f-369d36e3837e"
+ "urn:01c14a4b-ed94-4cd7-aecf-b1cf5dbd0636",
+ "urn:1e4f098b-80d9-4ada-b2b4-b771609d447f",
+ "urn:1e5f7ab0-fe79-4408-9285-7703f62ada81",
+ "urn:3b5a7e2d-88da-4698-9bd2-d28b7924cca7",
+ "urn:47081172-561d-45b2-966f-017725144a5a",
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+ "urn:5ede64d7-ed6a-43e8-9d84-48c85ba3337d",
+ "urn:6a709cf3-59bd-4bef-8036-427403483640",
+ "urn:a8c28eb9-afad-491e-a43e-db03a1be3b6a",
+ "urn:b0870209-65e9-4f07-bb0e-04a01421ebca",
+ "urn:b85d2b6f-cd72-46a9-9170-9e771394d1c3",
+ "urn:f66a5afb-048b-42f9-9463-57d589c88e3f"
]
},
{
- "@id": "urn:b361905e-407f-4981-8e58-3208f23a069a",
+ "@id": "urn:201ec870-0145-4a31-9d4a-0cbac8184ca4",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:9a03f285-dfcd-410d-bb99-8b0ebbe3ef20",
- "urn:b8d7c546-8d76-4977-902e-54a5f98165f9"
+ "urn:7f2241be-00ff-42bb-a0ff-019307d039e3",
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]
},
{
- "@id": "urn:3360db04-b715-4330-b177-7ab1cbce8211",
+ "@id": "urn:b5713225-c925-41a4-8859-f1a45cb98b2f",
"Label": "pngappend",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
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- "urn:bf004824-b637-4840-942f-369d36e3837e"
+ "urn:01c14a4b-ed94-4cd7-aecf-b1cf5dbd0636",
+ "urn:1e4f098b-80d9-4ada-b2b4-b771609d447f",
+ "urn:1e5f7ab0-fe79-4408-9285-7703f62ada81",
+ "urn:3b5a7e2d-88da-4698-9bd2-d28b7924cca7",
+ "urn:47081172-561d-45b2-966f-017725144a5a",
+ "urn:48ef0bfa-2e36-4e1d-b1cd-a8c2ae60de83",
+ "urn:5ede64d7-ed6a-43e8-9d84-48c85ba3337d",
+ "urn:6a709cf3-59bd-4bef-8036-427403483640",
+ "urn:a8c28eb9-afad-491e-a43e-db03a1be3b6a",
+ "urn:b0870209-65e9-4f07-bb0e-04a01421ebca",
+ "urn:b85d2b6f-cd72-46a9-9170-9e771394d1c3",
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]
},
{
- "@id": "urn:3aa74700-0b41-45a3-9889-68aad2d2e060",
+ "@id": "urn:7852bcb8-5b20-4e3d-b988-b3d0a7cd856a",
"Label": "pngappend",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
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- "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8"
+ "urn:52627452-6a11-4548-851b-68d0c1c1247a",
+ "urn:a909d3a6-899d-4094-8057-76e748420573"
]
},
{
- "@id": "urn:9bc9d34b-4426-4e61-9d88-ef8ef4e54805",
+ "@id": "urn:4a0a738c-5446-434b-b37e-185850b2c815",
"Label": "rm",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:14cc38ee-b9f4-4f09-8da4-2ff6893c9da8",
- "urn:b3e881ab-5017-474d-ab20-1ff4734e60f1"
+ "urn:08a67d0f-edac-465d-a658-7b36158e5bdc",
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]
},
{
- "@id": "urn:5e650fe4-797e-43ba-a8e5-78407a74f7b4",
+ "@id": "urn:52df3fa4-d453-4873-a4e7-7cff42bb45f6",
"Label": "rm",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:127a38fe-34a4-4248-9396-9b5106b4bca0"
+ "urn:a909d3a6-899d-4094-8057-76e748420573"
]
},
{
- "@id": "urn:94d83b6c-0071-40c5-b3ad-9687a6570107",
+ "@id": "urn:3338d962-1dc5-43c4-8b75-720ca98dd570",
"Label": "mcflirt",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:dda7883b-7b5a-4449-bac3-ffcbe0ef3bf2"
+ "urn:35e0e07b-52b0-4383-bec9-d458e83b8764"
]
},
{
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+ "@id": "urn:40dbdf46-570c-41fc-95d3-253dbe2e58c5",
"Label": "Make directory",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8",
+ "@id": "urn:f8a1c91e-1034-4376-98f7-2013730c5cc8",
"Label": "mv",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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- "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1",
- "urn:bbe97082-e102-4703-8c89-979834092600"
+ "urn:160924fb-36a2-4ec4-b294-904d4e626c07",
+ "urn:283dfd64-9894-47e8-b68c-de1c4ff418b7",
+ "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d",
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]
},
{
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+ "@id": "urn:aba916e9-f3ed-4c02-926d-b0522187522f",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1"
+ "urn:283dfd64-9894-47e8-b68c-de1c4ff418b7"
]
},
{
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+ "@id": "urn:845fd8cc-b941-4771-9a49-9b1e33707282",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1"
+ "urn:283dfd64-9894-47e8-b68c-de1c4ff418b7"
]
},
{
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+ "@id": "urn:4c567742-826b-41a5-9e89-3e4737f1161d",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca"
+ "urn:a6cf3443-a7a0-40c4-9036-dfeb288a68a3"
]
},
{
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+ "@id": "urn:c84b6522-8dec-4ded-aa5d-84852adab29c",
"Label": "fslmaths",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
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+ "urn:36b08c61-b83f-4357-8020-44cbf06f0fe0"
]
},
{
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+ "@id": "urn:4afc874f-94c0-4c10-9aa6-0817491b5286",
"Label": "bet2",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
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+ "urn:934646fa-7bbc-4805-a09f-9f5610ab15fc"
]
},
{
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+ "@id": "urn:134af596-b966-4d6d-b1de-8e018a339753",
"Label": "immv",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:0aa34890-8756-4bfc-90db-e611bc459fb7"
+ "urn:4ee7d8c0-5b6f-4a09-922b-93a7fddcb451"
]
},
{
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+ "@id": "urn:e9d6c052-dd8d-4200-8d7b-befe83645890",
"Label": "fslmaths",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
},
{
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+ "@id": "urn:294a7e16-60f3-471c-8de2-b6a3dede683c",
"Label": "fslstats",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
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+ "urn:226d8aa2-90c8-464e-8eee-e3633304c512"
]
},
{
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"Label": "fslmaths",
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]
},
{
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"Label": "fslstats",
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- "urn:543ec73e-7a7b-4f1c-b0f2-5e4faa4a024a"
+ "urn:36b08c61-b83f-4357-8020-44cbf06f0fe0"
]
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{
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"Label": "fslmaths",
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]
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{
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"Label": "fslmaths",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
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{
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"Label": "fslmaths",
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]
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"Label": "susan",
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]
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{
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"Label": "fslmaths",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
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{
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"Label": "fslmaths",
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+ "urn:898da8f5-a63a-4248-84b6-c59a933aec05"
]
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{
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"Label": "fslmaths",
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"Used": [
- "urn:e386f822-5553-4832-8d3d-145ad7886285"
+ "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3"
]
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"Label": "fslmaths",
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- "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
- "urn:e386f822-5553-4832-8d3d-145ad7886285"
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]
},
{
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"Label": "imrm",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:bf572fa3-0641-448f-900b-a0d0b1b22531"
+ "urn:2601600d-77ad-47b1-943f-527dce2f3c41"
]
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
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+ "urn:68c80596-8a3a-41ec-abd1-1b5cb9f3908f"
]
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{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
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+ "urn:48daa469-7980-4aef-8da7-ad179b504481"
]
},
{
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"Label": "rm",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:fa82d500-9b52-455b-842d-f82094ef7a6a"
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]
},
{
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"Label": "Make directory",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Label": "fslFixText",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:0651b820-6157-4a1d-a001-93201fb81bda"
+ "urn:f59764b8-a925-44d9-8cc7-4e70fb2b3d1b"
]
},
{
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"Label": "Make directory",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
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"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Label": "fslFixText",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
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+ "urn:741a7638-5305-4e8c-b932-63bbac46e5b4"
]
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{
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"Label": "film_gls",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con --fcon=design.fts",
"Used": []
},
{
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"Label": "smoothest",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 98 -m mask -r stats/res4d > stats/smoothness",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
+ "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
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]
},
{
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"Label": "echo",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat2 -mas mask thresh_zstat2",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
},
{
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"Label": "echo",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "echo 38352 > thresh_zstat2.vol",
"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat3 -mas mask thresh_zstat3",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
+ "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
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]
},
{
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"Label": "echo",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "echo 38352 > thresh_zstat3.vol",
"Used": []
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zfstat1 -mas mask thresh_zfstat1",
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- "urn:bdda387f-4e42-4010-969a-58d6c75a23ae"
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]
},
{
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"Label": "echo",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "echo 38352 > thresh_zfstat1.vol",
"Used": []
},
{
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+ "@id": "urn:76cf5f17-a795-4078-8068-c9e841f985ec",
"Label": "ptoz",
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+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
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"Label": "cluster",
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"Used": [
- "urn:40667860-a8a0-4bbb-8e21-a110c83b1cf2",
- "urn:df85adc5-0547-478e-a8d0-34cb2391ce58"
+ "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610",
+ "urn:d1ae6edb-eb2d-4090-8a91-27b487473beb"
]
},
{
- "@id": "urn:2461ed0f-a5f5-47b8-96f4-be8d20fc72ec",
+ "@id": "urn:5ecaa27a-d8dc-48bf-acb6-e3c9283ad0b8",
"Label": "cluster2html",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:37c3c064-fdc2-41a0-9c52-90aac989eb63"
+ "urn:f15fe524-f568-4e93-9286-fc790afe24eb"
]
},
{
- "@id": "urn:caf58ed5-15de-4ac6-aa9d-3a9c22c728fc",
+ "@id": "urn:a1805d3b-baeb-4707-b217-71a4d28ace1b",
"Label": "ptoz",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
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"Label": "cluster",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat2 -t 3.090232 --othresh=thresh_zstat2 -o cluster_mask_zstat2 --connectivity=26 --olmax=lmax_zstat2.txt --scalarname=Z --voxuncthresh -c stats/cope2 > cluster_zstat2.txt",
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- "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7"
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+ "urn:cc63cbf1-a938-4f36-94b0-28d7334c06ff"
]
},
{
- "@id": "urn:b082c399-b8dc-4e48-bc93-46517e9ad1b3",
+ "@id": "urn:d8d7376b-a591-4123-974d-081e6e33896a",
"Label": "cluster2html",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat2",
"Used": [
- "urn:11f223e3-299f-4f87-b5c6-b2cd5e69c374"
+ "urn:d33474de-c1e1-4d6c-a0f2-db992f31c561"
]
},
{
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+ "@id": "urn:2be229a2-3fbe-4acb-9aaf-e280530aa938",
"Label": "ptoz",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:1c5facbc-99e5-4301-ba64-ab4aadc48e17",
+ "@id": "urn:454dc845-1967-46e8-9b90-69b929477b23",
"Label": "cluster",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
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- "urn:75142b97-c286-40c1-a0df-a19fee33956c",
- "urn:a5773a3d-e278-40b2-b7a2-d22deb1d7ac4"
+ "urn:4963497e-481b-4679-a1f7-425b747b8db9",
+ "urn:53cb7ce5-86d5-486f-b549-3d7bc5744529"
]
},
{
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+ "@id": "urn:198081c3-d54d-4afa-8c05-56a43bd2ec90",
"Label": "cluster2html",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat3",
"Used": [
- "urn:636d3259-22bf-4dd3-a14a-b564569cac0d"
+ "urn:8d068463-26b0-4236-8937-fcb1118a01eb"
]
},
{
- "@id": "urn:589b1c78-c52c-4441-951b-48ba0f8ae0bd",
+ "@id": "urn:e4b3bf0b-1072-4d12-85a9-40d9fba0c427",
"Label": "ptoz",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:954dc233-a400-4356-98f9-d818f2b94a91",
+ "@id": "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
"Label": "cluster",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zfstat1 -t 3.090232 --othresh=thresh_zfstat1 -o cluster_mask_zfstat1 --connectivity=26 --olmax=lmax_zfstat1.txt --scalarname=Z --voxuncthresh > cluster_zfstat1.txt",
"Used": [
- "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15"
+ "urn:b38636c2-8db1-4744-9952-28a75ff3368d"
]
},
{
- "@id": "urn:d09a9e6e-3b93-45ac-bc47-55d3f9553c11",
+ "@id": "urn:8154353f-62f4-4f33-a5e0-b25cfb3e0bf4",
"Label": "cluster2html",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zfstat1",
"Used": [
- "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148"
+ "urn:3459f83d-9b42-4196-9684-d7762bb4bd34"
]
},
{
- "@id": "urn:63092bb5-c00b-4806-ada8-4e675ca40481",
+ "@id": "urn:24a27a0a-d8aa-421e-b5f2-6d2b89af0b86",
"Label": "fslstats",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:40667860-a8a0-4bbb-8e21-a110c83b1cf2"
+ "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610"
]
},
{
- "@id": "urn:b6cfbd28-f1b1-428c-8aee-21fa321a24c3",
+ "@id": "urn:c73fa496-d31f-4802-97a4-ed7e422f2b73",
"Label": "fslstats",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat2 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:266d9fa3-6f0b-4e1d-b2b2-aaaabb98cef2"
+ "urn:cc63cbf1-a938-4f36-94b0-28d7334c06ff"
]
},
{
- "@id": "urn:3de80e83-be49-40e6-9e70-c25dd5f971ad",
+ "@id": "urn:3aedf6ae-6545-476c-b838-cf17ff552bbd",
"Label": "fslstats",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat3 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:a5773a3d-e278-40b2-b7a2-d22deb1d7ac4"
+ "urn:53cb7ce5-86d5-486f-b549-3d7bc5744529"
]
},
{
- "@id": "urn:c32531f4-eacb-40a9-923b-70b1748c51c5",
+ "@id": "urn:13d034fa-73d1-442e-a6c5-5225daf2683f",
"Label": "fslstats",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zfstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15"
+ "urn:b38636c2-8db1-4744-9952-28a75ff3368d"
]
},
{
- "@id": "urn:58f887a8-b7b6-4ae0-ac2a-6f8113ecf719",
+ "@id": "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
"Label": "overlay",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090292 7.429559 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:af9f6f85-8adc-4ef9-a88c-8402725f2373",
+ "@id": "urn:0a80926c-2513-4239-bf14-d648691c34ee",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:a4bcce4e-9230-4c91-afc0-6657745b8701"
+ "urn:a020ff0c-b5e2-4414-a32c-0791ca1dd749"
]
},
{
- "@id": "urn:cb81e16e-cab3-408f-93d8-37aefc195994",
+ "@id": "urn:44a77ffc-f60b-4a4a-8561-f1cdbfa30a32",
"Label": "cp",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:e289288b-2ab9-40af-bfb8-5ccf11862589"
+ "urn:588a7629-618c-407b-ba9b-2f1ecac124d7"
]
},
{
- "@id": "urn:012baa80-344e-4625-9fe2-288360cec634",
+ "@id": "urn:057a0867-62eb-4701-9db0-41598da4c88d",
"Label": "overlay",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat2 3.090292 7.429559 rendered_thresh_zstat2",
"Used": []
},
{
- "@id": "urn:8433fb76-022b-4846-b2d4-fdc2cbeae320",
+ "@id": "urn:9c34070e-67f7-4161-8228-2532bcf88bc7",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat2 -A 750 rendered_thresh_zstat2.png",
"Used": [
- "urn:42974bae-1dd8-4079-a97d-4ba1ccc9632e"
+ "urn:acd0d873-2205-4bcf-8552-465bb5afba1f"
]
},
{
- "@id": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
+ "@id": "urn:7365d26e-619c-4e80-a058-964fa937d9e5",
"Label": "overlay",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat3 3.090292 7.429559 rendered_thresh_zstat3",
"Used": []
},
{
- "@id": "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87",
+ "@id": "urn:91bcc4fd-63dd-4ccd-b200-8f3db9ecd468",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat3 -A 750 rendered_thresh_zstat3.png",
"Used": [
- "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79"
+ "urn:2752a703-c278-4a04-895e-e9719f256693"
]
},
{
- "@id": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "@id": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10",
"Label": "overlay",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zfstat1 3.090292 7.429559 rendered_thresh_zfstat1",
"Used": []
},
{
- "@id": "urn:a424e26a-4756-4ebf-aee7-78caa8508f49",
+ "@id": "urn:adb1b0ff-e8c1-4355-9b01-b20a5b01cf0b",
"Label": "slicer",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zfstat1 -A 750 rendered_thresh_zfstat1.png",
"Used": [
- "urn:7c2e9e77-f441-4a6e-a902-d2101c32b8eb"
+ "urn:535bc829-b0d7-4089-a924-ada0c271af18"
]
},
{
- "@id": "urn:f7b45616-d40f-4f94-9390-20175b6abab7",
+ "@id": "urn:f19f51ad-5e08-412b-b80a-9023c70693b4",
"Label": "Make directory",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5",
+ "@id": "urn:0571739d-afb1-4fc4-85a8-64b608b3ddc1",
"Label": "tsplot",
- "AssociatedWith": "urn:b889cc5f-d33a-4375-9707-5241f6701604",
+ "AssociatedWith": "urn:83061624-d009-4f4b-8ae0-b5a6a300ae13",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:e4549dc8-e7dc-4d2d-a4fc-5aef29e6af69",
+ "@id": "urn:7e9b4723-0041-48af-a1c6-2f7853be68af",
"Label": "sub-01_task-tonecounting_bold",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
@@ -757,25 +757,25 @@
}
},
{
- "@id": "urn:dda7883b-7b5a-4449-bac3-ffcbe0ef3bf2",
+ "@id": "urn:35e0e07b-52b0-4383-bec9-d458e83b8764",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:b4a86db6-024c-43d1-a350-f0d1da9a6e0a",
+ "GeneratedBy": "urn:d1ec081b-dca9-4e34-b453-c9369a7d8f14",
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}
},
{
- "@id": "urn:b64e7dcb-f9fd-480c-b8d1-f72de36ef22a",
+ "@id": "urn:214821d7-ad17-4c86-8e25-55b7d3cf8238",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:b8097281-e20e-4997-a059-1965f255d018",
+ "GeneratedBy": "urn:5a331a8f-133d-42f1-9cd8-db061bfd5b10",
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}
},
{
- "@id": "urn:64729fa6-5fa8-4e4c-9622-e340d68a72fc",
+ "@id": "urn:580d3f39-2ed1-4d19-a7cb-afc1dca96dcd",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/example_func.nii.gz",
"digest": {
@@ -783,7 +783,7 @@
}
},
{
- "@id": "urn:3fd0f707-15fa-407a-9224-edfda6528cb1",
+ "@id": "urn:3ef69f43-addd-4b3e-a08d-72e58ac1cc5e",
"Label": "sub-01_T1w_brain",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
@@ -791,7 +791,7 @@
}
},
{
- "@id": "urn:f7465d5c-46f7-490e-a5a2-08d59b567b0d",
+ "@id": "urn:0255d49b-7932-4898-932c-f76b2883d865",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -799,31 +799,31 @@
}
},
{
- "@id": "urn:33c0adb5-01c5-4303-a15c-09d7f72fe426",
+ "@id": "urn:e7b3d762-06a3-4ab8-b5a0-36d56b8ca686",
"Label": "fsl_FIR_basis.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat",
- "GeneratedBy": "urn:70bfd749-6110-4cc8-8de4-e88be8987dd8"
+ "GeneratedBy": "urn:2486d696-f1a8-466b-ba4b-839949c75305"
},
{
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+ "@id": "urn:1228f105-1246-44de-ba34-4b6a2c0574be",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FIR_basis.feat/reg",
- "GeneratedBy": "urn:4f7fe1b2-ce65-4d83-98cd-a2992b80e685",
+ "GeneratedBy": "urn:f284d218-a06b-47db-b80f-bc5f8cbe08b9",
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}
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{
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+ "@id": "urn:7f2241be-00ff-42bb-a0ff-019307d039e3",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:951b9cd2-26a6-42d7-8125-f162f3a38fee",
+ "GeneratedBy": "urn:cf862659-769f-4670-a1c9-e8942ea215d6",
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}
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{
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+ "@id": "urn:6125b559-65da-4d84-91f6-f5e0bb74253d",
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
@@ -831,13 +831,13 @@
}
},
{
- "@id": "urn:f4f108d9-ad44-4f62-bef2-0214e3e76d69",
+ "@id": "urn:3cc4966c-5bed-4213-8972-39f8b5539223",
"Label": "",
"AtLocation": "",
- "GeneratedBy": "urn:e522e69f-2f06-4730-b9db-c7204a36f5a4"
+ "GeneratedBy": "urn:c2e3c6f9-ef9b-4224-81c0-d12f2387a4ab"
},
{
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+ "@id": "urn:d16e1d03-91c1-44be-b2e2-01f8510acb7c",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -845,16 +845,16 @@
}
},
{
- "@id": "urn:d2b88a58-b171-48dd-9b24-909c0df5133d",
+ "@id": "urn:51ab3eeb-51b3-4557-9bb6-321611d9b28b",
"Label": "highres2example_func.mat",
"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:5b10beae-c90a-4bd3-801e-3bba870ee006",
+ "GeneratedBy": "urn:b8510365-9a63-4fce-a710-1fac7f827369",
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}
},
{
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+ "@id": "urn:e6fbf256-8d35-47ec-876b-0357ad3e8ea9",
"Label": "example_func2highres",
"AtLocation": "example_func2highres",
"digest": {
@@ -862,250 +862,250 @@
}
},
{
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"AtLocation": "sla.png",
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{
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"AtLocation": "slb.png",
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{
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{
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{
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{
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{
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- "GeneratedBy": "urn:5b45b716-037e-42e9-a47c-f350030ae099",
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"AtLocation": "example_func2highres1.png",
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{
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{
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{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:3360db04-b715-4330-b177-7ab1cbce8211",
+ "GeneratedBy": "urn:b5713225-c925-41a4-8859-f1a45cb98b2f",
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"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:3aa74700-0b41-45a3-9889-68aad2d2e060",
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{
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"Label": "sl?.png",
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"digest": {
@@ -1113,25 +1113,25 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:94d83b6c-0071-40c5-b3ad-9687a6570107",
+ "GeneratedBy": "urn:3338d962-1dc5-43c4-8b75-720ca98dd570",
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{
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- "GeneratedBy": "urn:736f8ab3-cae1-4022-9c97-ba8843782a36",
+ "GeneratedBy": "urn:40dbdf46-570c-41fc-95d3-253dbe2e58c5",
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{
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+ "@id": "urn:93bf1748-0d66-4de9-8727-daad0227f807",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -1139,7 +1139,7 @@
}
},
{
- "@id": "urn:95dd9372-af2f-48c2-9239-2fa721e54fa1",
+ "@id": "urn:283dfd64-9894-47e8-b68c-de1c4ff418b7",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -1147,7 +1147,7 @@
}
},
{
- "@id": "urn:3d08452f-2ec9-47ad-be79-1d9fd0c690c2",
+ "@id": "urn:bf65fe1e-ad76-47f9-a992-39f329cd3457",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -1155,7 +1155,7 @@
}
},
{
- "@id": "urn:3ad61e65-704a-4488-8b98-355fd8537175",
+ "@id": "urn:ce42a61b-ef8f-4e71-8f12-7425fa64d4d5",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -1163,7 +1163,7 @@
}
},
{
- "@id": "urn:40705e2b-01dd-4e4b-a30f-4876f90382bb",
+ "@id": "urn:160924fb-36a2-4ec4-b294-904d4e626c07",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1171,7 +1171,7 @@
}
},
{
- "@id": "urn:bbe97082-e102-4703-8c89-979834092600",
+ "@id": "urn:5d41178a-42ce-4693-8b77-8e7c79d0157d",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1179,34 +1179,34 @@
}
},
{
- "@id": "urn:9f71d53e-4e02-4a4c-a895-35ba16cbe373",
+ "@id": "urn:5a7d3988-7a4e-412a-a2a9-f6f681725a3b",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:3a8fa6eb-a642-4a2b-983c-79bd02ca66f8",
+ "GeneratedBy": "urn:f8a1c91e-1034-4376-98f7-2013730c5cc8",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:5335c81d-8e46-452b-9092-fb041b634d5f",
+ "@id": "urn:8039243e-1237-4865-a4b3-f4d38e1cee10",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:230eecc7-aae1-43d0-af4a-f49dd70b07b1",
+ "GeneratedBy": "urn:aba916e9-f3ed-4c02-926d-b0522187522f",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:699344d3-19f3-46c0-98ae-3a9756df0bd8",
+ "@id": "urn:b90fa097-6626-4a52-92fa-1011aacdd585",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:6354be3e-5870-480b-a4e9-c0337b907c91",
+ "GeneratedBy": "urn:845fd8cc-b941-4771-9a49-9b1e33707282",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:646036ac-d41f-4613-83a2-1ab3a0d849ca",
+ "@id": "urn:a6cf3443-a7a0-40c4-9036-dfeb288a68a3",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1214,34 +1214,34 @@
}
},
{
- "@id": "urn:68c34e3d-c21c-423c-8152-3fe74f2cf2a2",
+ "@id": "urn:b9c6adb1-025e-452c-b725-c94944c871d2",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:ac0cbc3a-d528-41ac-9614-661e260ac537",
+ "GeneratedBy": "urn:4c567742-826b-41a5-9e89-3e4737f1161d",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:ae1735e0-33c8-4a6b-9a2d-f92b51e75ae8",
+ "@id": "urn:934646fa-7bbc-4805-a09f-9f5610ab15fc",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:d1e011d7-e565-4bea-850c-263729ba79cd",
+ "GeneratedBy": "urn:c84b6522-8dec-4ded-aa5d-84852adab29c",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:bdda387f-4e42-4010-969a-58d6c75a23ae",
+ "@id": "urn:4d84c4a2-4d4a-4c24-bebe-a6c923523ebd",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:008ecd09-9993-4235-84a2-a437a35dab54",
+ "GeneratedBy": "urn:4afc874f-94c0-4c10-9aa6-0817491b5286",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:0aa34890-8756-4bfc-90db-e611bc459fb7",
+ "@id": "urn:4ee7d8c0-5b6f-4a09-922b-93a7fddcb451",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1249,106 +1249,106 @@
}
},
{
- "@id": "urn:753c1b0c-e222-4f15-8866-5546c1c4ba3d",
+ "@id": "urn:ce34796c-ecbb-473e-aabd-9aaac62ef33c",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:1778c562-63a6-473a-baaf-fac05a57a5ba",
+ "GeneratedBy": "urn:134af596-b966-4d6d-b1de-8e018a339753",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:eb164190-0156-408a-8695-eabc2105da90",
+ "@id": "urn:226d8aa2-90c8-464e-8eee-e3633304c512",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:8745b76c-58c7-4318-8c6d-394b5a2929a9",
+ "GeneratedBy": "urn:e9d6c052-dd8d-4200-8d7b-befe83645890",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:d62b2ec3-829d-47f0-8be5-78951d973045",
+ "@id": "urn:a6beb099-d9b4-462b-9aee-41068713356a",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:12313157-10eb-4297-9463-d87018825ae9",
+ "GeneratedBy": "urn:b0947fdc-fe74-4e3d-8a30-2db1da4ce71b",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:bc40716c-b325-40dd-81fe-ffe9e270e07f",
+ "@id": "urn:ace6277e-bc4d-46d7-b056-76ac6741a493",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:dc001804-b15a-44be-ad41-70c5ddbc74cb",
+ "GeneratedBy": "urn:f55ea7eb-d8d5-4913-a6fa-ee8e7ae533e4",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:586156d3-de9c-47d0-aaa3-8c640989f434",
+ "@id": "urn:fed1518d-3e15-43d4-8c52-eec8ebe6c1ef",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:c46590f7-4d38-4ee9-a0ba-28911704bd72",
+ "GeneratedBy": "urn:21e521a1-5a90-48de-bc39-16737d89f891",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:577dbeef-ee03-40d7-aa64-023f1045a060",
+ "@id": "urn:1940a888-fea7-4526-b90b-8eff68400ec1",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:130b871a-526a-49f0-aedb-a4fd309f803f",
+ "GeneratedBy": "urn:63d224d0-eb64-4a30-a939-811117bae908",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:ba826ece-23e7-4e53-99b9-4b46aaad83a1",
+ "@id": "urn:898da8f5-a63a-4248-84b6-c59a933aec05",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:3ce38cf8-d9ad-4bb8-a6ee-d7c5c0a18511",
+ "GeneratedBy": "urn:50e20ccc-b165-4f42-9835-b7ed07183397",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:3e7153c9-1e34-421c-b825-35cd8d74eb15",
+ "@id": "urn:660fe90e-75ea-435d-8db6-d226d404baef",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:0ca949c1-667d-4f2c-899b-823a46887441",
+ "GeneratedBy": "urn:5a12057b-7894-4658-8885-bf8772cdd0cf",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:e386f822-5553-4832-8d3d-145ad7886285",
+ "@id": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:d66a89e0-e899-4368-b615-3138cf30c215",
+ "GeneratedBy": "urn:9d077082-757f-4630-99ce-4cea132a877d",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:bf572fa3-0641-448f-900b-a0d0b1b22531",
+ "@id": "urn:2601600d-77ad-47b1-943f-527dce2f3c41",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:cbaacc0b-fa57-4e78-8f67-1518f03bd398",
+ "GeneratedBy": "urn:24494591-d5d7-4500-ad04-ae114c3334f9",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:b6fa3c79-0f4b-43ca-9e68-105676040d46",
+ "@id": "urn:33ff81af-1444-46c3-a060-f926d0ced8ae",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:77b55fda-08f6-4167-aaa8-81a868cd06bb",
+ "GeneratedBy": "urn:5818684f-eb4f-4926-ab68-239aef10f315",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:69000e1a-e90e-4fe9-9148-a4e7bab105bc",
+ "@id": "urn:68c80596-8a3a-41ec-abd1-1b5cb9f3908f",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1356,25 +1356,25 @@
}
},
{
- "@id": "urn:56d76a74-54b9-4c18-94ef-0e7ffee7589d",
+ "@id": "urn:48daa469-7980-4aef-8da7-ad179b504481",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:fad5fe04-ff55-413d-ac3c-b845eb60abe7",
+ "GeneratedBy": "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:22332602-c1dd-46ac-8021-349e698a0939",
+ "@id": "urn:162a1740-734c-4e43-8413-04fa22e9ac88",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:5c4586db-865a-4612-818d-aedbe8a7214c",
+ "GeneratedBy": "urn:1abaf4b3-3b8b-47a5-9bef-ea9e15727931",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:fa82d500-9b52-455b-842d-f82094ef7a6a",
+ "@id": "urn:8ddb5caa-1d83-4fa7-81bc-bc33c94e9de0",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1382,16 +1382,16 @@
}
},
{
- "@id": "urn:f3864eb5-3dee-4f42-aebc-78dac92cd7ea",
+ "@id": "urn:f48bc076-8f2e-47d0-b651-3a12200ba777",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:357c4736-e0f2-4459-a14e-8796a5614330",
+ "GeneratedBy": "urn:fcb04b90-a3a3-4c4d-b8db-b5c2e2f07f5d",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:0651b820-6157-4a1d-a001-93201fb81bda",
+ "@id": "urn:f59764b8-a925-44d9-8cc7-4e70fb2b3d1b",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1399,22 +1399,22 @@
}
},
{
- "@id": "urn:4305cc71-294c-407a-be2e-082e60ec59c2",
+ "@id": "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:c6797c80-a805-4854-ae91-70a8444c022d"
+ "GeneratedBy": "urn:63ad4bc7-4d97-46bc-b872-48b4e3cc971d"
},
{
- "@id": "urn:14538410-322b-433e-89a1-fb485be42a81",
+ "@id": "urn:f0385465-4dbd-48ce-9470-433ea4f5b4ef",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:496059e9-1914-47b7-998c-2b3ab7cef31e",
+ "GeneratedBy": "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:f9444c1b-dbca-4dc3-b0e8-69fb0f84eaab",
+ "@id": "urn:741a7638-5305-4e8c-b932-63bbac46e5b4",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1422,13 +1422,13 @@
}
},
{
- "@id": "urn:c27daab7-7b46-4a97-aef8-e9def2558de6",
+ "@id": "urn:c928a696-a036-4263-b227-10fed64c9e8e",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:8387f2d4-1fd6-4431-b2d2-fb5c9be44109"
+ "GeneratedBy": "urn:a4cb1cd3-5946-4299-bda9-a293aea387b1"
},
{
- "@id": "urn:3a0e0646-3ab7-484c-95b6-6cb11ae88870",
+ "@id": "urn:6a389401-d37b-4c0e-89e2-a748ed2a46af",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1436,16 +1436,16 @@
}
},
{
- "@id": "urn:223f4f8a-3be2-4725-8506-7e8836fba053",
+ "@id": "urn:360c6e24-8ef1-4e78-a20c-4f1e6ebabc67",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:3c1ac51f-9d28-4ce9-a5ee-787dc723fe39",
+ "GeneratedBy": "urn:e5b81464-47db-4542-8dc2-69a1ddd77020",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:83df4d40-0769-4504-832a-88276820c98a",
+ "@id": "urn:e7fa77d8-7c17-453f-bf44-06a83aa361fb",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1453,16 +1453,16 @@
}
},
{
- "@id": "urn:40667860-a8a0-4bbb-8e21-a110c83b1cf2",
+ "@id": "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:44d74964-f3dc-46e0-a792-cd386dd5389f",
+ "GeneratedBy": "urn:0132a039-6f29-43c3-95e5-c1f46d2f6919",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:6b9530f5-6075-4b7d-873b-15df208d2e88",
+ "@id": "urn:03d5f94b-379d-43ba-82a1-346e22e37619",
"Label": "zstat2",
"AtLocation": "stats/zstat2",
"digest": {
@@ -1470,16 +1470,16 @@
}
},
{
- "@id": "urn:266d9fa3-6f0b-4e1d-b2b2-aaaabb98cef2",
+ "@id": "urn:cc63cbf1-a938-4f36-94b0-28d7334c06ff",
"Label": "thresh_zstat2",
"AtLocation": "thresh_zstat2",
- "GeneratedBy": "urn:44183f80-97dc-4bbb-be0f-10eedc9caec1",
+ "GeneratedBy": "urn:4405e61e-5f17-478e-8619-f860c4f23e39",
"digest": {
"sha256": "fe707ed68d72f4376668be45a2030f2d00fa81534a3e95bf92b6a499fa8595bd"
}
},
{
- "@id": "urn:372bd721-7ab0-4667-b4b6-a5412ee5062f",
+ "@id": "urn:f4931a39-0143-4666-b2d0-ea5a028c7585",
"Label": "zstat3",
"AtLocation": "stats/zstat3",
"digest": {
@@ -1487,16 +1487,16 @@
}
},
{
- "@id": "urn:a5773a3d-e278-40b2-b7a2-d22deb1d7ac4",
+ "@id": "urn:53cb7ce5-86d5-486f-b549-3d7bc5744529",
"Label": "thresh_zstat3",
"AtLocation": "thresh_zstat3",
- "GeneratedBy": "urn:f9aa4808-f717-4c6f-a4b1-0a6939095264",
+ "GeneratedBy": "urn:2420bc5d-17a3-48d3-9182-fcca102bd8bf",
"digest": {
"sha256": "d0f88769369dc8215d7373817e8f9a48482b508bb9deb2ca29904069bb23f484"
}
},
{
- "@id": "urn:6fac3dd4-3655-4d3d-a4f5-73b727d0283d",
+ "@id": "urn:d2d3e2a4-d1c8-4526-981d-515d6e512abc",
"Label": "zfstat1",
"AtLocation": "stats/zfstat1",
"digest": {
@@ -1504,16 +1504,16 @@
}
},
{
- "@id": "urn:2cf7336e-cc7b-4dc7-80e4-7fbd39e41e15",
+ "@id": "urn:b38636c2-8db1-4744-9952-28a75ff3368d",
"Label": "thresh_zfstat1",
"AtLocation": "thresh_zfstat1",
- "GeneratedBy": "urn:ccb1560a-9028-47f0-ab4c-966f54c83553",
+ "GeneratedBy": "urn:90f71712-65b6-4afd-9375-13f368a3ae90",
"digest": {
"sha256": "e4e927e247bdf8ff3b58b41cbb9db7643b27df1f7578c506950eb4b1ca2d0031"
}
},
{
- "@id": "urn:df85adc5-0547-478e-a8d0-34cb2391ce58",
+ "@id": "urn:d1ae6edb-eb2d-4090-8a91-27b487473beb",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1521,25 +1521,25 @@
}
},
{
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"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
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}
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{
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+ "@id": "urn:0bb1792b-9b25-46e4-b72e-c2be6f624712",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:8e23621e-af1f-4f36-aa91-fe74af747392",
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"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
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{
- "@id": "urn:37c3c064-fdc2-41a0-9c52-90aac989eb63",
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"AtLocation": "cluster_zstat1",
"digest": {
@@ -1547,7 +1547,7 @@
}
},
{
- "@id": "urn:40f61898-bf4a-46a7-9bd8-4190732dcdb7",
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"digest": {
@@ -1555,25 +1555,25 @@
}
},
{
- "@id": "urn:ba3fdc68-178d-4cf7-ad77-704f1b52cedd",
+ "@id": "urn:3190be3b-d808-4789-a6b2-90c5db0bb314",
"Label": "cluster_mask_zstat2",
"AtLocation": "cluster_mask_zstat2",
- "GeneratedBy": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
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}
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{
- "@id": "urn:1ae03796-c374-4c1d-b521-97bc6aeb3c76",
+ "@id": "urn:f0423d9e-54a2-4f80-a53f-e1dd94b3a947",
"Label": "cope2",
"AtLocation": "stats/cope2",
- "GeneratedBy": "urn:9157ac14-4b38-4ffb-9216-f2597912fe25",
+ "GeneratedBy": "urn:d78dd409-4c35-499c-9671-cf9bfce87925",
"digest": {
"sha256": "5f073baabd78c1c473fed55b511738f0ffe30d9fc1f23352a16ec058daacd88c"
}
},
{
- "@id": "urn:11f223e3-299f-4f87-b5c6-b2cd5e69c374",
+ "@id": "urn:d33474de-c1e1-4d6c-a0f2-db992f31c561",
"Label": "cluster_zstat2",
"AtLocation": "cluster_zstat2",
"digest": {
@@ -1581,7 +1581,7 @@
}
},
{
- "@id": "urn:75142b97-c286-40c1-a0df-a19fee33956c",
+ "@id": "urn:4963497e-481b-4679-a1f7-425b747b8db9",
"Label": "cope3",
"AtLocation": "stats/cope3",
"digest": {
@@ -1589,25 +1589,25 @@
}
},
{
- "@id": "urn:d59db5b5-4ab3-4475-bb6e-9e3510819631",
+ "@id": "urn:bade994c-bfbf-48ef-952e-593582deab90",
"Label": "cluster_mask_zstat3",
"AtLocation": "cluster_mask_zstat3",
- "GeneratedBy": "urn:1c5facbc-99e5-4301-ba64-ab4aadc48e17",
+ "GeneratedBy": "urn:454dc845-1967-46e8-9b90-69b929477b23",
"digest": {
"sha256": "fac31b7cc91c4dbb519375fa9238cfde00689381b0783d7e3b623a937b9f51d0"
}
},
{
- "@id": "urn:fe68686f-5fe0-4994-a9b1-200e446ff6b9",
+ "@id": "urn:459a96aa-645a-4262-b5e8-68460f4c9e9d",
"Label": "cope3",
"AtLocation": "stats/cope3",
- "GeneratedBy": "urn:1c5facbc-99e5-4301-ba64-ab4aadc48e17",
+ "GeneratedBy": "urn:454dc845-1967-46e8-9b90-69b929477b23",
"digest": {
"sha256": "4f5e165fb3b62e5ef5397e9f93b4572ba23f3ffe3c9f118e8a2a9cba52e2fe0e"
}
},
{
- "@id": "urn:636d3259-22bf-4dd3-a14a-b564569cac0d",
+ "@id": "urn:8d068463-26b0-4236-8937-fcb1118a01eb",
"Label": "cluster_zstat3",
"AtLocation": "cluster_zstat3",
"digest": {
@@ -1615,16 +1615,16 @@
}
},
{
- "@id": "urn:6a2d483a-c551-4640-840d-afcc913d7b0c",
+ "@id": "urn:3c9d6937-f35d-43bb-968a-f06ed6b2a0a8",
"Label": "cluster_mask_zfstat1",
"AtLocation": "cluster_mask_zfstat1",
- "GeneratedBy": "urn:954dc233-a400-4356-98f9-d818f2b94a91",
+ "GeneratedBy": "urn:1bf86114-bffa-44fe-a6e3-93a863200efc",
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"sha256": "3523a5abe83ae8c76dd74f74632bc34163aac475152d48a6b79f37eca7dfe022"
}
},
{
- "@id": "urn:3ae2add0-3e15-43a4-8ed1-2a271df38148",
+ "@id": "urn:3459f83d-9b42-4196-9684-d7762bb4bd34",
"Label": "cluster_zfstat1",
"AtLocation": "cluster_zfstat1",
"digest": {
@@ -1632,25 +1632,25 @@
}
},
{
- "@id": "urn:a4bcce4e-9230-4c91-afc0-6657745b8701",
+ "@id": "urn:a020ff0c-b5e2-4414-a32c-0791ca1dd749",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:58f887a8-b7b6-4ae0-ac2a-6f8113ecf719",
+ "GeneratedBy": "urn:6b561749-90cb-4ca3-b23e-29c9ffbe9085",
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"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:51f3d7f5-903a-4125-a257-f7bc9e65398b",
+ "@id": "urn:34aa4304-4007-4181-a467-db010e088b05",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:af9f6f85-8adc-4ef9-a88c-8402725f2373",
+ "GeneratedBy": "urn:0a80926c-2513-4239-bf14-d648691c34ee",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:e289288b-2ab9-40af-bfb8-5ccf11862589",
+ "@id": "urn:588a7629-618c-407b-ba9b-2f1ecac124d7",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1658,82 +1658,82 @@
}
},
{
- "@id": "urn:a7c0d8c8-7be5-4ebc-8f07-ebd395edf9a2",
+ "@id": "urn:e70ba5ee-87b0-42bd-a44c-5efde9c9bfed",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:cb81e16e-cab3-408f-93d8-37aefc195994",
+ "GeneratedBy": "urn:44a77ffc-f60b-4a4a-8561-f1cdbfa30a32",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:42974bae-1dd8-4079-a97d-4ba1ccc9632e",
+ "@id": "urn:acd0d873-2205-4bcf-8552-465bb5afba1f",
"Label": "rendered_thresh_zstat2",
"AtLocation": "rendered_thresh_zstat2",
- "GeneratedBy": "urn:012baa80-344e-4625-9fe2-288360cec634",
+ "GeneratedBy": "urn:057a0867-62eb-4701-9db0-41598da4c88d",
"digest": {
"sha256": "b988cb8ba2b862b6fa88f223fcd3279c70e2ea217477bd1ec664c023be079cad"
}
},
{
- "@id": "urn:6ed86163-23f8-47e8-89ec-54d1da8e4826",
+ "@id": "urn:c650b95a-c9bf-4612-b47a-eedf376d79f9",
"Label": "rendered_thresh_zstat2.png",
"AtLocation": "rendered_thresh_zstat2.png",
- "GeneratedBy": "urn:8433fb76-022b-4846-b2d4-fdc2cbeae320",
+ "GeneratedBy": "urn:9c34070e-67f7-4161-8228-2532bcf88bc7",
"digest": {
"sha256": "0d60298d9eb509148075cbac8a22e6a95de919f17a069624fb42f86c29e1e199"
}
},
{
- "@id": "urn:fb0604a6-1759-4f62-97f1-fc18df7e0e79",
+ "@id": "urn:2752a703-c278-4a04-895e-e9719f256693",
"Label": "rendered_thresh_zstat3",
"AtLocation": "rendered_thresh_zstat3",
- "GeneratedBy": "urn:84181693-0714-48f4-9e3b-b1b52f2f8877",
+ "GeneratedBy": "urn:7365d26e-619c-4e80-a058-964fa937d9e5",
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"sha256": "baac012afec8f9407f78df00034058a245d984bb1b1f86843d46a04a7eaa5b3d"
}
},
{
- "@id": "urn:a4725cde-22c1-43e1-bb39-8ca323359467",
+ "@id": "urn:17c44a15-af08-4f20-80dc-8d6a00fb19a0",
"Label": "rendered_thresh_zstat3.png",
"AtLocation": "rendered_thresh_zstat3.png",
- "GeneratedBy": "urn:04b2168c-1bb1-445f-b71d-0bc0f29ada87",
+ "GeneratedBy": "urn:91bcc4fd-63dd-4ccd-b200-8f3db9ecd468",
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}
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{
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"Label": "rendered_thresh_zfstat1",
"AtLocation": "rendered_thresh_zfstat1",
- "GeneratedBy": "urn:6fec5948-e934-4d57-885e-2f9ff5bb37ab",
+ "GeneratedBy": "urn:5c3f74df-5e15-416e-8c19-763fdf4fac10",
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}
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{
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+ "@id": "urn:308ee1ba-15be-4db5-a4f2-9e4ad49adee8",
"Label": "rendered_thresh_zfstat1.png",
"AtLocation": "rendered_thresh_zfstat1.png",
- "GeneratedBy": "urn:a424e26a-4756-4ebf-aee7-78caa8508f49",
+ "GeneratedBy": "urn:adb1b0ff-e8c1-4355-9b01-b20a5b01cf0b",
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}
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{
- "@id": "urn:49ddb519-977c-4811-810f-148fd1d470bf",
+ "@id": "urn:5a7ec459-4af7-4ecb-9669-f5681bfecdf9",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:f7b45616-d40f-4f94-9390-20175b6abab7",
+ "GeneratedBy": "urn:f19f51ad-5e08-412b-b80a-9023c70693b4",
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"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
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{
- "@id": "urn:b998fe7f-cac5-417b-a893-9c24f9d9c772",
+ "@id": "urn:8fff7e64-4f79-487c-8d5e-d71cf1c63f20",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:33aca4fb-d789-4ab3-96b7-d6f51bb3f6c5",
+ "GeneratedBy": "urn:0571739d-afb1-4fc4-85a8-64b608b3ddc1",
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diff --git a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png
index 577277c05..f49147e6c 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_fir_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
index 3a6deaaa1..9afbbbff1 100644
--- a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "@id": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,540 +13,540 @@
],
"Activities": [
{
- "@id": "urn:7567208c-e138-45bd-92fd-e04cbbbe5798",
+ "@id": "urn:b2625755-9228-4f29-9cdc-9e2e311271b4",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:5f833946-20fb-421f-bad6-7314076eefc9"
+ "urn:85d5d55e-0277-41ff-9bbb-1dd2833ef461"
]
},
{
- "@id": "urn:664b43fb-669a-401f-ae8b-84fe61d94430",
+ "@id": "urn:b6285a9f-3c3b-4835-8421-b287dd391f8a",
"Label": "fslroi",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:f0341414-568b-486a-a4d1-510de6bfe1df"
+ "urn:496fc0fe-61c9-4f9f-9f38-fda4fc784cd0"
]
},
{
- "@id": "urn:b21e6503-bf58-4c64-af2c-a7dd75598c0b",
+ "@id": "urn:98687417-079d-459f-ab4a-89047b25a9ea",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
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- "urn:b85c808d-47e1-4a93-9a2a-5dfa71c1ef7f"
+ "urn:26845403-e157-4c37-9a6e-c1eeaeae3b18",
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]
},
{
- "@id": "urn:d53e0107-1254-40e5-86e7-d8d9c3e13410",
+ "@id": "urn:0a236937-57ed-4fa9-8a42-42c9f451dcab",
"Label": "Make directory",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_double_gamma.feat/reg",
"Used": []
},
{
- "@id": "urn:5a684948-c866-433e-85cb-f5badd6af3ee",
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"Used": [
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]
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"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
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"Used": [
- "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac"
+ "urn:1f300416-cb44-4146-9f15-9c00172b67c2"
]
},
{
- "@id": "urn:4678ecbb-8466-49c4-84f4-5e092e99ada6",
+ "@id": "urn:f5e2dc55-f182-4797-a887-a3ef2bcdffbb",
"Label": "epi_reg",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:4e751535-4490-4cab-a8d0-fd2b0f897f07",
+ "@id": "urn:ee1dc8c2-1f47-49cd-be91-a9401a7b67e3",
"Label": "convert_xfm",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
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"Used": [
- "urn:b91a4495-095e-4698-850a-7413ec6cbcab"
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]
},
{
- "@id": "urn:8577bb07-1c01-44d3-bb9d-7aaa8458e8cc",
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"Label": "slicer",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:888face6-0e08-4aa6-8bda-c8a0262c4cb1",
- "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15"
+ "urn:106c67ad-3cda-4b75-9642-0d563c02bba6",
+ "urn:e050691d-f536-4747-9ebe-064e710a975e"
]
},
{
- "@id": "urn:67db5a25-584e-4f04-9359-ff4346af6040",
+ "@id": "urn:9c2c6c31-e6f6-4773-a202-95c36cda8dc2",
"Label": "pngappend",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:017d5cbd-ff1f-4475-9735-a22b07004037",
- "urn:0d2993cf-287d-4c90-9beb-3fc68b677049",
- "urn:3e320bc6-bbc2-4e05-ba6b-c6954f914af3",
- "urn:468f97b6-fcd4-424e-8298-910a84f5dee9",
- "urn:4eb9bfc6-31fe-4f23-b060-da82621ef6b7",
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- "urn:628b15c9-964e-46ad-8a6a-82fcee469f97",
- "urn:9f0735c4-b92d-4170-8956-a61e7015f205",
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- "urn:ba31de6b-e88d-443c-8864-b0d51d5f35ff",
- "urn:c539699d-a880-484f-9bd4-c583ac826a98",
- "urn:fabf4f69-def8-49d7-9611-c11f35a72be7"
+ "urn:0c95da24-bf76-40de-be8e-720ca4a8bc09",
+ "urn:2abffd1a-63a7-49a5-a031-c8a4bcbc73e0",
+ "urn:2b724579-87a4-402f-aeb6-403c1971174d",
+ "urn:3990b2ab-c24a-4737-a70a-2d9e95fae845",
+ "urn:447643b3-2ead-4c2d-911b-fdd63add854c",
+ "urn:521fc7ba-4582-4997-8637-e76a4c3b4be8",
+ "urn:8d81ce98-861a-4f2b-9039-8451b7987185",
+ "urn:b69ed67d-30d0-4ac4-b43a-90f19d8aeb04",
+ "urn:c4f4cc11-80af-41f1-af25-079c326a068c",
+ "urn:ce5318f7-cbe7-499e-bbb5-4ad119b79e07",
+ "urn:e65f2878-6f13-488c-ac81-1600790903d6",
+ "urn:eb1300ed-f917-4b8d-be12-a9b6917ab7c7"
]
},
{
- "@id": "urn:88bd7bdd-d84f-40ba-8642-3b33286e3b08",
+ "@id": "urn:2b56fc0d-dbd7-46b0-a6b9-e669e98c5221",
"Label": "slicer",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:888face6-0e08-4aa6-8bda-c8a0262c4cb1",
- "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15"
+ "urn:106c67ad-3cda-4b75-9642-0d563c02bba6",
+ "urn:e050691d-f536-4747-9ebe-064e710a975e"
]
},
{
- "@id": "urn:1cbd903f-9c67-4046-8bb4-7f88a62e7436",
+ "@id": "urn:f9f72209-8280-4c0d-9ad5-3aa395011ee5",
"Label": "pngappend",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
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- "urn:0d2993cf-287d-4c90-9beb-3fc68b677049",
- "urn:3e320bc6-bbc2-4e05-ba6b-c6954f914af3",
- "urn:468f97b6-fcd4-424e-8298-910a84f5dee9",
- "urn:4eb9bfc6-31fe-4f23-b060-da82621ef6b7",
- "urn:5597e536-cc2e-4140-a887-f9cf062a7cc8",
- "urn:628b15c9-964e-46ad-8a6a-82fcee469f97",
- "urn:9f0735c4-b92d-4170-8956-a61e7015f205",
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- "urn:ba31de6b-e88d-443c-8864-b0d51d5f35ff",
- "urn:c539699d-a880-484f-9bd4-c583ac826a98",
- "urn:fabf4f69-def8-49d7-9611-c11f35a72be7"
+ "urn:0c95da24-bf76-40de-be8e-720ca4a8bc09",
+ "urn:2abffd1a-63a7-49a5-a031-c8a4bcbc73e0",
+ "urn:2b724579-87a4-402f-aeb6-403c1971174d",
+ "urn:3990b2ab-c24a-4737-a70a-2d9e95fae845",
+ "urn:447643b3-2ead-4c2d-911b-fdd63add854c",
+ "urn:521fc7ba-4582-4997-8637-e76a4c3b4be8",
+ "urn:8d81ce98-861a-4f2b-9039-8451b7987185",
+ "urn:b69ed67d-30d0-4ac4-b43a-90f19d8aeb04",
+ "urn:c4f4cc11-80af-41f1-af25-079c326a068c",
+ "urn:ce5318f7-cbe7-499e-bbb5-4ad119b79e07",
+ "urn:e65f2878-6f13-488c-ac81-1600790903d6",
+ "urn:eb1300ed-f917-4b8d-be12-a9b6917ab7c7"
]
},
{
- "@id": "urn:94ee237c-3ace-498a-bde4-6dc285a62fc1",
+ "@id": "urn:42d37dd6-d765-4c36-9825-248bdd6eb840",
"Label": "pngappend",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:2257b871-d997-456a-8ba3-63bf7a39192f",
- "urn:c7abed1c-541a-416f-a69b-7d91ad6de028"
+ "urn:b0983ddd-77c6-48b2-96ad-529163046e5d",
+ "urn:f48b918e-8e21-44ec-b84d-7c582c5a29f2"
]
},
{
- "@id": "urn:d20ce534-d9dd-4432-befb-e4af83255cad",
+ "@id": "urn:aa6d4ca9-bdd4-4043-bb1a-1c493d201709",
"Label": "rm",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:04cf21b4-d8f2-416b-91dc-098aaede3b3b",
- "urn:c7abed1c-541a-416f-a69b-7d91ad6de028"
+ "urn:55f46847-0304-40b3-aab6-776cde3785ce",
+ "urn:b0983ddd-77c6-48b2-96ad-529163046e5d"
]
},
{
- "@id": "urn:ae0d63b9-8eea-4635-a229-46d0e077f4f6",
+ "@id": "urn:ca48fbe3-fd32-4b98-a794-b2d50cfc94ae",
"Label": "rm",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:2257b871-d997-456a-8ba3-63bf7a39192f"
+ "urn:f48b918e-8e21-44ec-b84d-7c582c5a29f2"
]
},
{
- "@id": "urn:e1f4504e-a931-4560-b135-c4b165528bc3",
+ "@id": "urn:af8c28a8-5dc0-4329-bccc-d4c58b03fc04",
"Label": "mcflirt",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:f0341414-568b-486a-a4d1-510de6bfe1df"
+ "urn:496fc0fe-61c9-4f9f-9f38-fda4fc784cd0"
]
},
{
- "@id": "urn:1b69e3f5-5564-4aa3-a5c9-de11f6e13e18",
+ "@id": "urn:e5e87b5f-4e21-4b1b-86b8-747ce7b162c0",
"Label": "Make directory",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:571d1fdc-8ad5-4ae2-8dbe-bfb8d5bee9e0",
+ "@id": "urn:00dbf366-54b8-44e2-a25b-f34d7db1afbf",
"Label": "mv",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
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- "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184",
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- "urn:ae169208-f61b-4a71-a1f2-33e0b026a76c"
+ "urn:4219a51e-94f7-49c2-be23-054e53c83d37",
+ "urn:4734b4e5-933f-4fdc-9dc7-555961628229",
+ "urn:663637f2-5620-4759-a680-1c5ddfc99c25",
+ "urn:7ba4801a-9b3b-4646-8ce8-77214178f7c3",
+ "urn:c55f0b91-2dee-40fd-8b2e-1843c2fc9952",
+ "urn:c9aa26ff-a1f8-4824-8a96-f91a726f789c"
]
},
{
- "@id": "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70",
+ "@id": "urn:aa032346-1a0e-461e-b69f-7697e1f73b33",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184"
+ "urn:c55f0b91-2dee-40fd-8b2e-1843c2fc9952"
]
},
{
- "@id": "urn:2d5ccef6-0f80-48b9-925a-36720b12df94",
+ "@id": "urn:537f0fb7-be91-447d-b3dd-c7e95ce9c200",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184"
+ "urn:c55f0b91-2dee-40fd-8b2e-1843c2fc9952"
]
},
{
- "@id": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
+ "@id": "urn:a4a646de-b7a0-4dd2-93a0-d55c2f3ffc75",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:ee8550a1-3a25-4bd3-b41f-5f9db3c2b519"
+ "urn:68616a4a-44c8-43d3-9035-7ad71ff8bd0a"
]
},
{
- "@id": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7",
+ "@id": "urn:9c28fa49-958c-469e-9d9f-31081c05a563",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473"
+ "urn:63b76a0e-b4f2-4599-95b6-fb194a899ec3"
]
},
{
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+ "@id": "urn:1a0509f4-dbd8-4122-af97-3a1c14419a3f",
"Label": "bet2",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:998c136b-89ab-434d-a383-742a8fe2cce7"
+ "urn:5763e116-fe67-4fb0-972d-bf4760c3f5e5"
]
},
{
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+ "@id": "urn:8456218e-78ef-4c11-8d99-f270f00b2481",
"Label": "immv",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:5fef3b34-c5f1-40d0-9aea-2f73c630a76d"
+ "urn:ffedd072-2d42-4cf8-8bf2-84da700e838d"
]
},
{
- "@id": "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "@id": "urn:74bb7b16-b4b4-4b3c-b7a7-2c2a95a127af",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:43ef2542-539e-48ab-a49a-8da522fc39f0",
- "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473"
+ "urn:63b76a0e-b4f2-4599-95b6-fb194a899ec3",
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428"
]
},
{
- "@id": "urn:eba8226f-0e46-44a0-8db3-f971ccf0da26",
+ "@id": "urn:caabbac7-5662-469e-80c8-63186c9f3a8e",
"Label": "fslstats",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d"
+ "urn:24e41c86-95da-4c99-b4b3-6b48de8f3d39"
]
},
{
- "@id": "urn:1a23fb57-c14c-4da3-9204-95c4e584f280",
+ "@id": "urn:f2c5b2f0-2b16-4aed-b7b1-c4c79b48829c",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d"
+ "urn:24e41c86-95da-4c99-b4b3-6b48de8f3d39"
]
},
{
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+ "@id": "urn:85da9c16-cb15-4fa2-a44b-202952ce4f61",
"Label": "fslstats",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473"
+ "urn:63b76a0e-b4f2-4599-95b6-fb194a899ec3"
]
},
{
- "@id": "urn:476c572f-a2bc-434d-9299-303b612766fb",
+ "@id": "urn:4e820c15-dc72-4417-9dad-09b740df92af",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:43ef2542-539e-48ab-a49a-8da522fc39f0"
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428"
]
},
{
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+ "@id": "urn:e608032d-6321-462f-92a6-a13cc4ca94a9",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:43ef2542-539e-48ab-a49a-8da522fc39f0",
- "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473"
+ "urn:63b76a0e-b4f2-4599-95b6-fb194a899ec3",
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428"
]
},
{
- "@id": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
+ "@id": "urn:9e2aa402-d146-4ea3-b337-917465257bd5",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da"
+ "urn:27593d35-ad2c-40ff-ba78-f0f3e8dc375d"
]
},
{
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+ "@id": "urn:5bda6fc2-3033-4108-9a3e-87e0c93691e9",
"Label": "susan",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da"
+ "urn:27593d35-ad2c-40ff-ba78-f0f3e8dc375d"
]
},
{
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+ "@id": "urn:beecffb3-93e6-441e-8729-4b285103ada4",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:b9777891-96c9-4d17-bc32-87980e3082c4"
+ "urn:26378a56-bbda-457f-b322-26a81a09886a",
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428"
]
},
{
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+ "@id": "urn:31b73e00-842f-4304-96f0-996fd85f1cf6",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:b9777891-96c9-4d17-bc32-87980e3082c4"
+ "urn:26378a56-bbda-457f-b322-26a81a09886a"
]
},
{
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+ "@id": "urn:39cc62c0-9656-46b8-b8b2-5f3566e0ee64",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:dee1e7d2-c686-4cbf-b6a8-e0b9a487316d"
+ "urn:6725e589-d545-44b7-b424-835064eefd93"
]
},
{
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+ "@id": "urn:6cef7006-c4f5-402d-a5b3-073a3393ce5f",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:ff9d2e07-fb6b-455d-9b57-97f81076b8f6"
+ "urn:431bd2f0-e1e0-4381-8f3b-6cc8cc8e6d72",
+ "urn:6725e589-d545-44b7-b424-835064eefd93"
]
},
{
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+ "@id": "urn:98eb07b2-ad19-45b5-838e-7d07c298d486",
"Label": "imrm",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:ff9d2e07-fb6b-455d-9b57-97f81076b8f6"
+ "urn:431bd2f0-e1e0-4381-8f3b-6cc8cc8e6d72"
]
},
{
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+ "@id": "urn:074502ee-77ef-447c-bd80-e6772427a1fe",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:dc81bcc2-7d97-408d-91ba-5edf765cf2c7"
+ "urn:1a52d737-915e-4d9b-8a1d-38631ed6d379"
]
},
{
- "@id": "urn:23f0145c-5038-48f3-923d-9dc25d3fba95",
+ "@id": "urn:6e5cc1ab-1c41-4b1a-9829-4deaca8b0167",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6"
+ "urn:2dd5beac-645f-442e-a765-5df8fb47c335"
]
},
{
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+ "@id": "urn:5e9efed4-3b10-43c0-a768-ea923c907d92",
"Label": "rm",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:66e9a593-4c31-41b9-95f3-d37201741051"
+ "urn:3c47d177-cff0-479e-a57d-37eb9ab1a4c4"
]
},
{
- "@id": "urn:7bd9021a-8ece-4eae-8527-15966a3238e0",
+ "@id": "urn:9f766c8b-1209-4ab4-8bb2-121b77094e6a",
"Label": "Make directory",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:f3920868-80ba-4883-a1b3-ab0fb63e9d35",
+ "@id": "urn:646dabb8-4043-4c1a-afb1-8b0961daea4a",
"Label": "fslFixText",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:cea95345-35be-4d64-8df3-d28bc89704ac"
+ "urn:ed3b68a3-f636-46e4-a09a-34a5efd2930e"
]
},
{
- "@id": "urn:cb25ef56-6a4a-4fd5-8796-a09c2ecc1733",
+ "@id": "urn:3f4a68bc-b2d6-4695-92e4-1eaf496365cf",
"Label": "Make directory",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:66a6c02a-7aed-4920-a165-fbbbefe73c7f",
+ "@id": "urn:bda90502-0355-42f7-b366-d17f5e34a690",
"Label": "fslFixText",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:ff8dc197-561e-4ac9-8789-fe98fdd482fe"
+ "urn:0e1b6288-0e69-48eb-bc7d-ff62118220b7"
]
},
{
- "@id": "urn:6bad6d78-8409-49b4-b9f4-e4fe6a252494",
+ "@id": "urn:0a273a8b-bf6c-4fac-8fbc-7ab70f744064",
"Label": "film_gls",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
- "@id": "urn:a9b05b37-91c1-4fc8-8744-6d437d5ca73b",
+ "@id": "urn:09f8f839-8937-4170-8d1c-c5beab63d0b2",
"Label": "smoothest",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
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- "urn:43ef2542-539e-48ab-a49a-8da522fc39f0",
- "urn:bf6e9b43-33c5-4777-addd-1b726f712d5e"
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428",
+ "urn:ff4e038e-aca9-4dd5-8e66-e4b5cbb2e507"
]
},
{
- "@id": "urn:45320a4c-88f2-4d46-aab7-8f2ed1459d9a",
+ "@id": "urn:4d5b1a26-5ca1-4151-8aa9-8bb8be7e49aa",
"Label": "fslmaths",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
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- "urn:43ef2542-539e-48ab-a49a-8da522fc39f0",
- "urn:79638e82-9f85-4be7-b17a-4a2cce96034c"
+ "urn:3f6ffef3-5208-4159-ae62-ec1f56f34b35",
+ "urn:ba9d4722-7841-4186-9cda-4a34276e2428"
]
},
{
- "@id": "urn:b572d524-8479-4dc8-8805-c1cae356fc84",
+ "@id": "urn:b2f73718-a51b-4452-9e31-8fc9b4017970",
"Label": "echo",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:b0be6445-9afb-4e3f-a7c1-33449fd2a793",
+ "@id": "urn:543ded4f-3858-4174-96f2-31bdfaa6a8bd",
"Label": "ptoz",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
- "@id": "urn:b236da14-0060-43c1-8ae8-a2ca27c4743a",
+ "@id": "urn:dbf4cddc-cc53-45dd-bdb8-ceefca12fb5d",
"Label": "cluster",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 3.090232 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z --voxuncthresh -c stats/cope1 > cluster_zstat1.txt",
"Used": [
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- "urn:e8d672f1-86f4-413e-839c-28b56632cd75"
+ "urn:816004d4-9b13-493f-998d-3f296343dadc",
+ "urn:f1aeab90-fd5b-4b5b-8551-9b4b5206e3cc"
]
},
{
- "@id": "urn:35c1f502-94fe-4cbc-aef7-63f633acd45e",
+ "@id": "urn:11ba212b-96f7-4c06-975e-5e3f33400f89",
"Label": "cluster2html",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:d888ce87-db52-42c4-86ec-7f5937747369"
+ "urn:611642a2-088a-4b7e-b2e8-65eab6f3b9a3"
]
},
{
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+ "@id": "urn:4c0d5d0d-40d3-411d-bdef-a620fad879ed",
"Label": "fslstats",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:e8d672f1-86f4-413e-839c-28b56632cd75"
+ "urn:f1aeab90-fd5b-4b5b-8551-9b4b5206e3cc"
]
},
{
- "@id": "urn:4a529a6f-ea0b-4554-b924-20f9e84a6d17",
+ "@id": "urn:085a4987-65f9-4842-bea9-60b04382d7ff",
"Label": "overlay",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.090718 7.041752 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:0823c534-eb6d-474b-bb65-02c92e9c5d39",
+ "@id": "urn:c16c40fe-a46b-4a0c-b7f0-66e09b55fce4",
"Label": "slicer",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:012b9ea7-02e5-4a39-b991-96afb57aff29"
+ "urn:2e84766b-f6b6-4e5a-8853-b27071e11e03"
]
},
{
- "@id": "urn:aba7b203-7855-4289-bd83-d494632ab053",
+ "@id": "urn:23dee5cc-e5e2-4b05-bb2e-499cb3caf1c4",
"Label": "cp",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56"
+ "urn:a5e54cc0-c748-449e-9d2b-66e126287db3"
]
},
{
- "@id": "urn:4b6c76de-2ef4-4b43-8d3c-e6c0e5003853",
+ "@id": "urn:bce53a79-dc25-46e4-83ed-c469956ade7b",
"Label": "Make directory",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:6afdcda2-2b02-4320-acef-8b40a7b03680",
+ "@id": "urn:f94e103c-66d5-4680-b4e6-f5f7c734c9fd",
"Label": "tsplot",
- "AssociatedWith": "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "AssociatedWith": "urn:240d1a60-392a-46d3-b3ac-0dde12607797",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
{
- "@id": "urn:5f833946-20fb-421f-bad6-7314076eefc9",
+ "@id": "urn:85d5d55e-0277-41ff-9bbb-1dd2833ef461",
"Label": "sub-01_task-tonecounting_bold",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
@@ -554,25 +554,25 @@
}
},
{
- "@id": "urn:f0341414-568b-486a-a4d1-510de6bfe1df",
+ "@id": "urn:496fc0fe-61c9-4f9f-9f38-fda4fc784cd0",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:7567208c-e138-45bd-92fd-e04cbbbe5798",
+ "GeneratedBy": "urn:b2625755-9228-4f29-9cdc-9e2e311271b4",
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}
},
{
- "@id": "urn:2f4ce27c-6f45-4c41-b2f6-5c56cd245544",
+ "@id": "urn:57e2f46d-dd77-4e80-91e3-0ca1293cc9eb",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:664b43fb-669a-401f-ae8b-84fe61d94430",
+ "GeneratedBy": "urn:b6285a9f-3c3b-4835-8421-b287dd391f8a",
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"digest": {
@@ -910,25 +910,25 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:e1f4504e-a931-4560-b135-c4b165528bc3",
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{
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"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:1b69e3f5-5564-4aa3-a5c9-de11f6e13e18",
+ "GeneratedBy": "urn:e5e87b5f-4e21-4b1b-86b8-747ce7b162c0",
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{
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"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -936,7 +936,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -944,7 +944,7 @@
}
},
{
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+ "@id": "urn:4734b4e5-933f-4fdc-9dc7-555961628229",
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"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -952,7 +952,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -960,7 +960,7 @@
}
},
{
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"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -968,7 +968,7 @@
}
},
{
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"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -976,34 +976,34 @@
}
},
{
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"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:571d1fdc-8ad5-4ae2-8dbe-bfb8d5bee9e0",
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}
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{
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- "GeneratedBy": "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70",
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}
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{
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"AtLocation": "trans.png",
- "GeneratedBy": "urn:2d5ccef6-0f80-48b9-925a-36720b12df94",
+ "GeneratedBy": "urn:537f0fb7-be91-447d-b3dd-c7e95ce9c200",
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}
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{
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"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1011,34 +1011,34 @@
}
},
{
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"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
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}
},
{
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+ "@id": "urn:5763e116-fe67-4fb0-972d-bf4760c3f5e5",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7",
+ "GeneratedBy": "urn:9c28fa49-958c-469e-9d9f-31081c05a563",
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},
{
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+ "@id": "urn:ba9d4722-7841-4186-9cda-4a34276e2428",
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- "GeneratedBy": "urn:89c4e160-0920-4f79-8e68-1b551e450cfd",
+ "GeneratedBy": "urn:1a0509f4-dbd8-4122-af97-3a1c14419a3f",
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}
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{
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+ "@id": "urn:ffedd072-2d42-4cf8-8bf2-84da700e838d",
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"digest": {
@@ -1046,106 +1046,106 @@
}
},
{
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+ "@id": "urn:514bd95f-6c3c-4b0b-83b3-1ab8e268df15",
"Label": "mask",
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- "GeneratedBy": "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d",
+ "GeneratedBy": "urn:8456218e-78ef-4c11-8d99-f270f00b2481",
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{
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+ "@id": "urn:24e41c86-95da-4c99-b4b3-6b48de8f3d39",
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"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "GeneratedBy": "urn:74bb7b16-b4b4-4b3c-b7a7-2c2a95a127af",
"digest": {
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}
},
{
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"Label": "mask",
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- "GeneratedBy": "urn:1a23fb57-c14c-4da3-9204-95c4e584f280",
+ "GeneratedBy": "urn:f2c5b2f0-2b16-4aed-b7b1-c4c79b48829c",
"digest": {
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}
},
{
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"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:476c572f-a2bc-434d-9299-303b612766fb",
+ "GeneratedBy": "urn:4e820c15-dc72-4417-9dad-09b740df92af",
"digest": {
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}
},
{
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+ "@id": "urn:27593d35-ad2c-40ff-ba78-f0f3e8dc375d",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:c586e728-fcc7-4e86-b211-dfc2ab5d386c",
+ "GeneratedBy": "urn:e608032d-6321-462f-92a6-a13cc4ca94a9",
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}
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{
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+ "@id": "urn:e92556b3-2f40-47a8-8e64-c9c27593b5b2",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
+ "GeneratedBy": "urn:9e2aa402-d146-4ea3-b337-917465257bd5",
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}
},
{
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+ "@id": "urn:26378a56-bbda-457f-b322-26a81a09886a",
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"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:3488314f-c550-4532-8db8-90bcec24624f",
+ "GeneratedBy": "urn:5bda6fc2-3033-4108-9a3e-87e0c93691e9",
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}
},
{
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+ "@id": "urn:4b5dd777-e83d-487e-8c2e-a160089f4f05",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9",
+ "GeneratedBy": "urn:beecffb3-93e6-441e-8729-4b285103ada4",
"digest": {
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}
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{
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+ "@id": "urn:6725e589-d545-44b7-b424-835064eefd93",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:38783393-8687-499e-af74-4c389b7a07f8",
+ "GeneratedBy": "urn:31b73e00-842f-4304-96f0-996fd85f1cf6",
"digest": {
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}
},
{
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+ "@id": "urn:431bd2f0-e1e0-4381-8f3b-6cc8cc8e6d72",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:ae9f3ec1-ab33-409a-8f91-a998a39193a1",
+ "GeneratedBy": "urn:39cc62c0-9656-46b8-b8b2-5f3566e0ee64",
"digest": {
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}
},
{
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+ "@id": "urn:aa0f5d9f-ef8f-40c7-ad6a-6674a7f9a4ff",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:02bac1d5-5bff-45e9-af9e-bd8cb8544e48",
+ "GeneratedBy": "urn:6cef7006-c4f5-402d-a5b3-073a3393ce5f",
"digest": {
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}
},
{
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+ "@id": "urn:1a52d737-915e-4d9b-8a1d-38631ed6d379",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1153,25 +1153,25 @@
}
},
{
- "@id": "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6",
+ "@id": "urn:2dd5beac-645f-442e-a765-5df8fb47c335",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:7687e560-68ce-415d-abaa-18a1c6b032df",
+ "GeneratedBy": "urn:074502ee-77ef-447c-bd80-e6772427a1fe",
"digest": {
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}
},
{
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+ "@id": "urn:661acb24-0d0e-4204-ac2c-8c254641df82",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:23f0145c-5038-48f3-923d-9dc25d3fba95",
+ "GeneratedBy": "urn:6e5cc1ab-1c41-4b1a-9829-4deaca8b0167",
"digest": {
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}
},
{
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+ "@id": "urn:3c47d177-cff0-479e-a57d-37eb9ab1a4c4",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,16 +1179,16 @@
}
},
{
- "@id": "urn:60181192-775f-4634-98d3-66d692c27341",
+ "@id": "urn:8676198f-410b-4255-8171-7673e732fe7f",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:7bd9021a-8ece-4eae-8527-15966a3238e0",
+ "GeneratedBy": "urn:9f766c8b-1209-4ab4-8bb2-121b77094e6a",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:cea95345-35be-4d64-8df3-d28bc89704ac",
+ "@id": "urn:ed3b68a3-f636-46e4-a09a-34a5efd2930e",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1196,22 +1196,22 @@
}
},
{
- "@id": "urn:89e608d8-2eb1-437b-a979-248aa6bb8bfb",
+ "@id": "urn:e3fbf26f-e9cf-49ac-b999-37978b1a2f26",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:f3920868-80ba-4883-a1b3-ab0fb63e9d35"
+ "GeneratedBy": "urn:646dabb8-4043-4c1a-afb1-8b0961daea4a"
},
{
- "@id": "urn:b858ca8c-00ce-4220-b42b-9fdbce0c54c5",
+ "@id": "urn:9eb675dd-d506-4c0c-8956-c50dce094ff3",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:cb25ef56-6a4a-4fd5-8796-a09c2ecc1733",
+ "GeneratedBy": "urn:3f4a68bc-b2d6-4695-92e4-1eaf496365cf",
"digest": {
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}
},
{
- "@id": "urn:ff8dc197-561e-4ac9-8789-fe98fdd482fe",
+ "@id": "urn:0e1b6288-0e69-48eb-bc7d-ff62118220b7",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1219,13 +1219,13 @@
}
},
{
- "@id": "urn:55c66188-f142-4cf4-a2ff-f4c281fa69b6",
+ "@id": "urn:5892f4d5-ff68-4975-b9c4-b358835454b7",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:66a6c02a-7aed-4920-a165-fbbbefe73c7f"
+ "GeneratedBy": "urn:bda90502-0355-42f7-b366-d17f5e34a690"
},
{
- "@id": "urn:bf6e9b43-33c5-4777-addd-1b726f712d5e",
+ "@id": "urn:ff4e038e-aca9-4dd5-8e66-e4b5cbb2e507",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1233,16 +1233,16 @@
}
},
{
- "@id": "urn:f30b3e68-c42c-4cf2-b4a2-3662c40763a4",
+ "@id": "urn:e4e69c8b-361e-47c9-b4b2-1f9791d75970",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:a9b05b37-91c1-4fc8-8744-6d437d5ca73b",
+ "GeneratedBy": "urn:09f8f839-8937-4170-8d1c-c5beab63d0b2",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
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+ "@id": "urn:3f6ffef3-5208-4159-ae62-ec1f56f34b35",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1250,16 +1250,16 @@
}
},
{
- "@id": "urn:e8d672f1-86f4-413e-839c-28b56632cd75",
+ "@id": "urn:f1aeab90-fd5b-4b5b-8551-9b4b5206e3cc",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:45320a4c-88f2-4d46-aab7-8f2ed1459d9a",
+ "GeneratedBy": "urn:4d5b1a26-5ca1-4151-8aa9-8bb8be7e49aa",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
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+ "@id": "urn:816004d4-9b13-493f-998d-3f296343dadc",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1267,25 +1267,25 @@
}
},
{
- "@id": "urn:8d7109c7-7ffa-45f0-be88-19d8cf59f902",
+ "@id": "urn:55edab04-2d8f-4fad-93b5-f00b8c4b1551",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:b236da14-0060-43c1-8ae8-a2ca27c4743a",
+ "GeneratedBy": "urn:dbf4cddc-cc53-45dd-bdb8-ceefca12fb5d",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:4cc74bde-de10-4407-9512-a9c834be1ceb",
+ "@id": "urn:3881f671-7091-4f65-ab4a-d62e230af38e",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:b236da14-0060-43c1-8ae8-a2ca27c4743a",
+ "GeneratedBy": "urn:dbf4cddc-cc53-45dd-bdb8-ceefca12fb5d",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:d888ce87-db52-42c4-86ec-7f5937747369",
+ "@id": "urn:611642a2-088a-4b7e-b2e8-65eab6f3b9a3",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1293,25 @@
}
},
{
- "@id": "urn:012b9ea7-02e5-4a39-b991-96afb57aff29",
+ "@id": "urn:2e84766b-f6b6-4e5a-8853-b27071e11e03",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:4a529a6f-ea0b-4554-b924-20f9e84a6d17",
+ "GeneratedBy": "urn:085a4987-65f9-4842-bea9-60b04382d7ff",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:d9243bae-0e1c-48ea-b2b8-d670ffa89dcd",
+ "@id": "urn:6f8efe1e-6e80-45f3-a30f-e770c90dc04b",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:0823c534-eb6d-474b-bb65-02c92e9c5d39",
+ "GeneratedBy": "urn:c16c40fe-a46b-4a0c-b7f0-66e09b55fce4",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:f95e4ec4-e974-4885-919b-99de5d3b3a56",
+ "@id": "urn:a5e54cc0-c748-449e-9d2b-66e126287db3",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1319,28 @@
}
},
{
- "@id": "urn:8c85596f-7fa2-43b1-8a9d-e343dd1250dc",
+ "@id": "urn:560a7372-548e-42fa-921d-24259ff5eb0c",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:aba7b203-7855-4289-bd83-d494632ab053",
+ "GeneratedBy": "urn:23dee5cc-e5e2-4b05-bb2e-499cb3caf1c4",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:8992ddf0-b6d9-4da5-86ae-aae8b06bf498",
+ "@id": "urn:3da4d702-a202-4bac-b707-054550bce11c",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:4b6c76de-2ef4-4b43-8d3c-e6c0e5003853",
+ "GeneratedBy": "urn:bce53a79-dc25-46e4-83ed-c469956ade7b",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:b27fcab0-8025-43f6-bc2b-e214f412c4f4",
+ "@id": "urn:d5d2f4ac-1c68-4e7a-9256-4caccf23d9b1",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:6afdcda2-2b02-4320-acef-8b40a7b03680",
+ "GeneratedBy": "urn:f94e103c-66d5-4680-b4e6-f5f7c734c9fd",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png
index 8f68b7162..d7d31cefd 100644
Binary files a/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png and b/examples/from_parsers/fsl/fsl_hrf_gammadiff_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
index 4de83d82a..1505664be 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "@id": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,572 +13,572 @@
],
"Activities": [
{
- "@id": "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b",
+ "@id": "urn:79e151a5-c648-4cae-93dd-b4eaa7c60136",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:b5f66e4e-2342-4065-8f7b-2c21b222d7b8"
+ "urn:590ba71a-c6d9-434e-a343-6f856119883b"
]
},
{
- "@id": "urn:a38e2601-9eb9-4a15-a0b4-bda9d367153f",
+ "@id": "urn:fc4e83c4-c47d-46a0-b475-3bff18608a56",
"Label": "fslroi",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:7cd6ecd7-6511-4f63-9962-952ebad0dcdb"
+ "urn:f8be5416-8122-419c-b982-29067b5dc5ea"
]
},
{
- "@id": "urn:678536c5-1572-466a-89e4-3051f34d7755",
+ "@id": "urn:8bd97ac6-43b4-427f-8481-3297908a83ef",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
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- "urn:ceb0c6bb-c4dd-48e4-b53a-5b01198dd651",
- "urn:d3630e97-6933-464a-97bb-ab45131ac706"
+ "urn:109585e9-fc1e-472d-a23c-92f69102aa1a",
+ "urn:b10d5108-8806-4746-a9d9-df7707480c86",
+ "urn:b42e214e-b817-49ea-b57e-688b5fe9413f"
]
},
{
- "@id": "urn:378c0ea8-a35a-472a-9347-ff979b23f462",
+ "@id": "urn:36cdfedd-cdbc-4de1-84e8-ed8b0a881a96",
"Label": "Make directory",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg",
"Used": []
},
{
- "@id": "urn:1a2225a3-bad6-407b-b80e-b03730489480",
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
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]
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{
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"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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"Used": [
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]
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"Label": "epi_reg",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
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"Label": "convert_xfm",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
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"Used": [
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]
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{
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"Label": "slicer",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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]
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{
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"Label": "pngappend",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
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+ "urn:dac866b4-d456-4117-8d49-7ed57506aee0"
]
},
{
- "@id": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
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"Label": "slicer",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:90d0ad49-8128-44dc-b6d3-40b269bf7e59"
+ "urn:70dbec60-b908-498d-826f-65d7633bb261",
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]
},
{
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"Label": "pngappend",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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- "urn:fa7f30ff-7045-4e3d-8ce0-8e53e0806051"
+ "urn:0b61184a-cac9-40b6-81dc-6872a83e0af4",
+ "urn:0d0e2d05-f309-4b04-a2a5-f10351b10b2c",
+ "urn:1a7df79f-5d60-474a-b28f-8b9b822bcc19",
+ "urn:2783a287-676c-45f3-9447-710c44eeaaf1",
+ "urn:7f0c003b-cd9b-46bd-a0cb-e23e674efa0c",
+ "urn:93d0927d-619a-4809-a4aa-a47a9cf6c9f9",
+ "urn:97404bf1-deb1-4e37-b199-2280209c6e16",
+ "urn:a5ae59a2-c246-483d-8555-2d6f0ad1dc75",
+ "urn:b916902c-b0c4-4efe-9041-e21b5b59aaae",
+ "urn:bc402a7d-a8df-41e0-bf0f-30a4f6f4eb5d",
+ "urn:c6d1eb8b-6f60-4d3c-88dd-dc6a63a8402c",
+ "urn:dac866b4-d456-4117-8d49-7ed57506aee0"
]
},
{
- "@id": "urn:fdf650bf-c3ed-431b-982a-c1758eadc379",
+ "@id": "urn:712101dd-72bf-4522-84bd-2206e7600948",
"Label": "pngappend",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:3922f9bd-f91d-449e-a730-8942b061fc06",
- "urn:ec4eff37-da73-479a-bf55-e1c024f86d2c"
+ "urn:791e3f41-1d41-4379-8c6f-783af998fdfc",
+ "urn:c1f580e0-28aa-4625-9252-217bc4bade24"
]
},
{
- "@id": "urn:a28dbf2b-52e6-497a-9a17-f8131d65ccdb",
+ "@id": "urn:a91c074f-a725-4f84-aa83-73630b62aadf",
"Label": "rm",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:24cd5583-0676-412c-8d30-869fc4bad772",
- "urn:3922f9bd-f91d-449e-a730-8942b061fc06"
+ "urn:0238939f-61b0-44a5-9e78-6dffb0b0b5e3",
+ "urn:c1f580e0-28aa-4625-9252-217bc4bade24"
]
},
{
- "@id": "urn:d9d77f6b-eeea-42be-bb7f-375ffe0ea710",
+ "@id": "urn:7d02c4a5-0008-481a-aefd-89d90a4f459b",
"Label": "rm",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:ec4eff37-da73-479a-bf55-e1c024f86d2c"
+ "urn:791e3f41-1d41-4379-8c6f-783af998fdfc"
]
},
{
- "@id": "urn:395f5c5b-e9ac-4840-9e36-f7d9f8378081",
+ "@id": "urn:98f15577-ff6b-46bc-9bf2-acb04558545b",
"Label": "mcflirt",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:7cd6ecd7-6511-4f63-9962-952ebad0dcdb"
+ "urn:f8be5416-8122-419c-b982-29067b5dc5ea"
]
},
{
- "@id": "urn:69393fe9-a34d-43a3-8146-b78f971c8599",
+ "@id": "urn:4c5b85fe-32e6-4d2c-b34c-8a2fc87aec51",
"Label": "Make directory",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:6def26df-f81f-41d3-b0ac-e5a601c7ce4e",
+ "@id": "urn:dc32a6ba-52b8-4331-8c20-c103684d9607",
"Label": "mv",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
- "urn:09da4b05-35ba-4775-a31f-b5833a8f2f71",
- "urn:c0524ec3-3ea6-4e3e-baba-417314d9af3d",
- "urn:cca9d05c-43fe-47b3-ada3-1c165bea6342",
- "urn:e30b077c-1b55-440f-8bea-abd13856532c",
- "urn:ef507610-583e-4af5-aaee-520301a7bdb0",
- "urn:fef7f3f0-8d54-45b9-be9d-dd4ae9560b00"
+ "urn:0e12140c-f0fa-4b1c-afdc-6b4072852687",
+ "urn:1ff46c81-17ab-417c-898c-5c967b8b6b74",
+ "urn:23375a72-1ee5-4128-8d10-54fabae7b00c",
+ "urn:58233196-f676-4b22-b7b6-d2a803c73967",
+ "urn:70a63de5-2bb7-4f9d-b86b-0a8330de087f",
+ "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe"
]
},
{
- "@id": "urn:dbf0bd54-d5d1-45cf-8aa7-b593bd3aacf5",
+ "@id": "urn:47a4a930-45a7-48f8-afc5-4e5281aa9e2c",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:ef507610-583e-4af5-aaee-520301a7bdb0"
+ "urn:23375a72-1ee5-4128-8d10-54fabae7b00c"
]
},
{
- "@id": "urn:441608e5-a5db-483b-988c-f52b353161c6",
+ "@id": "urn:a214e64f-f623-475a-addf-0f8f08afe372",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:ef507610-583e-4af5-aaee-520301a7bdb0"
+ "urn:23375a72-1ee5-4128-8d10-54fabae7b00c"
]
},
{
- "@id": "urn:a55793e4-f85a-4ac9-8d63-34f58119f00e",
+ "@id": "urn:3f2ecad8-a8e5-493a-8abc-0ab3f1401d31",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:956a31fd-030a-4e43-8e0b-eb06823cf052"
+ "urn:086ca1fc-cef0-4bd7-9a98-1418e4dd7814"
]
},
{
- "@id": "urn:ec9d7980-1d0b-42f4-96b5-51a4ff6c86d0",
+ "@id": "urn:c8fa209f-5ecb-443c-9b74-ba12277d8e19",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:063eaae6-6afd-45d0-ba57-b1629a475797"
+ "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0"
]
},
{
- "@id": "urn:d401069b-da20-48be-afbb-31e098f3b3b2",
+ "@id": "urn:da2f36c8-f656-4f6e-a4a8-8f2618a20752",
"Label": "bet2",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
- "urn:247ba477-f6f4-4359-bf5f-d3779573ecd7"
+ "urn:1daee25e-6e10-4a25-81f8-cf7861e3aaed"
]
},
{
- "@id": "urn:c28e8620-2d74-43ae-be27-e2028601d9bd",
+ "@id": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
"Label": "immv",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:bc3e9f42-d4b1-4642-97b0-5e6677575a1f"
+ "urn:4601a4cd-a630-418f-beb8-4815818cd73a"
]
},
{
- "@id": "urn:94571380-7577-41e6-a488-f0c5ea96db5e",
+ "@id": "urn:3bee4548-3d99-4d3b-8ecf-fe9fe26023a6",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
"Used": [
- "urn:063eaae6-6afd-45d0-ba57-b1629a475797",
- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe",
+ "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0"
]
},
{
- "@id": "urn:95dbbb1a-af6d-4133-8620-a928beb28b2c",
+ "@id": "urn:8b2c4ce3-6f47-46bc-b31b-3380285a85df",
"Label": "fslstats",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c"
+ "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43"
]
},
{
- "@id": "urn:e4eab963-3f85-4099-b44a-7c31510246e3",
+ "@id": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c"
+ "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43"
]
},
{
- "@id": "urn:760ad209-0e8d-4380-9167-6790e6cdbef4",
+ "@id": "urn:5d66c68e-3383-423b-a9a7-bc6dd08e0d21",
"Label": "fslstats",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:063eaae6-6afd-45d0-ba57-b1629a475797"
+ "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0"
]
},
{
- "@id": "urn:605488b5-e8b5-43a7-a87e-6bf4673c8dbd",
+ "@id": "urn:208eefab-d051-4765-bff4-67f1743005b2",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe"
]
},
{
- "@id": "urn:7fe5640e-c1ac-41e2-a390-5cfb10ed270c",
+ "@id": "urn:fa2f1c7b-7751-4b85-b51c-c0c7ff606a4e",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:063eaae6-6afd-45d0-ba57-b1629a475797",
- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe",
+ "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0"
]
},
{
- "@id": "urn:19c392b8-27a2-4289-8244-b4873e9ca58f",
+ "@id": "urn:792ea18a-543c-4720-bb39-266ed3d5a6f2",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:71033977-c543-4f01-b2cf-9b47a1244aae"
+ "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342"
]
},
{
- "@id": "urn:ea004d6b-2e31-45db-b3b4-7b0e08b96791",
+ "@id": "urn:2e21b4e4-5935-4855-8b93-dd5e88819342",
"Label": "susan",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:71033977-c543-4f01-b2cf-9b47a1244aae"
+ "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342"
]
},
{
- "@id": "urn:444a1daf-b77e-42d9-a1b3-56b1ad9ec433",
+ "@id": "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:5ea48616-c75d-40df-8da5-ecbca08599d0",
- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:497d8112-4d30-4d69-8445-f21e9299b37d",
+ "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe"
]
},
{
- "@id": "urn:5125d2d9-6492-4c8b-adf2-c5705cc01a67",
+ "@id": "urn:e5d28661-d83f-4e8e-a350-8605712fa18e",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:5ea48616-c75d-40df-8da5-ecbca08599d0"
+ "urn:497d8112-4d30-4d69-8445-f21e9299b37d"
]
},
{
- "@id": "urn:40123b3b-91ec-43ee-988a-93227bbb8fa9",
+ "@id": "urn:9961f831-35e9-477b-8d1f-3b47d84871b1",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:fa4f4013-2d53-44e1-bf16-4dcc0a0d3daf"
+ "urn:ca0cc3f3-fdbf-434f-9653-c4ecd0da4c6b"
]
},
{
- "@id": "urn:52207409-b5c7-42a2-a9f3-13fcebc29fa2",
+ "@id": "urn:ac8b5b17-4954-4507-b9ff-cc76b89ef95b",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
"Used": [
- "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3",
- "urn:fa4f4013-2d53-44e1-bf16-4dcc0a0d3daf"
+ "urn:ca0cc3f3-fdbf-434f-9653-c4ecd0da4c6b",
+ "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9"
]
},
{
- "@id": "urn:13f7d6e4-de0c-411e-a8e5-36e80edb89ff",
+ "@id": "urn:a78d4805-0251-477e-af6b-e6c89ff27f3b",
"Label": "imrm",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3"
+ "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9"
]
},
{
- "@id": "urn:9aa8be1f-d7bd-4ade-9c20-192c16d8b960",
+ "@id": "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0"
+ "urn:b0574ba8-bc8b-49a7-9b9f-aa4783c7800b"
]
},
{
- "@id": "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "@id": "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1",
"Label": "fslmaths",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:fdecdbd0-25b4-4a8f-a3d3-e9908b473677"
+ "urn:04ed6b15-acd8-4153-bd79-745075ff58fb"
]
},
{
- "@id": "urn:6b4c40e2-9e63-4713-84af-081da9537ef3",
+ "@id": "urn:6423345c-8fec-4562-af45-f57d0ffa4b58",
"Label": "rm",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:5e81132b-0af3-47d9-a5e3-016da536af9c"
+ "urn:f5266e11-6d2d-4f7c-bf3c-85b21c458104"
]
},
{
- "@id": "urn:b6710d0b-30c3-428b-b924-2051bc82cc7a",
+ "@id": "urn:7583d6d9-67d6-4bbc-a100-f16a38448de8",
"Label": "Make directory",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Label": "fslFixText",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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"Used": [
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]
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{
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"Label": "Make directory",
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"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
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"Used": [
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+ "urn:e7c2b1da-9d10-4647-b4dc-5b76e1756e66"
]
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{
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"Label": "mp_diffpow.sh",
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"Used": [
- "urn:315774d8-d488-4729-b1f0-85284457a2e3"
+ "urn:08f57df8-b9f5-4033-87f7-55fce2b3dcbf"
]
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"Label": "paste",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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"Used": []
},
{
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+ "@id": "urn:bd75912f-9996-4e47-a434-dce8b0d6fc39",
"Label": "paste",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
"Used": []
},
{
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+ "@id": "urn:45200e47-1c0a-48ef-af6f-0b5b06327076",
"Label": "feat_model",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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"Used": [
- "urn:e7e293a9-eed8-4907-8a4f-271b2c2e77d0"
+ "urn:47f2e70e-0f03-42ae-baee-8eb44818c65b"
]
},
{
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+ "@id": "urn:16753022-6cf4-41c0-8d10-bba03c02c719",
"Label": "film_gls",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
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+ "@id": "urn:20222870-633f-4598-b671-960cf3d572fa",
"Label": "smoothest",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 78 -m mask -r stats/res4d > stats/smoothness",
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- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:196d4e36-94b4-4ed6-bccd-fa569b52c996",
+ "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe"
]
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
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- "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37"
+ "urn:37683ca5-1963-41df-b40c-cd03888b8d3f",
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]
},
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+ "@id": "urn:64f1e5cf-a973-4928-a6c1-7de24f6ec447",
"Label": "echo",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
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+ "@id": "urn:0231e881-7455-4a1c-84ae-5e8f5912264a",
"Label": "ptoz",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/ptoz 0.001",
"Used": []
},
{
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+ "@id": "urn:036f1bf8-a8ac-4ebd-97dd-31bd186bddff",
"Label": "cluster",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
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- "urn:c3ea95c6-89ba-4b96-9a86-b4b166b94a52"
+ "urn:5a23202c-b202-40cf-9778-7330e983b71a",
+ "urn:e025346f-9151-462c-8434-0246918c24e7"
]
},
{
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+ "@id": "urn:52b4e335-e4b8-4778-824e-0640913d61fd",
"Label": "cluster2html",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:b1114cd8-a76d-4379-998a-9a2e4b6d4f5d"
+ "urn:375eb646-fef7-4012-935b-ac8f7b28dca1"
]
},
{
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"Label": "fslstats",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:7e832bb7-d40a-491a-9125-de21b2444e71"
+ "urn:e025346f-9151-462c-8434-0246918c24e7"
]
},
{
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"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 3.093412 5.467648 rendered_thresh_zstat1",
"Used": []
},
{
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+ "@id": "urn:e5a515f1-d016-4f08-a4bd-7718cb7309df",
"Label": "slicer",
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+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:6a5a682c-1df7-48eb-93e1-b320e412ec2e"
+ "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752"
]
},
{
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+ "@id": "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73",
"Label": "cp",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:d4a83aff-fe1a-478a-8c0b-3fdf85f08262"
+ "urn:c61b8756-1bed-4aeb-913d-cdf85bfe5fb4"
]
},
{
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+ "@id": "urn:32b98972-d2ee-4e72-8597-71810714a976",
"Label": "Make directory",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:f8cde05b-2019-414d-a458-eae315156b7f",
+ "@id": "urn:5caaba6c-e58e-47fb-8216-4f7e6345a328",
"Label": "tsplot",
- "AssociatedWith": "urn:d7d8cb58-f077-4a44-9c83-d0cc455a5cf2",
+ "AssociatedWith": "urn:b99d477f-b343-4baf-a037-4bd3d873e359",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
"Entities": [
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+ "@id": "urn:590ba71a-c6d9-434e-a343-6f856119883b",
"Label": "sub-01_task-tonecounting_bold",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
@@ -586,25 +586,25 @@
}
},
{
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+ "@id": "urn:f8be5416-8122-419c-b982-29067b5dc5ea",
"Label": "prefiltered_func_data",
"AtLocation": "prefiltered_func_data",
- "GeneratedBy": "urn:9c952d4e-87cf-4ea6-b03c-4af969fd056b",
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}
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{
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+ "@id": "urn:719afeb9-a1ed-4c0c-9b64-4b8d6aa33a9d",
"Label": "example_func",
"AtLocation": "example_func",
- "GeneratedBy": "urn:a38e2601-9eb9-4a15-a0b4-bda9d367153f",
+ "GeneratedBy": "urn:fc4e83c4-c47d-46a0-b475-3bff18608a56",
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+ "@id": "urn:109585e9-fc1e-472d-a23c-92f69102aa1a",
"Label": "example_func.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/example_func.nii.gz",
"digest": {
@@ -612,7 +612,7 @@
}
},
{
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"Label": "sub-01_T1w_brain",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain",
"digest": {
@@ -620,7 +620,7 @@
}
},
{
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+ "@id": "urn:b10d5108-8806-4746-a9d9-df7707480c86",
"Label": "MNI152_T1_2mm_brain",
"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -628,31 +628,31 @@
}
},
{
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+ "@id": "urn:091619d7-2630-497f-9e72-2c1237fcefc7",
"Label": "fsl_motion_reg_der.feat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat",
- "GeneratedBy": "urn:678536c5-1572-466a-89e4-3051f34d7755"
+ "GeneratedBy": "urn:8bd97ac6-43b4-427f-8481-3297908a83ef"
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{
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+ "@id": "urn:fa97c292-3cc3-49ca-bfd1-3d2096c6eeee",
"Label": "reg",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg_der.feat/reg",
- "GeneratedBy": "urn:378c0ea8-a35a-472a-9347-ff979b23f462",
+ "GeneratedBy": "urn:36cdfedd-cdbc-4de1-84e8-ed8b0a881a96",
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{
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+ "@id": "urn:70dbec60-b908-498d-826f-65d7633bb261",
"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:1a2225a3-bad6-407b-b80e-b03730489480",
+ "GeneratedBy": "urn:3a05e7d0-9801-405b-8bf1-1d8374bd2e13",
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}
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{
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+ "@id": "urn:ba2ddac7-ea39-45cc-b261-8e86907e891d",
"Label": "sub-01_T1w",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w",
"digest": {
@@ -660,13 +660,13 @@
}
},
{
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+ "@id": "urn:fec24f26-05bc-46b1-a308-e387bad0083c",
"Label": "",
"AtLocation": "",
- "GeneratedBy": "urn:77295b4e-c8b1-46f6-8adc-7322f4a5361a"
+ "GeneratedBy": "urn:3e0f8be8-e09a-4de1-8898-42148d574f5a"
},
{
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+ "@id": "urn:e3a00e98-0b9c-486c-9d45-661ad0f29c5c",
"Label": "example_func2highres.mat",
"AtLocation": "example_func2highres.mat",
"digest": {
@@ -674,16 +674,16 @@
}
},
{
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+ "@id": "urn:0b064394-077e-4c5a-b3da-8fc4bb051868",
"Label": "highres2example_func.mat",
"AtLocation": "highres2example_func.mat",
- "GeneratedBy": "urn:8d51b390-740e-4699-ba32-88d4f25ea861",
+ "GeneratedBy": "urn:345fc00b-87bb-4394-992d-88b581c53a1e",
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}
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+ "@id": "urn:da7c4a76-1cc5-4b5a-9b7a-aeee1f25a262",
"Label": "example_func2highres",
"AtLocation": "example_func2highres",
"digest": {
@@ -691,250 +691,250 @@
}
},
{
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"AtLocation": "sla.png",
- "GeneratedBy": "urn:e13f861b-3c6e-40be-b8cd-02eeee0e58ce",
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}
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{
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{
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{
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{
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"AtLocation": "example_func2highres1.png",
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{
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{
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{
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- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
+ "GeneratedBy": "urn:f21fb26e-c121-44f4-9518-59a3ba3cddfb",
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},
{
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},
{
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}
},
{
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}
},
{
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- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
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}
},
{
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"Label": "sli.png",
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- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
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}
},
{
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"Label": "slj.png",
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- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
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{
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"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
+ "GeneratedBy": "urn:f21fb26e-c121-44f4-9518-59a3ba3cddfb",
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}
},
{
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"Label": "sll.png",
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- "GeneratedBy": "urn:096ab662-5a1f-4198-86eb-36ec825f4a29",
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},
{
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"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:72eaa85b-1d14-43ec-b59b-ba9598401b53",
+ "GeneratedBy": "urn:3fb67843-9a96-48ae-b535-b18a05d6de44",
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{
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"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:fdf650bf-c3ed-431b-982a-c1758eadc379",
+ "GeneratedBy": "urn:712101dd-72bf-4522-84bd-2206e7600948",
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},
{
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+ "@id": "urn:0238939f-61b0-44a5-9e78-6dffb0b0b5e3",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -942,25 +942,25 @@
}
},
{
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+ "@id": "urn:cfbdc37d-4f9f-4297-b2ed-b01ff2a85ed0",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:395f5c5b-e9ac-4840-9e36-f7d9f8378081",
+ "GeneratedBy": "urn:98f15577-ff6b-46bc-9bf2-acb04558545b",
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{
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"AtLocation": "mc",
- "GeneratedBy": "urn:69393fe9-a34d-43a3-8146-b78f971c8599",
+ "GeneratedBy": "urn:4c5b85fe-32e6-4d2c-b34c-8a2fc87aec51",
"digest": {
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{
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"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -968,7 +968,7 @@
}
},
{
- "@id": "urn:ef507610-583e-4af5-aaee-520301a7bdb0",
+ "@id": "urn:23375a72-1ee5-4128-8d10-54fabae7b00c",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -976,7 +976,7 @@
}
},
{
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+ "@id": "urn:d61ba711-53ab-409c-b0f7-ca672b380ffe",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -984,7 +984,7 @@
}
},
{
- "@id": "urn:c0524ec3-3ea6-4e3e-baba-417314d9af3d",
+ "@id": "urn:1ff46c81-17ab-417c-898c-5c967b8b6b74",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -992,7 +992,7 @@
}
},
{
- "@id": "urn:e30b077c-1b55-440f-8bea-abd13856532c",
+ "@id": "urn:70a63de5-2bb7-4f9d-b86b-0a8330de087f",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1000,7 +1000,7 @@
}
},
{
- "@id": "urn:cca9d05c-43fe-47b3-ada3-1c165bea6342",
+ "@id": "urn:58233196-f676-4b22-b7b6-d2a803c73967",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1008,34 +1008,34 @@
}
},
{
- "@id": "urn:5339cda2-af48-4857-970f-5101e41df618",
+ "@id": "urn:bab102ed-4797-4fa1-84b8-fa18fe447a52",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:6def26df-f81f-41d3-b0ac-e5a601c7ce4e",
+ "GeneratedBy": "urn:dc32a6ba-52b8-4331-8c20-c103684d9607",
"digest": {
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}
},
{
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"Label": "rot.png",
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- "GeneratedBy": "urn:dbf0bd54-d5d1-45cf-8aa7-b593bd3aacf5",
+ "GeneratedBy": "urn:47a4a930-45a7-48f8-afc5-4e5281aa9e2c",
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}
},
{
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+ "@id": "urn:e83d851c-9631-44c8-8c4f-5ffd4bb94feb",
"Label": "trans.png",
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- "GeneratedBy": "urn:441608e5-a5db-483b-988c-f52b353161c6",
+ "GeneratedBy": "urn:a214e64f-f623-475a-addf-0f8f08afe372",
"digest": {
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}
},
{
- "@id": "urn:956a31fd-030a-4e43-8e0b-eb06823cf052",
+ "@id": "urn:086ca1fc-cef0-4bd7-9a98-1418e4dd7814",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1043,34 +1043,34 @@
}
},
{
- "@id": "urn:348b02c5-3388-42a3-90af-a610d35d440d",
+ "@id": "urn:4a81a54c-f691-4024-8f90-299b7e38f7fc",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:a55793e4-f85a-4ac9-8d63-34f58119f00e",
+ "GeneratedBy": "urn:3f2ecad8-a8e5-493a-8abc-0ab3f1401d31",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:247ba477-f6f4-4359-bf5f-d3779573ecd7",
+ "@id": "urn:1daee25e-6e10-4a25-81f8-cf7861e3aaed",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:ec9d7980-1d0b-42f4-96b5-51a4ff6c86d0",
+ "GeneratedBy": "urn:c8fa209f-5ecb-443c-9b74-ba12277d8e19",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:f64a3d35-0ede-4fc7-87a1-edc41e2efc37",
+ "@id": "urn:5b5798a2-a216-41fb-8cb0-ef650c5c95fe",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:d401069b-da20-48be-afbb-31e098f3b3b2",
+ "GeneratedBy": "urn:da2f36c8-f656-4f6e-a4a8-8f2618a20752",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:bc3e9f42-d4b1-4642-97b0-5e6677575a1f",
+ "@id": "urn:4601a4cd-a630-418f-beb8-4815818cd73a",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1078,106 +1078,106 @@
}
},
{
- "@id": "urn:abfb5142-c999-4e6e-ae9e-27cbe9f09a1d",
+ "@id": "urn:aec43d8a-1acf-483e-839f-a6b9d0413d1e",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:c28e8620-2d74-43ae-be27-e2028601d9bd",
+ "GeneratedBy": "urn:5532669b-e4be-439f-ad6c-7eaec203e36d",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:9e26b4b4-7e71-499b-96ae-a1c4ede8344c",
+ "@id": "urn:68d31ef2-236f-48f3-a4db-d45f22bfcc43",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:94571380-7577-41e6-a488-f0c5ea96db5e",
+ "GeneratedBy": "urn:3bee4548-3d99-4d3b-8ecf-fe9fe26023a6",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:4414d31d-9eaf-4d18-b375-04f3314a1039",
+ "@id": "urn:36658aad-0153-4170-8fe1-747d75a6cc5b",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:e4eab963-3f85-4099-b44a-7c31510246e3",
+ "GeneratedBy": "urn:e23fad7b-8ec6-4e75-ad8d-dc6ac8a84649",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:dced5c1d-04b9-4ce8-9f1f-929ef0c1d8c7",
+ "@id": "urn:9b52e42b-e126-46e8-8f25-8f5aaaa31b85",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:605488b5-e8b5-43a7-a87e-6bf4673c8dbd",
+ "GeneratedBy": "urn:208eefab-d051-4765-bff4-67f1743005b2",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:71033977-c543-4f01-b2cf-9b47a1244aae",
+ "@id": "urn:5bbc1c18-26eb-4371-a51f-6060dc8d9342",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:7fe5640e-c1ac-41e2-a390-5cfb10ed270c",
+ "GeneratedBy": "urn:fa2f1c7b-7751-4b85-b51c-c0c7ff606a4e",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:c5644168-63b9-4e5f-b32b-354c7481a6b3",
+ "@id": "urn:08254780-9d70-4efc-8615-576ba6205e13",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:19c392b8-27a2-4289-8244-b4873e9ca58f",
+ "GeneratedBy": "urn:792ea18a-543c-4720-bb39-266ed3d5a6f2",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:5ea48616-c75d-40df-8da5-ecbca08599d0",
+ "@id": "urn:497d8112-4d30-4d69-8445-f21e9299b37d",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:ea004d6b-2e31-45db-b3b4-7b0e08b96791",
+ "GeneratedBy": "urn:2e21b4e4-5935-4855-8b93-dd5e88819342",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:18c43dee-e923-4c54-9293-0d45d34598fc",
+ "@id": "urn:a11d9f65-21e9-4639-956e-2670338fb5a4",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:444a1daf-b77e-42d9-a1b3-56b1ad9ec433",
+ "GeneratedBy": "urn:8c4fb7bc-b852-4995-9c0d-f57f3bc4ff9d",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:fa4f4013-2d53-44e1-bf16-4dcc0a0d3daf",
+ "@id": "urn:ca0cc3f3-fdbf-434f-9653-c4ecd0da4c6b",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:5125d2d9-6492-4c8b-adf2-c5705cc01a67",
+ "GeneratedBy": "urn:e5d28661-d83f-4e8e-a350-8605712fa18e",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:c0cf9bfd-dcce-45e6-a6f6-27dbd33dd9a3",
+ "@id": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:40123b3b-91ec-43ee-988a-93227bbb8fa9",
+ "GeneratedBy": "urn:9961f831-35e9-477b-8d1f-3b47d84871b1",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:2e5f2dfb-470a-43c5-95a0-5dbecb68ecd6",
+ "@id": "urn:aa1738e1-fffa-413c-b8ed-5027efbeb699",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:52207409-b5c7-42a2-a9f3-13fcebc29fa2",
+ "GeneratedBy": "urn:ac8b5b17-4954-4507-b9ff-cc76b89ef95b",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:6c839333-833f-49bb-a38e-fde96e9ae7f0",
+ "@id": "urn:b0574ba8-bc8b-49a7-9b9f-aa4783c7800b",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1185,25 +1185,25 @@
}
},
{
- "@id": "urn:fdecdbd0-25b4-4a8f-a3d3-e9908b473677",
+ "@id": "urn:04ed6b15-acd8-4153-bd79-745075ff58fb",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:9aa8be1f-d7bd-4ade-9c20-192c16d8b960",
+ "GeneratedBy": "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:30f2c87d-f28f-4a74-8d93-0c761ca96317",
+ "@id": "urn:5a0983f2-8f5b-4f8c-a9b9-1dd457e1bcea",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:a39d779d-35f9-4d5b-bd4e-775ab902dd6a",
+ "GeneratedBy": "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:5e81132b-0af3-47d9-a5e3-016da536af9c",
+ "@id": "urn:f5266e11-6d2d-4f7c-bf3c-85b21c458104",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1211,16 +1211,16 @@
}
},
{
- "@id": "urn:3a79788e-4c74-4a65-b4c6-27115e8884d6",
+ "@id": "urn:762aa6c1-c623-4250-9ef9-83a1d18c9045",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:b6710d0b-30c3-428b-b924-2051bc82cc7a",
+ "GeneratedBy": "urn:7583d6d9-67d6-4bbc-a100-f16a38448de8",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:14ffc75c-d323-4058-9fb3-fa7ecd7fb992",
+ "@id": "urn:09658342-b347-432e-a0ca-39ead0b8b6bb",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1228,22 +1228,22 @@
}
},
{
- "@id": "urn:4d37d4cb-b4a6-442a-b3a5-39d657df0ece",
+ "@id": "urn:5c04b2ac-9263-4f7e-84b9-e4b1c26db771",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:c2ff4c68-2abb-4b70-908a-6844e3ed2b58"
+ "GeneratedBy": "urn:695559a1-9da1-4abf-8ffd-18797ec1ce59"
},
{
- "@id": "urn:03ad30da-5d39-489d-9db4-1594a32ed253",
+ "@id": "urn:a6a2bf4f-efef-4293-a5db-8d1df9698c89",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:12ac620f-52b9-4e67-9ca4-2c6ed0706ca2",
+ "GeneratedBy": "urn:2dca8497-bcdb-4c8a-ba3a-74d6a617f12e",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:5fd5670b-c661-4d9f-852f-fdb5238e0773",
+ "@id": "urn:e7c2b1da-9d10-4647-b4dc-5b76e1756e66",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1251,24 +1251,24 @@
}
},
{
- "@id": "urn:f544d8ad-bd4e-46e4-9508-a4aefe1e0432",
+ "@id": "urn:98f0c556-3b7f-45cf-8a9d-ef78175900aa",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:b096695f-7087-450e-9140-ce73eb052e67"
+ "GeneratedBy": "urn:2b9a4fd8-fd99-49a5-b619-58384b71b798"
},
{
- "@id": "urn:315774d8-d488-4729-b1f0-85284457a2e3",
+ "@id": "urn:08f57df8-b9f5-4033-87f7-55fce2b3dcbf",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "mc/prefiltered_func_data_mcf.par"
},
{
- "@id": "urn:d1f48085-4938-4fac-a690-a8a1bef178f0",
+ "@id": "urn:76206d61-8a55-4e68-85d7-f2214a93ab8e",
"Label": "prefiltered_func_data_mcf_diff",
"AtLocation": "mc/prefiltered_func_data_mcf_diff",
- "GeneratedBy": "urn:4a199e13-d903-4746-8a05-4c28d3f24786"
+ "GeneratedBy": "urn:5c7b80bb-a52c-4191-8763-48cd3ae1992f"
},
{
- "@id": "urn:e7e293a9-eed8-4907-8a4f-271b2c2e77d0",
+ "@id": "urn:47f2e70e-0f03-42ae-baee-8eb44818c65b",
"Label": "design",
"AtLocation": "design",
"digest": {
@@ -1276,7 +1276,7 @@
}
},
{
- "@id": "urn:eb856fcf-6bbd-4aca-b994-a5f4f046b424",
+ "@id": "urn:196d4e36-94b4-4ed6-bccd-fa569b52c996",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1284,16 +1284,16 @@
}
},
{
- "@id": "urn:ff64e210-7ac9-4c70-add6-986f2c290fcd",
+ "@id": "urn:d74ef598-3595-4ced-97fd-75c5dc103e00",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:76213b1a-bbf3-4212-a463-8865023f1bda",
+ "GeneratedBy": "urn:20222870-633f-4598-b671-960cf3d572fa",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:318d11c1-328d-4b91-827d-74de938fd19b",
+ "@id": "urn:37683ca5-1963-41df-b40c-cd03888b8d3f",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1301,16 +1301,16 @@
}
},
{
- "@id": "urn:7e832bb7-d40a-491a-9125-de21b2444e71",
+ "@id": "urn:e025346f-9151-462c-8434-0246918c24e7",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:c488ce52-4a39-4f48-acd7-4f48bc1a64f0",
+ "GeneratedBy": "urn:86e2b612-99e2-477b-b627-e50595fb6deb",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:c3ea95c6-89ba-4b96-9a86-b4b166b94a52",
+ "@id": "urn:5a23202c-b202-40cf-9778-7330e983b71a",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1318,25 +1318,25 @@
}
},
{
- "@id": "urn:9a249a9d-60cf-4aa9-bc09-0a7819af0bbf",
+ "@id": "urn:d41e9730-95ec-44d7-ac3c-a3309e68ae23",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:13d39e25-fa20-4c1c-b5b1-db78848a2997",
+ "GeneratedBy": "urn:036f1bf8-a8ac-4ebd-97dd-31bd186bddff",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:036fc19d-7265-42c9-b036-b83c683c11e7",
+ "@id": "urn:4bbd25ac-bbe4-49bf-8e89-d892ecfe2ae9",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:13d39e25-fa20-4c1c-b5b1-db78848a2997",
+ "GeneratedBy": "urn:036f1bf8-a8ac-4ebd-97dd-31bd186bddff",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:b1114cd8-a76d-4379-998a-9a2e4b6d4f5d",
+ "@id": "urn:375eb646-fef7-4012-935b-ac8f7b28dca1",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1344,25 +1344,25 @@
}
},
{
- "@id": "urn:6a5a682c-1df7-48eb-93e1-b320e412ec2e",
+ "@id": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:c400fe05-4ace-4790-b645-b588133520a5",
+ "GeneratedBy": "urn:f5ef2e53-bcf3-4dcb-96f7-1b2ae394587a",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:55c204fc-4ef2-4bab-b845-fd5c543a7a0b",
+ "@id": "urn:1bcb7d2f-7e08-4b01-b7c0-eb7804e396d7",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:69ebc693-1dc1-4aa5-9816-62b678317767",
+ "GeneratedBy": "urn:e5a515f1-d016-4f08-a4bd-7718cb7309df",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:d4a83aff-fe1a-478a-8c0b-3fdf85f08262",
+ "@id": "urn:c61b8756-1bed-4aeb-913d-cdf85bfe5fb4",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1370,28 +1370,28 @@
}
},
{
- "@id": "urn:d2f0229f-3103-408c-840b-198e212f80b7",
+ "@id": "urn:94d92ce2-3775-4ebf-893b-44c9e3d6dc68",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:939b337b-342a-417d-a5df-9d8b0577f496",
+ "GeneratedBy": "urn:5b94b6ab-5880-496b-8f90-d0158d2e2d73",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:6bbd0a71-c593-4f62-a7b7-4d10f75aaf00",
+ "@id": "urn:1afc17e0-5955-442d-8cba-a87e39830089",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:9c283eeb-3683-4f35-966a-6cee22e62921",
+ "GeneratedBy": "urn:32b98972-d2ee-4e72-8597-71810714a976",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:e5955845-059f-4888-9f31-10a84ecd3afd",
+ "@id": "urn:a7cf4d8b-0646-448e-9f96-fa0ee0c60dd7",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:f8cde05b-2019-414d-a458-eae315156b7f",
+ "GeneratedBy": "urn:5caaba6c-e58e-47fb-8216-4f7e6345a328",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png
index 38f6dcd12..bc525bb56 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_der_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
index e1002a725..9149d9daa 100644
--- a/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_motion_reg_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "@id": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,565 +13,565 @@
],
"Activities": [
{
- "@id": "urn:ac8b5b17-4954-4507-b9ff-cc76b89ef95b",
+ "@id": "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266",
"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:37f82981-5933-4f9e-9690-5aacde57b42e"
+ "urn:2a713eec-eb1a-4ace-9328-7e0d28524daa"
]
},
{
- "@id": "urn:aa1738e1-fffa-413c-b8ed-5027efbeb699",
+ "@id": "urn:a46ad4e6-5621-4686-b06f-2f4c85f6fded",
"Label": "fslroi",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:e1d15475-ff8f-4283-85cf-e17fe947c022"
+ "urn:fd1d4aff-2275-4cf2-a575-8ee7b01253b0"
]
},
{
- "@id": "urn:e06a687b-df2b-48e6-8c5f-a2c14a0b1980",
+ "@id": "urn:beff7ab6-7cd1-4cc4-a241-5a6e8d8024ef",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
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- "urn:b51223eb-e691-4d0b-9b2b-21688c76b1f1"
+ "urn:6d9c0313-572b-46d4-acdc-537652e3b978",
+ "urn:a2983d0b-37f1-46b8-8815-5532cf9dd9f4",
+ "urn:abe0ec4f-41d6-4388-83b3-816399fb430b"
]
},
{
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+ "@id": "urn:4663d55e-670a-44cf-94de-46cc8a947ede",
"Label": "Make directory",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_motion_reg.feat/reg",
"Used": []
},
{
- "@id": "urn:f5266e11-6d2d-4f7c-bf3c-85b21c458104",
+ "@id": "urn:b627d50b-31e2-462e-b4f6-a5e381e2a660",
"Label": "fslmaths",
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+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
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]
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
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"Used": [
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]
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"Label": "epi_reg",
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+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
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"Label": "convert_xfm",
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"Used": [
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]
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"Label": "slicer",
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+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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]
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"Label": "pngappend",
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"Label": "slicer",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
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"Label": "pngappend",
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"Label": "pngappend",
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"Label": "rm",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
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- "urn:9cd152ef-df9c-4f65-8ab3-4cf1246b8ed1"
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"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:f5ef2e53-bcf3-4dcb-96f7-1b2ae394587a"
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+ "@id": "urn:20cab6a3-3a47-4335-b31b-e6fdcece720f",
"Label": "mcflirt",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
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]
},
{
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"Label": "Make directory",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/bin/mkdir -p mc",
"Used": []
},
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"Label": "mv",
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"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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+ "urn:079d7cac-4058-4041-9cf2-90593a76d661",
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"Label": "fsl_tsplot",
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- "urn:06eef3af-6ad7-48cb-8b69-1ff6facdaa33"
+ "urn:9b76cb45-76f2-4b42-bc20-232970f00ce2"
]
},
{
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+ "@id": "urn:ff7f29d1-5dce-4121-bffc-d7f8b99ded43",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:06eef3af-6ad7-48cb-8b69-1ff6facdaa33"
+ "urn:9b76cb45-76f2-4b42-bc20-232970f00ce2"
]
},
{
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+ "@id": "urn:8686801c-6354-4d39-80f7-52a85f1e1b00",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:394dee60-f149-43ca-a524-03059a7b9cee"
+ "urn:378d2b0f-09ba-4f38-b77d-549ea7a15246"
]
},
{
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+ "@id": "urn:f28f2fa6-6cb8-4300-9866-8d4918e9b493",
"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:3bf36bd4-a425-4266-9c15-e89373b35211"
+ "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae"
]
},
{
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+ "@id": "urn:6add6bab-95e0-411c-be61-24f213edbb8c",
"Label": "bet2",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
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+ "urn:5eb19834-e313-4f3e-9e36-ada7e9e336ce"
]
},
{
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+ "@id": "urn:9f91de42-958b-4994-a2a1-cd5df69db358",
"Label": "immv",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
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+ "urn:824606da-683f-4db1-8310-2850ded25d2f"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:55fc28fb-de6a-46a5-9b3a-8e8ddfddbff8"
+ "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae",
+ "urn:ac651414-4de1-42cd-a173-ad519f6e16a6"
]
},
{
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+ "@id": "urn:c7532fdd-ac39-43ff-acdd-62f316b3f815",
"Label": "fslstats",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:7cb60c42-3c85-481f-9aca-b86d2fc5dbd0"
+ "urn:e90963c7-4df4-4e92-90a6-11df69e7316b"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:7cb60c42-3c85-481f-9aca-b86d2fc5dbd0"
+ "urn:e90963c7-4df4-4e92-90a6-11df69e7316b"
]
},
{
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"Label": "fslstats",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:3bf36bd4-a425-4266-9c15-e89373b35211"
+ "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae"
]
},
{
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+ "@id": "urn:4bd66238-a389-4bff-9a22-dfff5c122f77",
"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:55fc28fb-de6a-46a5-9b3a-8e8ddfddbff8"
+ "urn:ac651414-4de1-42cd-a173-ad519f6e16a6"
]
},
{
- "@id": "urn:0b66eade-b9cf-457f-a7a8-520a4b9771de",
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:55fc28fb-de6a-46a5-9b3a-8e8ddfddbff8"
+ "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae",
+ "urn:ac651414-4de1-42cd-a173-ad519f6e16a6"
]
},
{
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+ "@id": "urn:45354d21-9918-4d74-ab12-ab46e2456b13",
"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:e0cf6796-f3d4-4408-801a-580d81d2167d"
+ "urn:7f65789c-9a04-408a-b158-bb43c2962ac1"
]
},
{
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+ "@id": "urn:ee75043c-c987-4b82-a8bd-a4ddd3561414",
"Label": "susan",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:e0cf6796-f3d4-4408-801a-580d81d2167d"
+ "urn:7f65789c-9a04-408a-b158-bb43c2962ac1"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:9f99c103-7de0-43ce-b4d8-fd4eda8b8506"
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
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+ "urn:9dea77f8-7d51-4663-a542-723d7fe4bae5"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:096b2bb0-07a4-4e58-bb1b-fde0c7781fc9"
+ "urn:6b8a71c3-0cda-469b-aafd-ac593f5cc414"
]
},
{
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"Label": "fslmaths",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:14ce5791-494b-4a0b-a1a6-701796a26de3"
+ "urn:2cb9bdac-3da5-4505-a8d5-4858a059c59d",
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]
},
{
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+ "@id": "urn:96e62f9d-b1bc-4d08-8a56-80c4267c1dde",
"Label": "imrm",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:14ce5791-494b-4a0b-a1a6-701796a26de3"
+ "urn:2cb9bdac-3da5-4505-a8d5-4858a059c59d"
]
},
{
- "@id": "urn:727ab8db-ebd4-4d1e-9f24-9b2471be1cfa",
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"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:4aed242b-89cb-413f-a4af-892df17b2585"
+ "urn:02351260-94bb-4c70-a587-11e2b342d24a"
]
},
{
- "@id": "urn:b8905fc6-7f60-457b-ac15-bdaba9e4ea83",
+ "@id": "urn:f4ae569c-0764-4af2-bbf4-bba99716197e",
"Label": "fslmaths",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:40085074-470f-40a7-8592-5cfde205f538"
+ "urn:31972545-5912-43dc-ad05-41b1982cf51e"
]
},
{
- "@id": "urn:c888973b-7c65-4992-a202-25b5dc13375c",
+ "@id": "urn:6e926570-0c7d-4610-98ac-8cbb9779eceb",
"Label": "rm",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:cf4823ef-3d1f-43bb-b014-d95d7677f3ab"
+ "urn:f52b1da6-54af-4ef5-b883-eef4570d66b1"
]
},
{
- "@id": "urn:69d846d5-f7c6-4c06-a249-6e6214cbbf0f",
+ "@id": "urn:2a0f2321-a75e-4613-b39e-0462b3551323",
"Label": "Make directory",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:9e5b02ef-3ed2-4f0f-96ec-59134e367424",
+ "@id": "urn:f0482e54-ccc8-49e0-aed4-703c4a8469ee",
"Label": "fslFixText",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:20bb5ec6-2f0e-43b7-862c-bcae7b5f0c2f"
+ "urn:9fd8ffd2-1776-4af3-a24c-acdeaff9cf12"
]
},
{
- "@id": "urn:7422254b-05f7-476f-9a0f-4e86f4333240",
+ "@id": "urn:c26758f0-d786-468a-b6a1-e340a63d1835",
"Label": "Make directory",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:ee78b807-2592-4d04-a5fe-a598c79a8f54",
+ "@id": "urn:69027950-f2cb-40ce-9227-567626ceeece",
"Label": "fslFixText",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:99743df4-ee90-462d-bbfe-52cce238b77d"
+ "urn:7f7a3a8b-9f54-4bea-9795-d3eda4abf34c"
]
},
{
- "@id": "urn:1430ed23-73d6-42db-8269-2236d93df758",
+ "@id": "urn:e3c381f4-cc66-424c-9d66-89012fc3da27",
"Label": "cp",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "cp mc/prefiltered_func_data_mcf.par mc/prefiltered_func_data_mcf_final.par",
"Used": [
- "urn:3eefdc1a-c3e2-427b-be45-b122ff464a33"
+ "urn:765c228f-2359-49dd-ad0b-097cb05b8bf1"
]
},
{
- "@id": "urn:3135e215-2b94-4562-8b8e-a48f87f57f2d",
+ "@id": "urn:fde8bbd8-c433-4a4b-a258-4ccd58a6e898",
"Label": "paste",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "paste -d ' ' mc/prefiltered_func_data_mcf_final.par > confoundevs.txt",
"Used": []
},
{
- "@id": "urn:a02be499-7cc7-4d58-bfd0-6a560cfea4a4",
+ "@id": "urn:22d071c8-f1be-42e8-82f2-13a71d0f0998",
"Label": "feat_model",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/feat_model design confoundevs.txt",
"Used": [
- "urn:b1ffe3d9-ecc1-40f5-b3c4-b2a6dd8a0b7c"
+ "urn:ac338e03-8c6a-4d36-a540-1e90fe86db13"
]
},
{
- "@id": "urn:bd3ca465-bdf8-4c4b-bb01-4fb8ab6d1942",
+ "@id": "urn:e0b55535-1ed2-485c-afc5-1a0f64f8d8fe",
"Label": "film_gls",
- "AssociatedWith": "urn:eda0a5ba-c917-4844-b0db-b2d718610ab9",
+ "AssociatedWith": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
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]
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]
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]
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},
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]
},
{
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},
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}
],
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"digest": {
@@ -579,25 +579,25 @@
}
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@@ -605,7 +605,7 @@
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@@ -613,7 +613,7 @@
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@@ -621,31 +621,31 @@
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@@ -653,13 +653,13 @@
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@@ -667,16 +667,16 @@
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@@ -684,250 +684,250 @@
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{
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"AtLocation": "sll.png",
- "GeneratedBy": "urn:98f0c556-3b7f-45cf-8a9d-ef78175900aa",
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}
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{
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"AtLocation": "example_func2highres1.png",
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{
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"AtLocation": "sla.png",
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}
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{
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"Label": "slb.png",
"AtLocation": "slb.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
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}
},
{
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"Label": "slc.png",
"AtLocation": "slc.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
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}
},
{
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"AtLocation": "sld.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"AtLocation": "sle.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
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}
},
{
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"Label": "slf.png",
"AtLocation": "slf.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"Label": "slg.png",
"AtLocation": "slg.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"Label": "slh.png",
"AtLocation": "slh.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"AtLocation": "sli.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"Label": "slj.png",
"AtLocation": "slj.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"Label": "slk.png",
"AtLocation": "slk.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
- "@id": "urn:0369ec03-893d-47e1-92a6-e77ecd990622",
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"Label": "sll.png",
"AtLocation": "sll.png",
- "GeneratedBy": "urn:b8f972d9-f226-43b2-91a6-6c23a9e2d752",
+ "GeneratedBy": "urn:ded84b0d-d146-4dc9-b41d-e0ce0c61bb2a",
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}
},
{
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"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:cd3b4ccd-e2c1-44f1-b372-4b7152273b09",
+ "GeneratedBy": "urn:b443b44b-2dc5-4e12-87db-2bfc68ea356f",
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}
},
{
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+ "@id": "urn:e5e4090a-a4ea-4043-b74f-f7256d572210",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:593fce14-4a1b-4d64-bfaa-b0f7fd3ce024",
+ "GeneratedBy": "urn:5bf68f22-01ae-4964-a4f6-61566ca7444a",
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}
},
{
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+ "@id": "urn:33d51e81-49cf-46d0-b182-d658d33a9b70",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -935,25 +935,25 @@
}
},
{
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+ "@id": "urn:8e9dd447-40ed-4518-b363-7b3ec7685fae",
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"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:9aff8a3b-3ab3-40d1-b5a4-c720945178d9",
+ "GeneratedBy": "urn:20cab6a3-3a47-4335-b31b-e6fdcece720f",
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}
},
{
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+ "@id": "urn:c67f6a4c-debf-480b-b592-a07da7bbf6ce",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:e215ad6e-d4e7-4b13-9ba1-5353b1dddee0",
+ "GeneratedBy": "urn:ddf41957-b1fb-417a-9cca-3a6e7b8759f3",
"digest": {
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}
},
{
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+ "@id": "urn:2e352c4d-358e-4891-ad71-62332c3426f9",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -961,7 +961,7 @@
}
},
{
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+ "@id": "urn:9b76cb45-76f2-4b42-bc20-232970f00ce2",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -969,7 +969,7 @@
}
},
{
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+ "@id": "urn:079d7cac-4058-4041-9cf2-90593a76d661",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -977,7 +977,7 @@
}
},
{
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+ "@id": "urn:08ecdced-5275-4da3-b272-5f8764017e2c",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -985,7 +985,7 @@
}
},
{
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+ "@id": "urn:c92087a6-3795-4d7f-bf8d-e88741c51954",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -993,7 +993,7 @@
}
},
{
- "@id": "urn:89e387c3-e856-481e-8055-7ae25e760a36",
+ "@id": "urn:9b4cae5d-4de4-4e98-ad24-dc42a0b9e38c",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -1001,34 +1001,34 @@
}
},
{
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"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:b185efef-8306-47df-9b4e-4d359d1ed28a",
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}
},
{
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"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:ea9ce4ff-53f7-45de-a21b-ccab8b353caf",
+ "GeneratedBy": "urn:02bf0272-90eb-449e-b7c2-12a1c3be169e",
"digest": {
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}
},
{
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"AtLocation": "trans.png",
- "GeneratedBy": "urn:1d0e7df0-934e-4348-b758-3e3f0fd2d999",
+ "GeneratedBy": "urn:ff7f29d1-5dce-4121-bffc-d7f8b99ded43",
"digest": {
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}
},
{
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+ "@id": "urn:378d2b0f-09ba-4f38-b77d-549ea7a15246",
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"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1036,34 +1036,34 @@
}
},
{
- "@id": "urn:52163e9a-5b61-49c5-8a41-ffb9e4014483",
+ "@id": "urn:718d8d0d-3d99-4491-a744-63bba1e72fa3",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:81c37383-2699-4e08-9b37-d05476f53749",
+ "GeneratedBy": "urn:8686801c-6354-4d39-80f7-52a85f1e1b00",
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}
},
{
- "@id": "urn:253de491-b4d6-4138-ba37-a6eb6dd22228",
+ "@id": "urn:5eb19834-e313-4f3e-9e36-ada7e9e336ce",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:31c9b029-310d-4021-aa62-c0dbd25fc2e0",
+ "GeneratedBy": "urn:f28f2fa6-6cb8-4300-9866-8d4918e9b493",
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}
},
{
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"Label": "mask",
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- "GeneratedBy": "urn:e681cd2e-df3c-4488-a64d-0261a6b46929",
+ "GeneratedBy": "urn:6add6bab-95e0-411c-be61-24f213edbb8c",
"digest": {
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}
},
{
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+ "@id": "urn:824606da-683f-4db1-8310-2850ded25d2f",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1071,106 +1071,106 @@
}
},
{
- "@id": "urn:c88080b6-995a-41c4-88ce-a7d6c176e52f",
+ "@id": "urn:7d46adc6-f120-4f44-8c70-ad3b8eaa5890",
"Label": "mask",
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- "GeneratedBy": "urn:6c569e45-9361-462c-bded-a5959c6c2e84",
+ "GeneratedBy": "urn:9f91de42-958b-4994-a2a1-cd5df69db358",
"digest": {
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}
},
{
- "@id": "urn:7cb60c42-3c85-481f-9aca-b86d2fc5dbd0",
+ "@id": "urn:e90963c7-4df4-4e92-90a6-11df69e7316b",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:d62cb163-faad-415d-b1a8-afb62b829694",
+ "GeneratedBy": "urn:b454e49b-12d9-4aff-94c3-3fd59398132c",
"digest": {
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}
},
{
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"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:601dd07b-c372-4753-ae81-340c406e60c7",
+ "GeneratedBy": "urn:ab15cd3f-1b9d-4006-9c10-7c7816794d53",
"digest": {
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}
},
{
- "@id": "urn:64ef5f8f-e0b2-469c-a5bc-3abbef036f7e",
+ "@id": "urn:703a45c1-fcbe-4d35-adda-d89aca9c8e21",
"Label": "mask",
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- "GeneratedBy": "urn:4ab0a510-1e34-41b9-a913-9db8b8c40537",
+ "GeneratedBy": "urn:4bd66238-a389-4bff-9a22-dfff5c122f77",
"digest": {
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}
},
{
- "@id": "urn:e0cf6796-f3d4-4408-801a-580d81d2167d",
+ "@id": "urn:7f65789c-9a04-408a-b158-bb43c2962ac1",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:0b66eade-b9cf-457f-a7a8-520a4b9771de",
+ "GeneratedBy": "urn:f81c36df-64ce-49ff-b928-c7ddf0b4c8c3",
"digest": {
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}
},
{
- "@id": "urn:3f7a5206-52c1-41b7-aa5a-aad9f9eccf59",
+ "@id": "urn:e2361583-12d5-4b48-87ee-8480606b9e53",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:f80e3c61-fdee-42ff-bc7a-b3bdc1dafba4",
+ "GeneratedBy": "urn:45354d21-9918-4d74-ab12-ab46e2456b13",
"digest": {
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@@ -1178,25 +1178,25 @@
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{
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{
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@@ -1204,16 +1204,16 @@
}
},
{
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"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:69d846d5-f7c6-4c06-a249-6e6214cbbf0f",
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{
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+ "@id": "urn:9fd8ffd2-1776-4af3-a24c-acdeaff9cf12",
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"digest": {
@@ -1221,22 +1221,22 @@
}
},
{
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"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:9e5b02ef-3ed2-4f0f-96ec-59134e367424"
+ "GeneratedBy": "urn:f0482e54-ccc8-49e0-aed4-703c4a8469ee"
},
{
- "@id": "urn:c6ed5643-9338-4f2c-ac91-1d0e6af17437",
+ "@id": "urn:6134bd82-c6ba-4031-a0f6-1da02585d5eb",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:7422254b-05f7-476f-9a0f-4e86f4333240",
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}
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{
- "@id": "urn:99743df4-ee90-462d-bbfe-52cce238b77d",
+ "@id": "urn:7f7a3a8b-9f54-4bea-9795-d3eda4abf34c",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1244,24 +1244,24 @@
}
},
{
- "@id": "urn:fbe8da44-f727-45b4-acea-f9c466ce910f",
+ "@id": "urn:89fee5f0-1524-467f-8e87-4af5ee8abd9f",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:ee78b807-2592-4d04-a5fe-a598c79a8f54"
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},
{
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"AtLocation": "mc/prefiltered_func_data_mcf.par"
},
{
- "@id": "urn:489ee359-4af7-4f70-b93c-6fd638b112b3",
+ "@id": "urn:3c4a0424-458f-413d-b5ae-2f4a556b4d38",
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"AtLocation": "mc/prefiltered_func_data_mcf_final.par",
- "GeneratedBy": "urn:1430ed23-73d6-42db-8269-2236d93df758"
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},
{
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"Label": "design",
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"digest": {
@@ -1269,7 +1269,7 @@
}
},
{
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+ "@id": "urn:2a2831db-7ec1-4ea8-9870-d9e7a2776e5b",
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"digest": {
@@ -1277,16 +1277,16 @@
}
},
{
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+ "@id": "urn:815262c7-f8be-4a52-a3f7-b7110b0a1f1a",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:990c7146-147f-4591-9407-8fc0f6f7ca55",
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"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
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+ "@id": "urn:3b79334f-2482-4ea7-94d4-6e6090623211",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1294,16 +1294,16 @@
}
},
{
- "@id": "urn:dfe0e715-e555-4e6f-aa5c-8b7fcf92bf1f",
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"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:da97f2d0-d3e2-463f-b3b1-b405e013599e",
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"digest": {
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}
},
{
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"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1311,25 +1311,25 @@
}
},
{
- "@id": "urn:1489a1c9-788b-4219-a4c8-e214343a4228",
+ "@id": "urn:f6eacf00-2ad7-46ea-b5f3-43d8902e19fd",
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"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:e88ac25a-1920-4693-b775-d9aa77d9e2b5",
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}
},
{
- "@id": "urn:77b1a6d4-2c81-4425-86ca-3199c1c5a801",
+ "@id": "urn:0eef9786-fe6e-44cf-a869-6c0bdb1489fe",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:e88ac25a-1920-4693-b775-d9aa77d9e2b5",
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}
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{
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+ "@id": "urn:6931cd5d-dcc9-413c-beb2-c8f59fc9c740",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1337,25 +1337,25 @@
}
},
{
- "@id": "urn:d8b82d32-0f19-46cb-9355-082f1a0568eb",
+ "@id": "urn:4affc0e0-f2f6-410c-98cd-dda7019b68ed",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:3600cb48-ad73-46e5-8e0c-5eb61601e385",
+ "GeneratedBy": "urn:15e50e77-cee7-49b7-9400-55c59f732a08",
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}
},
{
- "@id": "urn:2d19aac9-48f4-41ee-b21f-e77731c5a2ed",
+ "@id": "urn:0add8a2e-685b-4ffb-b51c-33fe56d30fa7",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:bf7337de-6268-4c59-abef-5961f97933b6",
+ "GeneratedBy": "urn:260212da-3b7a-4a16-ba6c-820e5c061d98",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:0af5be90-ef9c-41eb-a027-c2d10d4e3069",
+ "@id": "urn:f0961f03-78cc-43e3-b7c3-fda09a73d42c",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1363,28 +1363,28 @@
}
},
{
- "@id": "urn:9559ee13-769c-4c10-9e77-a66c989afa4c",
+ "@id": "urn:fc2b1774-c34b-4a1f-9d9b-3fd5d889cd04",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:c38d3fd6-4413-4aeb-af2c-a4ba9e52d1ea",
+ "GeneratedBy": "urn:66f8141e-8fd0-4ffc-9853-8005134fb5f4",
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"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:dfc7f499-0b68-4f62-9327-6d5997de2574",
+ "@id": "urn:472415a7-8fa4-47d7-90a9-d77af101c59b",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:1f5d1568-320b-4372-8466-ae06afa84270",
+ "GeneratedBy": "urn:d8674169-2dfa-45af-ae52-683c72874335",
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"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
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+ "@id": "urn:235e03ab-4e6d-43fa-947c-18213c5b8159",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:bb1014cd-1635-4785-a243-d3065a59835f",
+ "GeneratedBy": "urn:22c77196-50f1-4441-b41b-4a8abad44eb9",
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diff --git a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png
index d39439bab..853e2d303 100644
Binary files a/examples/from_parsers/fsl/fsl_motion_reg_report_log.png and b/examples/from_parsers/fsl/fsl_motion_reg_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
index da728922f..778a698aa 100644
--- a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "@id": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,533 +13,533 @@
],
"Activities": [
{
- "@id": "urn:51edc49b-aeb0-441f-94e9-bd7d8a34438f",
+ "@id": "urn:65393bc8-f970-412f-9ce9-6614d4d6200a",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold prefiltered_func_data -odt float",
"Used": [
- "urn:c536bc02-2e99-4f33-80fa-2049cdf59bf2"
+ "urn:c65ad0ab-2625-4563-8b53-45bd217dfa41"
]
},
{
- "@id": "urn:6f8690c8-59d4-435b-bde0-3a7bbd870e45",
+ "@id": "urn:1afe2e30-81b6-43e6-97ee-869c7c2e8a2b",
"Label": "fslroi",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:e78b162c-1f30-4cdf-863a-8e2c248887f0"
+ "urn:aad4164b-37cd-491c-964b-2a23d48dfe04"
]
},
{
- "@id": "urn:8d1b4cad-4104-4023-a010-1b4f7ef2a12b",
+ "@id": "urn:9f3489e8-3177-45d1-a55e-0af7bb8c0eab",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mainfeatreg -F 6.00 -d /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat -l /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/logs/feat2_pre -R /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_unwarp.html -r /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/report_reg.html -i /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/example_func.nii.gz -h /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain -w BBR -x 90 -s /usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain -y 12 -z 90",
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- "urn:f8cb0e67-b771-4013-aef5-f3570952ec55"
+ "urn:8197e7e1-580a-4d2f-8865-764f9d032b4d",
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]
},
{
- "@id": "urn:927ff65e-1d3e-4803-8c17-18433a1607c1",
+ "@id": "urn:2b9671d2-998a-4437-8282-c857b0bf8b84",
"Label": "Make directory",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/mkdir -p /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_cluster_p005.feat/reg",
"Used": []
},
{
- "@id": "urn:584dcc11-4282-4005-a233-aa247685f735",
+ "@id": "urn:ae52c4d2-ee76-4d3f-8d33-b37c3a397491",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w_brain highres",
"Used": [
- "urn:f8cb0e67-b771-4013-aef5-f3570952ec55"
+ "urn:8219f30c-b029-404f-8ee3-680e7b1dd0c7"
]
},
{
- "@id": "urn:c62f9d14-a51a-4fee-8038-d735433b3e7c",
+ "@id": "urn:1327e337-d81d-49cc-a010-e9f4b6232e95",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL/sub-01_T1w highres_head",
"Used": [
- "urn:432fd184-6d95-4966-bc34-3703aaebc045"
+ "urn:e0d079fd-d9b3-4dbd-92b4-21710d49451a"
]
},
{
- "@id": "urn:d16c50a6-7f32-4b74-b8f3-8f9c5a14d796",
+ "@id": "urn:30060837-43de-42b1-a901-a966b492fa52",
"Label": "epi_reg",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/epi_reg --epi=example_func --t1=highres_head --t1brain=highres --out=example_func2highres",
"Used": []
},
{
- "@id": "urn:ec08b899-bdfa-4f0f-b3fd-8671c1ceea3d",
+ "@id": "urn:56bffbdb-2bf5-4ebc-88bf-4d7d108899b4",
"Label": "convert_xfm",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/convert_xfm -inverse -omat highres2example_func.mat example_func2highres.mat",
"Used": [
- "urn:155a15be-dfc8-497f-bcab-b479fbce21c2"
+ "urn:b0423bcb-4c6f-4b95-9cbc-1e2a31b97037"
]
},
{
- "@id": "urn:d1727f99-2840-4f61-b0fc-7a3b7833c964",
+ "@id": "urn:82e635ea-824f-4ef5-b896-040362923cbb",
"Label": "slicer",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer example_func2highres highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
"Used": [
- "urn:6f070701-23cb-4ab5-a385-af737f811d7e",
- "urn:d2ea33ae-1f76-4b44-890c-f3d725d21da4"
+ "urn:c89add60-b4b1-41a4-94b1-23047048d2c7",
+ "urn:e2e90b8e-55c9-43cb-bbab-e1a8c6d4584c"
]
},
{
- "@id": "urn:bfcf1d25-38e5-4fc5-8102-eaf19af9b7e3",
+ "@id": "urn:7556cc7a-14ba-46ba-a8f2-ba3d98f37993",
"Label": "pngappend",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres1.png",
"Used": [
- "urn:2bce5358-e3e1-4ebc-b87f-e4997de984a5",
- "urn:5e17a001-8b17-426f-b998-3a9e2f1ac345",
- "urn:680dcb93-a5e5-4c9c-90c1-fc944c597c01",
- "urn:8456e1f8-f2ca-4e15-ba7d-728b19b628b1",
- "urn:8be00b9f-a0ec-4b9b-9f74-afa0e2539204",
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- "urn:d49a081f-daeb-41bb-9197-1595d0e07b8c",
- "urn:e7565259-771d-4514-b0f8-511867fdf0d4",
- "urn:efbf8bd2-204f-4308-a8a6-b38ea3ed3659"
+ "urn:0bb7f8f0-ead9-444b-a9e6-6c0157149a22",
+ "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "urn:6b72f628-1ec4-4a98-ae8a-929cba33bab5",
+ "urn:6cf7055e-62c3-4f57-a23f-a7329d0408af",
+ "urn:84e58995-014d-4089-bad8-578e23399b07",
+ "urn:84e80130-5c98-46ec-ad2f-28ae98a0c8f4",
+ "urn:c00ec312-9c80-4217-b67b-1cf38581bceb",
+ "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "urn:d7b90546-6df6-4147-886e-d0b0fb295f71",
+ "urn:e94747f0-7a3b-43a1-bcee-7b6ec209dd64",
+ "urn:ea755f41-a00d-4582-be8c-86b8d98cf377",
+ "urn:f6190e92-0bca-4a32-925c-34273712fa92"
]
},
{
- "@id": "urn:6eadba50-fb9c-4d7e-bf72-1b88f1ca5a88",
+ "@id": "urn:5422727e-31da-43ce-91ad-bfbc9f42b164",
"Label": "slicer",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer highres example_func2highres -s 2 -x 0.35 sla.png -x 0.45 slb.png -x 0.55 slc.png -x 0.65 sld.png -y 0.35 sle.png -y 0.45 slf.png -y 0.55 slg.png -y 0.65 slh.png -z 0.35 sli.png -z 0.45 slj.png -z 0.55 slk.png -z 0.65 sll.png",
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- "urn:d2ea33ae-1f76-4b44-890c-f3d725d21da4"
+ "urn:c89add60-b4b1-41a4-94b1-23047048d2c7",
+ "urn:e2e90b8e-55c9-43cb-bbab-e1a8c6d4584c"
]
},
{
- "@id": "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454",
+ "@id": "urn:91245685-6840-4d58-8b62-1ffe58f4fb9b",
"Label": "pngappend",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend sla.png slb.png slc.png sld.png sle.png slf.png slg.png slh.png sli.png slj.png slk.png sll.png example_func2highres2.png",
"Used": [
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- "urn:5e17a001-8b17-426f-b998-3a9e2f1ac345",
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- "urn:9aaacc92-ad1f-44d1-b791-010d10a306c4",
- "urn:9aaf2d76-fdcb-465d-9248-7743685b85e0",
- "urn:a436f385-0f2b-4f63-9e9f-3fc989a38ba4",
- "urn:d49a081f-daeb-41bb-9197-1595d0e07b8c",
- "urn:e7565259-771d-4514-b0f8-511867fdf0d4",
- "urn:efbf8bd2-204f-4308-a8a6-b38ea3ed3659"
+ "urn:0bb7f8f0-ead9-444b-a9e6-6c0157149a22",
+ "urn:4335828e-9ce9-4fa0-85c2-4a0d18b4394c",
+ "urn:6b72f628-1ec4-4a98-ae8a-929cba33bab5",
+ "urn:6cf7055e-62c3-4f57-a23f-a7329d0408af",
+ "urn:84e58995-014d-4089-bad8-578e23399b07",
+ "urn:84e80130-5c98-46ec-ad2f-28ae98a0c8f4",
+ "urn:c00ec312-9c80-4217-b67b-1cf38581bceb",
+ "urn:c77e6fc9-34cf-4f6e-b42e-3890d59a8e81",
+ "urn:d7b90546-6df6-4147-886e-d0b0fb295f71",
+ "urn:e94747f0-7a3b-43a1-bcee-7b6ec209dd64",
+ "urn:ea755f41-a00d-4582-be8c-86b8d98cf377",
+ "urn:f6190e92-0bca-4a32-925c-34273712fa92"
]
},
{
- "@id": "urn:a4173802-b0fc-4eb5-9016-9013f1a1852f",
+ "@id": "urn:2aba531a-f91f-455b-baf4-3d0e18c8c119",
"Label": "pngappend",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
"Used": [
- "urn:afe142bc-c35a-4051-910a-ef29f94fd623",
- "urn:da60e1fe-01dc-4dd7-a2e7-2daf34e5c853"
+ "urn:252514db-a544-4986-996e-fdaf40afdb46",
+ "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94"
]
},
{
- "@id": "urn:e86ccae2-61ff-42f0-b150-66e5f24bf34b",
+ "@id": "urn:aae79a0c-0b25-4947-bf7f-72e24d7e584a",
"Label": "rm",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
"Used": [
- "urn:678c01d1-55b3-48e4-80a7-50bd58e40b65",
- "urn:da60e1fe-01dc-4dd7-a2e7-2daf34e5c853"
+ "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94",
+ "urn:4994ee96-8a5f-4514-9409-283aac70c4aa"
]
},
{
- "@id": "urn:0409ad06-cf22-4cc1-b3e0-933604ab29b5",
+ "@id": "urn:bda7c9ed-226a-4b59-a89c-f3d9c8bba4f7",
"Label": "rm",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:afe142bc-c35a-4051-910a-ef29f94fd623"
+ "urn:252514db-a544-4986-996e-fdaf40afdb46"
]
},
{
- "@id": "urn:d5f274be-3cda-4bfc-bca6-4afcd1622e19",
+ "@id": "urn:c96b85ef-9bad-41dc-a413-025a5563094d",
"Label": "mcflirt",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:e78b162c-1f30-4cdf-863a-8e2c248887f0"
+ "urn:aad4164b-37cd-491c-964b-2a23d48dfe04"
]
},
{
- "@id": "urn:f5777f7f-afef-49f9-be4a-a93d2a957623",
+ "@id": "urn:21662e29-fc09-4b5e-8c02-31ca30ee9d23",
"Label": "Make directory",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
- "@id": "urn:4d3e09b8-a6d1-4cae-ab6e-518c9140be14",
+ "@id": "urn:8f5d1740-44de-48d3-8770-2d0f32d89de9",
"Label": "mv",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
"Used": [
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- "urn:7ba4e7c7-b024-4437-89fb-12b9fd6d684e",
- "urn:93b166eb-4469-4dae-9d65-435cb8462de2",
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- "urn:a3e80646-9e6a-421f-9d5d-36a21303d503",
- "urn:bc261f1d-b44d-4663-8826-2438b4367d0b"
+ "urn:01e67382-f8f7-4229-91ba-20b303bf197e",
+ "urn:257fb473-236f-41e3-a419-a9d60148e9be",
+ "urn:2821d248-72d4-4ecf-b631-7d7348247d46",
+ "urn:6bed399a-edb1-4db3-b058-05dc76a2f315",
+ "urn:839d773c-d1ea-428c-980b-5c45cbd39a55",
+ "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7"
]
},
{
- "@id": "urn:77eff1ab-01eb-4ea7-8085-3efbc9667ede",
+ "@id": "urn:25f83831-8237-4bcf-a95d-c1c43b678e9a",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:bc261f1d-b44d-4663-8826-2438b4367d0b"
+ "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7"
]
},
{
- "@id": "urn:28adcfaf-736c-4b8b-8bc3-d265bf0eba90",
+ "@id": "urn:64c5f41e-349c-42dd-a27f-95f04499e42a",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:bc261f1d-b44d-4663-8826-2438b4367d0b"
+ "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7"
]
},
{
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+ "@id": "urn:07f1d615-da56-4401-a194-3f2c26ee1978",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:87f188df-c23d-4aa0-bfb6-eb6dd111eab2"
+ "urn:88b502b2-3a2e-4ced-8185-8a16765901f3"
]
},
{
- "@id": "urn:7798a257-63de-4a1e-9e79-f2c54807c99f",
+ "@id": "urn:dcb5f57a-81cd-49cf-936d-37102a28864b",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
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- "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a"
+ "urn:f266cd82-e270-492d-8a34-0fd70149eda3"
]
},
{
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+ "@id": "urn:87e6336f-0546-4d51-8158-72b17abf6e90",
"Label": "bet2",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
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+ "urn:d0e0899e-adea-40d8-9ab3-eec5b6976039"
]
},
{
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+ "@id": "urn:38268715-5065-43de-85de-fcdd8865fc95",
"Label": "immv",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
- "urn:6fd8cde4-416a-4eef-bb49-901f85a600f3"
+ "urn:771a00ec-f716-4c32-b8e0-1d6bc6bd887b"
]
},
{
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+ "@id": "urn:e8c59636-f0da-46b6-812b-0911a423417e",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "urn:f266cd82-e270-492d-8a34-0fd70149eda3"
]
},
{
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+ "@id": "urn:7989ed26-c111-4c65-a7f2-c118f1201bff",
"Label": "fslstats",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
- "urn:032573f6-5228-40f3-aa2f-e69f7d20428b"
+ "urn:29c83b1d-da8b-4533-8855-222e99990b85"
]
},
{
- "@id": "urn:72a30876-bc78-42d5-96f1-e65d6204b602",
+ "@id": "urn:c2986c0c-ed72-4122-9a88-1a28862e6651",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
- "urn:032573f6-5228-40f3-aa2f-e69f7d20428b"
+ "urn:29c83b1d-da8b-4533-8855-222e99990b85"
]
},
{
- "@id": "urn:511e6233-0598-4ed9-830d-0c8a75fe69cd",
+ "@id": "urn:2b833511-6aef-47d4-9072-31e496874006",
"Label": "fslstats",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a"
+ "urn:f266cd82-e270-492d-8a34-0fd70149eda3"
]
},
{
- "@id": "urn:53a89cdd-70b9-4db2-b069-8c90ee557888",
+ "@id": "urn:3e7ea993-af25-4097-bcde-e19282d42de7",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7"
]
},
{
- "@id": "urn:2af7130a-5929-4c49-bc60-87d3679c56b6",
+ "@id": "urn:b90ae67f-f83f-4488-b865-b9ae7fd73bd6",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
- "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "urn:f266cd82-e270-492d-8a34-0fd70149eda3"
]
},
{
- "@id": "urn:16931ede-5125-43d4-9542-c658eabfe815",
+ "@id": "urn:ed331241-db7d-4bc0-8c44-35d1d4d65364",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:e20b44b2-308c-4a70-9d88-be65a8f8ca56"
+ "urn:90161d09-6f0c-46e4-9d1c-a16798b445cf"
]
},
{
- "@id": "urn:b9006899-0e5a-4b73-bba5-5fbe62aaaf70",
+ "@id": "urn:808246b0-cd67-4753-8f07-690754d4a9f8",
"Label": "susan",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:e20b44b2-308c-4a70-9d88-be65a8f8ca56"
+ "urn:90161d09-6f0c-46e4-9d1c-a16798b445cf"
]
},
{
- "@id": "urn:a4a341f2-26f6-412f-bbfa-19e14300ba36",
+ "@id": "urn:646c895a-c042-47ce-8c9e-f28f3cae2eee",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
- "urn:612ba8e4-a321-4ed5-a8db-f058c9714ee1"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55"
]
},
{
- "@id": "urn:86ec68f6-393f-4b22-8f91-3b172d8b9222",
+ "@id": "urn:0f4d6eea-0d6c-4fec-8a2d-9fefb6752db1",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
- "urn:612ba8e4-a321-4ed5-a8db-f058c9714ee1"
+ "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55"
]
},
{
- "@id": "urn:1efe54fd-8715-49eb-aada-13d6e2cdebee",
+ "@id": "urn:241de80c-b8e2-43b3-be20-f4200ac54a29",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:8965832a-ae7b-4dd0-a768-07c2add9c69a"
+ "urn:6305398a-67f9-40b5-8456-ff711cd48892"
]
},
{
- "@id": "urn:c1e1e658-7814-4772-9a8e-1f78cc2304f6",
+ "@id": "urn:9b09580c-b95c-4672-ac21-1789f9976135",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:49bf439f-38c7-4199-8e87-69c80fac13b1",
- "urn:8965832a-ae7b-4dd0-a768-07c2add9c69a"
+ "urn:6305398a-67f9-40b5-8456-ff711cd48892",
+ "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f"
]
},
{
- "@id": "urn:c458d0e0-760b-477e-ba6e-3738fb12899d",
+ "@id": "urn:8f8fe587-dd5a-43d2-9792-8b372f66297e",
"Label": "imrm",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:49bf439f-38c7-4199-8e87-69c80fac13b1"
+ "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f"
]
},
{
- "@id": "urn:3ed53110-62f4-4afb-b4d4-e532ba05c06d",
+ "@id": "urn:fac8ab5f-acb2-45d7-a176-6b27b1260cf1",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
"Used": [
- "urn:9d1166fb-e484-48db-a28a-5096b6f510ac"
+ "urn:8e8371ea-1da5-42d5-87e9-39e5dbce47ae"
]
},
{
- "@id": "urn:fc0613fa-5fd4-4495-8357-0cd8529d8039",
+ "@id": "urn:e744d76b-c5b8-44ba-a46a-d60b966b2cf2",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths filtered_func_data -Tmean mean_func",
"Used": [
- "urn:630c11dd-1330-4b11-acf6-38a25866bf9b"
+ "urn:29ae19fc-3f10-4560-b622-06a4f38fc36e"
]
},
{
- "@id": "urn:2145b1ec-29c9-4f38-8fae-e22b03e9d510",
+ "@id": "urn:5e13557d-67b9-492a-80c9-23771d8429e4",
"Label": "rm",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/rm -rf prefiltered_func_data*",
"Used": [
- "urn:794a1586-eeca-42d4-bd17-209350f2dca7"
+ "urn:69730e52-a1bd-4eab-90f1-d16b1134d0e5"
]
},
{
- "@id": "urn:9db814a8-1bcc-44c3-983e-9df4ee6fe2dd",
+ "@id": "urn:66567581-ae6f-4fef-b90e-0c2e1b58c105",
"Label": "Make directory",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:351af4c6-0a25-41b8-a04a-f7a9e1fbe0f4",
+ "@id": "urn:78a45f91-2706-45b4-a8a5-13de8e038981",
"Label": "fslFixText",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt custom_timing_files/ev1.txt",
"Used": [
- "urn:7ade7234-672e-4949-8cac-ddb7c085f8e3"
+ "urn:7f26712f-542f-4cab-b485-c34d61c39b26"
]
},
{
- "@id": "urn:e0f7df09-b3b6-46ed-bb81-f50f98b456b3",
+ "@id": "urn:68d1f283-8c1c-4996-96d0-8bd367625bef",
"Label": "Make directory",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "mkdir -p custom_timing_files",
"Used": []
},
{
- "@id": "urn:6b322220-2c90-483b-993b-6483d77b8a9d",
+ "@id": "urn:77014477-f46d-4f42-a5cc-62e47afe0b8c",
"Label": "fslFixText",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslFixText /storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt custom_timing_files/ev2.txt",
"Used": [
- "urn:37563603-83e1-4a1b-b5fd-3e44180f457c"
+ "urn:8adaf97f-5454-4af6-b15e-0af7e42fb528"
]
},
{
- "@id": "urn:bce0e9d4-45fc-4c6f-9aa7-73b7ed67b6d6",
+ "@id": "urn:465ee51d-ad40-4c2f-a28e-ca5554256ccc",
"Label": "film_gls",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/film_gls --in=filtered_func_data --rn=stats --pd=design.mat --thr=1000.0 --sa --ms=5 --con=design.con",
"Used": []
},
{
- "@id": "urn:5fc04da0-5344-458d-a448-2f39ee9b1aa8",
+ "@id": "urn:d036abd4-f374-4ca5-83ad-1f151c63f354",
"Label": "smoothest",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/smoothest -d 102 -m mask -r stats/res4d > stats/smoothness",
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
- "urn:f9a48e5b-69cd-4f1a-97e0-20b485db7038"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "urn:c65011b8-5ce9-4ef5-8fc3-3bbfe50987ab"
]
},
{
- "@id": "urn:70d7aa44-9486-4d80-a553-314541d0689f",
+ "@id": "urn:e784343f-88eb-4b8d-8447-9af21cf0b76a",
"Label": "fslmaths",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths stats/zstat1 -mas mask thresh_zstat1",
"Used": [
- "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
- "urn:52930724-156d-4201-a99f-92d0664a5726"
+ "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
+ "urn:cb7470f0-d59a-452e-ae07-d28403e45649"
]
},
{
- "@id": "urn:3ae6d58b-af74-4aba-b551-beafc94b9403",
+ "@id": "urn:6e408f66-20ca-482a-8005-ad8f3afa2a44",
"Label": "echo",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "echo 38352 > thresh_zstat1.vol",
"Used": []
},
{
- "@id": "urn:7229a79a-35b5-414f-bbef-a80c6a0aa382",
+ "@id": "urn:4dd470c8-0988-4c71-a5f7-fece23acbed2",
"Label": "cluster",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster -i thresh_zstat1 -t 2.3 --othresh=thresh_zstat1 -o cluster_mask_zstat1 --connectivity=26 --olmax=lmax_zstat1.txt --scalarname=Z -p 0.05 -d 0.70114 --volume=38352 -c stats/cope1 > cluster_zstat1.txt",
"Used": [
- "urn:4d776027-1b79-454d-b119-8be7428aa40a",
- "urn:53d6fe42-943b-4412-a88b-59d60f4676ce"
+ "urn:02264add-1973-4141-8387-b33615c07ee2",
+ "urn:e29308d3-e89c-4238-a244-1637a64a3c27"
]
},
{
- "@id": "urn:1e4af6db-76e5-4f56-bb88-54a17fafc89d",
+ "@id": "urn:925cff4d-fdf7-4657-9ec2-ce8b1557aaef",
"Label": "cluster2html",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/cluster2html . cluster_zstat1",
"Used": [
- "urn:3d020ecb-fd28-407c-b4ee-5440d1a2c024"
+ "urn:33a30fc8-a9d3-4f43-a4c8-ee348a2bf4cf"
]
},
{
- "@id": "urn:3da27e70-7531-4071-b13c-dfa3d43a7765",
+ "@id": "urn:fd791b55-91e2-4377-905f-cdf0a2180274",
"Label": "fslstats",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats thresh_zstat1 -l 0.0001 -R 2>/dev/null",
"Used": [
- "urn:4d776027-1b79-454d-b119-8be7428aa40a"
+ "urn:e29308d3-e89c-4238-a244-1637a64a3c27"
]
},
{
- "@id": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
+ "@id": "urn:48a6c19e-309b-418e-bd45-f0f33dfb3cb1",
"Label": "overlay",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/overlay 1 0 example_func -a thresh_zstat1 2.300208 7.488793 rendered_thresh_zstat1",
"Used": []
},
{
- "@id": "urn:b86afaa0-9f58-422b-a895-1d2c7f5252c1",
+ "@id": "urn:9e3c0116-5947-4998-8e67-a79ab55a637f",
"Label": "slicer",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/slicer rendered_thresh_zstat1 -A 750 rendered_thresh_zstat1.png",
"Used": [
- "urn:42662c59-30f0-487c-b0cc-2d69743b66b6"
+ "urn:f6036a07-8760-4628-bd77-3b22d8121ce4"
]
},
{
- "@id": "urn:0d0a0fe7-66f5-4922-b89f-3eede3d17736",
+ "@id": "urn:1620a2a7-9490-4365-8522-a8bb5461719f",
"Label": "cp",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:5634518e-8272-499c-ab40-b15f1a0d7d8a"
+ "urn:fd665767-b5b2-4d60-a6e6-23c46cdfdc3c"
]
},
{
- "@id": "urn:7924b172-2309-4669-ae81-a988e591655e",
+ "@id": "urn:e6be6791-8da7-4e56-b1a5-b8192775becc",
"Label": "Make directory",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "mkdir -p tsplot",
"Used": []
},
{
- "@id": "urn:3e6bfd7e-087f-4f51-afb1-882eb4cbe149",
+ "@id": "urn:7de17507-bdc9-4002-bf2d-2815ea50a192",
"Label": "tsplot",
- "AssociatedWith": "urn:45d976f3-c2d0-4772-96db-c01c35484f80",
+ "AssociatedWith": "urn:cd7bd294-0560-47ae-8c01-34ccdc77ac75",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
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@@ -547,25 +547,25 @@
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@@ -573,7 +573,7 @@
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@@ -581,7 +581,7 @@
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@@ -621,13 +621,13 @@
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@@ -635,16 +635,16 @@
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@@ -652,250 +652,250 @@
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"AtLocation": "sll.png",
- "GeneratedBy": "urn:6eadba50-fb9c-4d7e-bf72-1b88f1ca5a88",
+ "GeneratedBy": "urn:5422727e-31da-43ce-91ad-bfbc9f42b164",
"digest": {
"sha256": "0b9c965bbea7bb7d1f251ea0f2973f485727fbbc91357e30aee25ff9869f5009"
}
},
{
- "@id": "urn:da60e1fe-01dc-4dd7-a2e7-2daf34e5c853",
+ "@id": "urn:2fc4ff83-2a26-4a10-80bc-0102aa6d6e94",
"Label": "example_func2highres2.png",
"AtLocation": "example_func2highres2.png",
- "GeneratedBy": "urn:e2bedf66-d8ac-4e5e-9971-d9e5cca47454",
+ "GeneratedBy": "urn:91245685-6840-4d58-8b62-1ffe58f4fb9b",
"digest": {
"sha256": "4e622cf27c5f4d28786e7ccdc4e88253f4e5a855818d597ceec90fa78f0d437c"
}
},
{
- "@id": "urn:7946dc75-fa41-452e-8788-0845c4b1d736",
+ "@id": "urn:a63366cb-4305-471f-9c59-3eb80e99629e",
"Label": "example_func2highres.png",
"AtLocation": "example_func2highres.png",
- "GeneratedBy": "urn:a4173802-b0fc-4eb5-9016-9013f1a1852f",
+ "GeneratedBy": "urn:2aba531a-f91f-455b-baf4-3d0e18c8c119",
"digest": {
"sha256": "31960f4162da045cb9b73a0eb3cac33f09d5a2ec1f146f1e457c4a59f478f3e8"
}
},
{
- "@id": "urn:678c01d1-55b3-48e4-80a7-50bd58e40b65",
+ "@id": "urn:4994ee96-8a5f-4514-9409-283aac70c4aa",
"Label": "sl?.png",
"AtLocation": "sl?.png",
"digest": {
@@ -903,25 +903,25 @@
}
},
{
- "@id": "urn:798285b2-c0b7-47ff-9dd9-cd8db08a6f5a",
+ "@id": "urn:f266cd82-e270-492d-8a34-0fd70149eda3",
"Label": "prefiltered_func_data_mcf",
"AtLocation": "prefiltered_func_data_mcf",
- "GeneratedBy": "urn:d5f274be-3cda-4bfc-bca6-4afcd1622e19",
+ "GeneratedBy": "urn:c96b85ef-9bad-41dc-a413-025a5563094d",
"digest": {
"sha256": "83371e264d408de4f678b8182097b39c86bd0a618ca76af6d1dfee5db0903b78"
}
},
{
- "@id": "urn:5f1265e6-ae5c-49cc-825c-cfc8fb60e870",
+ "@id": "urn:133cc17d-bdb0-4a73-a87d-102c3a843276",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:f5777f7f-afef-49f9-be4a-a93d2a957623",
+ "GeneratedBy": "urn:21662e29-fc09-4b5e-8c02-31ca30ee9d23",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:7ba4e7c7-b024-4437-89fb-12b9fd6d684e",
+ "@id": "urn:839d773c-d1ea-428c-980b-5c45cbd39a55",
"Label": "prefiltered_func_data_mcf.mat",
"AtLocation": "prefiltered_func_data_mcf.mat",
"digest": {
@@ -929,7 +929,7 @@
}
},
{
- "@id": "urn:bc261f1d-b44d-4663-8826-2438b4367d0b",
+ "@id": "urn:96acc8d3-b1fb-411a-8a5e-0cd058d715e7",
"Label": "prefiltered_func_data_mcf.par",
"AtLocation": "prefiltered_func_data_mcf.par",
"digest": {
@@ -937,7 +937,7 @@
}
},
{
- "@id": "urn:9a5ec82b-4187-43d9-9c8e-a2884b7f56c6",
+ "@id": "urn:2821d248-72d4-4ecf-b631-7d7348247d46",
"Label": "prefiltered_func_data_mcf_abs.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms",
"digest": {
@@ -945,7 +945,7 @@
}
},
{
- "@id": "urn:74badce5-1fae-46aa-b055-750279abb84b",
+ "@id": "urn:01e67382-f8f7-4229-91ba-20b303bf197e",
"Label": "prefiltered_func_data_mcf_abs_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_abs_mean.rms",
"digest": {
@@ -953,7 +953,7 @@
}
},
{
- "@id": "urn:a3e80646-9e6a-421f-9d5d-36a21303d503",
+ "@id": "urn:6bed399a-edb1-4db3-b058-05dc76a2f315",
"Label": "prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -961,7 +961,7 @@
}
},
{
- "@id": "urn:93b166eb-4469-4dae-9d65-435cb8462de2",
+ "@id": "urn:257fb473-236f-41e3-a419-a9d60148e9be",
"Label": "prefiltered_func_data_mcf_rel_mean.rms",
"AtLocation": "prefiltered_func_data_mcf_rel_mean.rms",
"digest": {
@@ -969,34 +969,34 @@
}
},
{
- "@id": "urn:62721fb4-d252-4369-bdba-ca764ea274af",
+ "@id": "urn:5bce27f0-f599-4ab0-bf68-2d0e37a96f74",
"Label": "mc",
"AtLocation": "mc",
- "GeneratedBy": "urn:4d3e09b8-a6d1-4cae-ab6e-518c9140be14",
+ "GeneratedBy": "urn:8f5d1740-44de-48d3-8770-2d0f32d89de9",
"digest": {
"sha256": "a1a8fa7b1d2bf5bc0a263e95f926d3d9b656d2572455245d46edf48e93744ffa"
}
},
{
- "@id": "urn:3864259f-5550-45d1-b33a-9df348637636",
+ "@id": "urn:9c040cef-944e-4d83-a8d9-02bb210e9d8a",
"Label": "rot.png",
"AtLocation": "rot.png",
- "GeneratedBy": "urn:77eff1ab-01eb-4ea7-8085-3efbc9667ede",
+ "GeneratedBy": "urn:25f83831-8237-4bcf-a95d-c1c43b678e9a",
"digest": {
"sha256": "b8776603f8865a358b2273847d21e63491e7c2e10567fb640608dd47ba721f29"
}
},
{
- "@id": "urn:01fb4cd3-71f1-4d76-86fb-813344b065d1",
+ "@id": "urn:8c44dd51-35e1-4b89-8524-f882421e5782",
"Label": "trans.png",
"AtLocation": "trans.png",
- "GeneratedBy": "urn:28adcfaf-736c-4b8b-8bc3-d265bf0eba90",
+ "GeneratedBy": "urn:64c5f41e-349c-42dd-a27f-95f04499e42a",
"digest": {
"sha256": "496eac1d0ac15e80928780c73766c7791a1707291b2b9a6d1781c2f6a38de3cd"
}
},
{
- "@id": "urn:87f188df-c23d-4aa0-bfb6-eb6dd111eab2",
+ "@id": "urn:88b502b2-3a2e-4ced-8185-8a16765901f3",
"Label": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"AtLocation": "prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms",
"digest": {
@@ -1004,34 +1004,34 @@
}
},
{
- "@id": "urn:b134ff18-cea0-4fd7-ba7c-462a43576f99",
+ "@id": "urn:9b37749a-3351-487a-8ae2-eb5aca1a5d50",
"Label": "disp.png",
"AtLocation": "disp.png",
- "GeneratedBy": "urn:638257a8-0895-48d4-8016-cc60c84f7b3e",
+ "GeneratedBy": "urn:07f1d615-da56-4401-a194-3f2c26ee1978",
"digest": {
"sha256": "c4615e07e04f0c390d969482634cb62e81d47c818d2866ee866ec9c64a5350fd"
}
},
{
- "@id": "urn:a7145494-e97e-4d07-b1fa-a6f4cc8156c7",
+ "@id": "urn:d0e0899e-adea-40d8-9ab3-eec5b6976039",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:7798a257-63de-4a1e-9e79-f2c54807c99f",
+ "GeneratedBy": "urn:dcb5f57a-81cd-49cf-936d-37102a28864b",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:0056d03a-3a4e-4ad8-a792-e032a7a1b1d4",
+ "@id": "urn:0e9519ef-e62c-48ff-9874-02d6bbe82cc7",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:e3618e9c-6936-4acc-ad62-398e8f716185",
+ "GeneratedBy": "urn:87e6336f-0546-4d51-8158-72b17abf6e90",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:6fd8cde4-416a-4eef-bb49-901f85a600f3",
+ "@id": "urn:771a00ec-f716-4c32-b8e0-1d6bc6bd887b",
"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1039,106 +1039,106 @@
}
},
{
- "@id": "urn:06fc7b28-440a-443f-a1ac-d27d1cd48948",
+ "@id": "urn:db065346-363d-4ba1-826a-e17bbdd3fcaf",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:6b5d0405-4cd3-4e91-b83e-54bfc4060735",
+ "GeneratedBy": "urn:38268715-5065-43de-85de-fcdd8865fc95",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:032573f6-5228-40f3-aa2f-e69f7d20428b",
+ "@id": "urn:29c83b1d-da8b-4533-8855-222e99990b85",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:a9d7e700-eb28-4f95-96f4-fbb2d456c47a",
+ "GeneratedBy": "urn:e8c59636-f0da-46b6-812b-0911a423417e",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:13bef169-ea6a-41ed-afa2-64eda95838bd",
+ "@id": "urn:0f339db7-b6d0-472c-86d9-935025f1e945",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:72a30876-bc78-42d5-96f1-e65d6204b602",
+ "GeneratedBy": "urn:c2986c0c-ed72-4122-9a88-1a28862e6651",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:39a676f4-77df-40f8-acb2-7e28c6080cb9",
+ "@id": "urn:090659f4-2b0a-4c91-a339-d6eb664a39bd",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:53a89cdd-70b9-4db2-b069-8c90ee557888",
+ "GeneratedBy": "urn:3e7ea993-af25-4097-bcde-e19282d42de7",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:e20b44b2-308c-4a70-9d88-be65a8f8ca56",
+ "@id": "urn:90161d09-6f0c-46e4-9d1c-a16798b445cf",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:2af7130a-5929-4c49-bc60-87d3679c56b6",
+ "GeneratedBy": "urn:b90ae67f-f83f-4488-b865-b9ae7fd73bd6",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:5f22ddf2-67d3-4126-8597-d39382d590d7",
+ "@id": "urn:e97db26f-22a5-423d-ac55-e88ca7ffbfaf",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:16931ede-5125-43d4-9542-c658eabfe815",
+ "GeneratedBy": "urn:ed331241-db7d-4bc0-8c44-35d1d4d65364",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:612ba8e4-a321-4ed5-a8db-f058c9714ee1",
+ "@id": "urn:dbd5fbb8-de1d-4d1f-958d-7bb195badc55",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:b9006899-0e5a-4b73-bba5-5fbe62aaaf70",
+ "GeneratedBy": "urn:808246b0-cd67-4753-8f07-690754d4a9f8",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:6f18de40-659b-4703-ac67-3e1ef791e7dd",
+ "@id": "urn:ad95a8e0-1090-4d6a-97da-f496eb5bb94d",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:a4a341f2-26f6-412f-bbfa-19e14300ba36",
+ "GeneratedBy": "urn:646c895a-c042-47ce-8c9e-f28f3cae2eee",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:8965832a-ae7b-4dd0-a768-07c2add9c69a",
+ "@id": "urn:6305398a-67f9-40b5-8456-ff711cd48892",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:86ec68f6-393f-4b22-8f91-3b172d8b9222",
+ "GeneratedBy": "urn:0f4d6eea-0d6c-4fec-8a2d-9fefb6752db1",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:49bf439f-38c7-4199-8e87-69c80fac13b1",
+ "@id": "urn:9bbddc14-8c3b-4b30-87dd-6d3f0423692f",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:1efe54fd-8715-49eb-aada-13d6e2cdebee",
+ "GeneratedBy": "urn:241de80c-b8e2-43b3-be20-f4200ac54a29",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:3be0b06d-d28f-40c3-ae8f-7e5ee3a243bc",
+ "@id": "urn:2a166a8b-0df5-48e7-885f-3dd1049a4a6e",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:c1e1e658-7814-4772-9a8e-1f78cc2304f6",
+ "GeneratedBy": "urn:9b09580c-b95c-4672-ac21-1789f9976135",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:9d1166fb-e484-48db-a28a-5096b6f510ac",
+ "@id": "urn:8e8371ea-1da5-42d5-87e9-39e5dbce47ae",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1146,25 +1146,25 @@
}
},
{
- "@id": "urn:630c11dd-1330-4b11-acf6-38a25866bf9b",
+ "@id": "urn:29ae19fc-3f10-4560-b622-06a4f38fc36e",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:3ed53110-62f4-4afb-b4d4-e532ba05c06d",
+ "GeneratedBy": "urn:fac8ab5f-acb2-45d7-a176-6b27b1260cf1",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:de06699c-4240-4cb5-ac86-00f497114b13",
+ "@id": "urn:12ce83c3-7028-4d69-afb7-ac47d8663d65",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:fc0613fa-5fd4-4495-8357-0cd8529d8039",
+ "GeneratedBy": "urn:e744d76b-c5b8-44ba-a46a-d60b966b2cf2",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:794a1586-eeca-42d4-bd17-209350f2dca7",
+ "@id": "urn:69730e52-a1bd-4eab-90f1-d16b1134d0e5",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1172,16 +1172,16 @@
}
},
{
- "@id": "urn:5ea303c9-2001-4005-8ea5-e21dc774c2ed",
+ "@id": "urn:60c33d10-55ae-4161-b566-42216c3f0dc8",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:9db814a8-1bcc-44c3-983e-9df4ee6fe2dd",
+ "GeneratedBy": "urn:66567581-ae6f-4fef-b90e-0c2e1b58c105",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:7ade7234-672e-4949-8cac-ddb7c085f8e3",
+ "@id": "urn:7f26712f-542f-4cab-b485-c34d61c39b26",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1189,22 +1189,22 @@
}
},
{
- "@id": "urn:c6d90bd6-3dfb-4883-8769-e2c8ee94f629",
+ "@id": "urn:26f9a9dc-3402-4c47-b515-59febac8369e",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:351af4c6-0a25-41b8-a04a-f7a9e1fbe0f4"
+ "GeneratedBy": "urn:78a45f91-2706-45b4-a8a5-13de8e038981"
},
{
- "@id": "urn:ecb26611-af49-4f77-9041-82a002d7c2d5",
+ "@id": "urn:f9a6acf6-a5e0-4fff-9cd4-5518dd375af4",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:e0f7df09-b3b6-46ed-bb81-f50f98b456b3",
+ "GeneratedBy": "urn:68d1f283-8c1c-4996-96d0-8bd367625bef",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:37563603-83e1-4a1b-b5fd-3e44180f457c",
+ "@id": "urn:8adaf97f-5454-4af6-b15e-0af7e42fb528",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1212,13 +1212,13 @@
}
},
{
- "@id": "urn:83c705c4-10e0-4063-9745-7ebce793f929",
+ "@id": "urn:07a8d6a6-64b2-42fe-80b4-2b1eac1eb9e7",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:6b322220-2c90-483b-993b-6483d77b8a9d"
+ "GeneratedBy": "urn:77014477-f46d-4f42-a5cc-62e47afe0b8c"
},
{
- "@id": "urn:f9a48e5b-69cd-4f1a-97e0-20b485db7038",
+ "@id": "urn:c65011b8-5ce9-4ef5-8fc3-3bbfe50987ab",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1226,16 +1226,16 @@
}
},
{
- "@id": "urn:b968a2b7-1ab3-4918-a943-f019e88bf502",
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"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:5fc04da0-5344-458d-a448-2f39ee9b1aa8",
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{
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+ "@id": "urn:cb7470f0-d59a-452e-ae07-d28403e45649",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1243,16 +1243,16 @@
}
},
{
- "@id": "urn:4d776027-1b79-454d-b119-8be7428aa40a",
+ "@id": "urn:e29308d3-e89c-4238-a244-1637a64a3c27",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:70d7aa44-9486-4d80-a553-314541d0689f",
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{
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+ "@id": "urn:02264add-1973-4141-8387-b33615c07ee2",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1260,25 +1260,25 @@
}
},
{
- "@id": "urn:85f8c26a-fb6e-4a28-b689-84fc0a73caa9",
+ "@id": "urn:876e299e-293c-40ca-9120-31b5a862d278",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:7229a79a-35b5-414f-bbef-a80c6a0aa382",
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}
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{
- "@id": "urn:056dd331-56c7-4481-9025-6a972c52f7af",
+ "@id": "urn:6110816b-7ef2-4df2-9454-12e5e7d9f8f3",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:7229a79a-35b5-414f-bbef-a80c6a0aa382",
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}
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{
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+ "@id": "urn:33a30fc8-a9d3-4f43-a4c8-ee348a2bf4cf",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1286,25 +1286,25 @@
}
},
{
- "@id": "urn:42662c59-30f0-487c-b0cc-2d69743b66b6",
+ "@id": "urn:f6036a07-8760-4628-bd77-3b22d8121ce4",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:2f56c0f2-f0d5-4997-9cb7-dc9136310252",
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"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:95e20196-ea50-47d2-85d2-5ca1fceaeb1e",
+ "@id": "urn:ab3c4e2c-eac4-499d-83f7-ac40b11b2893",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:b86afaa0-9f58-422b-a895-1d2c7f5252c1",
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"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
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+ "@id": "urn:fd665767-b5b2-4d60-a6e6-23c46cdfdc3c",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1312,28 +1312,28 @@
}
},
{
- "@id": "urn:c78c31e5-b426-479e-962a-b525066ac296",
+ "@id": "urn:0f140c41-9200-4788-864b-b308f1f6bbba",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:0d0a0fe7-66f5-4922-b89f-3eede3d17736",
+ "GeneratedBy": "urn:1620a2a7-9490-4365-8522-a8bb5461719f",
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"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
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{
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+ "@id": "urn:11e8ed87-b70c-4982-96a9-a139509bc82e",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:7924b172-2309-4669-ae81-a988e591655e",
+ "GeneratedBy": "urn:e6be6791-8da7-4e56-b1a5-b8192775becc",
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}
},
{
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+ "@id": "urn:932a5b83-fa80-448a-a1c3-dedfd1901952",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:3e6bfd7e-087f-4f51-afb1-882eb4cbe149",
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"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
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diff --git a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png
index 289f33d92..7d3ae008c 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_clustfwep05_report_log.png differ
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
index 4dedfbd82..25dcb3d94 100644
--- a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
+++ b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "@id": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "FSL",
@@ -13,540 +13,540 @@
],
"Activities": [
{
- "@id": "urn:ac5590b1-bd70-4147-b25f-7328029e7372",
+ "@id": "urn:770417db-0b49-4407-baa9-5a149a92cbeb",
"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
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"Used": [
- "urn:08d57a05-4f66-4823-85e2-c934a8c15fa0"
+ "urn:efba00c8-2a39-48f4-940b-565cc201efb5"
]
},
{
- "@id": "urn:228beb26-f70c-48f3-9558-0bd838529fbe",
+ "@id": "urn:a7179e0e-f881-4aa3-afbb-90c9fc14b7bc",
"Label": "fslroi",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslroi prefiltered_func_data example_func 52 1",
"Used": [
- "urn:3db2bc04-8f31-4762-869a-f720e632d374"
+ "urn:151c4564-2b06-42e4-805f-a53e7471f4a6"
]
},
{
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+ "@id": "urn:5ad7a5b7-40a3-4380-acf7-c1ab546a53bd",
"Label": "mainfeatreg",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
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"Label": "Make directory",
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+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
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]
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"Label": "slicer",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
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+ "urn:43900715-a661-4411-9a8b-c5ffe9330f19",
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+ "urn:74707900-30d5-4930-b467-4a69f7a019c1",
+ "urn:a3042f5e-5d72-4015-97c0-e5b43d94a6b9",
+ "urn:ad8c2146-4bbe-408a-a107-9d9ba36aa1ec",
+ "urn:bc54bf5a-9fe8-4ff6-abfe-ff9c2ec60d4a",
+ "urn:c89142a2-cb00-4e74-a5fe-c88971d7120e",
+ "urn:da7df978-8511-4e8c-82bb-0453bfa8cf21",
+ "urn:e960ebac-d05a-4cf4-9343-37287329f1f5"
]
},
{
- "@id": "urn:21b670f4-1f25-468a-b105-e56765a5b70b",
+ "@id": "urn:b272bb59-0cae-4ac0-9775-73c7bb5b27a4",
"Label": "pngappend",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/pngappend example_func2highres1.png example_func2highres2.png example_func2highres.png",
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- "urn:5482f524-2167-48a2-92b1-ca1661bdf7e6",
- "urn:6a2cef36-9e48-44a3-ab46-7ceccdf60d22"
+ "urn:1a3f1526-ac54-4499-94a4-8b75b8d9007b",
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]
},
{
- "@id": "urn:11197429-a0be-4d37-9b04-890eb7b1f0f3",
+ "@id": "urn:9d4ba426-e4ef-4863-8c94-1a122c95de90",
"Label": "rm",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/bin/rm -f sl?.png example_func2highres2.png",
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- "urn:5482f524-2167-48a2-92b1-ca1661bdf7e6",
- "urn:80d150d5-a203-4fe1-8f28-78b7983e99d0"
+ "urn:9edd7dc8-198e-47f2-97a0-a0c502f60628",
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]
},
{
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"Label": "rm",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/bin/rm example_func2highres1.png",
"Used": [
- "urn:6a2cef36-9e48-44a3-ab46-7ceccdf60d22"
+ "urn:1a3f1526-ac54-4499-94a4-8b75b8d9007b"
]
},
{
- "@id": "urn:721222c6-a2fa-45a6-9a85-760de2229100",
+ "@id": "urn:783b074d-fd7b-4e3f-bc14-df2af149aa0b",
"Label": "mcflirt",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/mcflirt -in prefiltered_func_data -out prefiltered_func_data_mcf -mats -plots -reffile example_func -rmsrel -rmsabs -spline_final",
"Used": [
- "urn:3db2bc04-8f31-4762-869a-f720e632d374"
+ "urn:151c4564-2b06-42e4-805f-a53e7471f4a6"
]
},
{
- "@id": "urn:4b447554-1671-4506-954b-0b02f38eff39",
+ "@id": "urn:f0e1ca2a-5db1-405d-88fd-954cf41a91bf",
"Label": "Make directory",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/bin/mkdir -p mc",
"Used": []
},
{
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+ "@id": "urn:1c2384c0-5ef1-443d-a5ac-d36f29454823",
"Label": "mv",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/bin/mv -f prefiltered_func_data_mcf.mat prefiltered_func_data_mcf.par prefiltered_func_data_mcf_abs.rms prefiltered_func_data_mcf_abs_mean.rms prefiltered_func_data_mcf_rel.rms prefiltered_func_data_mcf_rel_mean.rms mc",
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- "urn:eb6fee87-8ce4-405c-b263-0e194b3767f6",
- "urn:f53f6f1c-8fa1-475d-9785-20fc21be0b8c"
+ "urn:3452a9ca-42b6-4997-bcca-cfb7b55db048",
+ "urn:4a757610-bffc-4f8b-86e5-cc5fb837b4cd",
+ "urn:8e066908-75d0-41b0-a0cf-9685bf3a5785",
+ "urn:a97cc948-6aa2-425a-b953-f1d83ceed350",
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]
},
{
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+ "@id": "urn:5f833946-20fb-421f-bad6-7314076eefc9",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated rotations (radians)' -u 1 --start=1 --finish=3 -a x,y,z -w 640 -h 144 -o rot.png",
"Used": [
- "urn:0e68eb6d-c08a-4a9f-abe3-d6da7513de35"
+ "urn:3452a9ca-42b6-4997-bcca-cfb7b55db048"
]
},
{
- "@id": "urn:b714a794-518e-413b-9c3f-abfa479130c3",
+ "@id": "urn:bc513e48-e7b0-4ce3-8108-092528fc45af",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf.par -t 'MCFLIRT estimated translations (mm)' -u 1 --start=4 --finish=6 -a x,y,z -w 640 -h 144 -o trans.png",
"Used": [
- "urn:0e68eb6d-c08a-4a9f-abe3-d6da7513de35"
+ "urn:3452a9ca-42b6-4997-bcca-cfb7b55db048"
]
},
{
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+ "@id": "urn:06bc5b94-8010-4257-9815-dade77c76107",
"Label": "fsl_tsplot",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fsl_tsplot -i prefiltered_func_data_mcf_abs.rms,prefiltered_func_data_mcf_rel.rms -t 'MCFLIRT estimated mean displacement (mm)' -u 1 -w 640 -h 144 -a absolute,relative -o disp.png",
"Used": [
- "urn:9a52fb33-7db4-4783-80ae-bce932c5429b"
+ "urn:b85c808d-47e1-4a93-9a2a-5dfa71c1ef7f"
]
},
{
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+ "@id": "urn:0aef9850-8080-416b-b56e-b15d2f9b7ad3",
"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
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"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -Tmean mean_func",
"Used": [
- "urn:1e5111e7-554a-4475-a3bd-eedf60f7af39"
+ "urn:060115b8-449f-4a4a-8cb5-b5ed45d61f56"
]
},
{
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+ "@id": "urn:5a684948-c866-433e-85cb-f5badd6af3ee",
"Label": "bet2",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/bet2 mean_func mask -f 0.3 -n -m",
"Used": [
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+ "urn:ace9ce86-0577-4528-9f67-f68406ca6064"
]
},
{
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+ "@id": "urn:f15dc3f1-5707-4d5e-af3f-7650223df45c",
"Label": "immv",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/immv mask_mask mask",
"Used": [
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+ "urn:e3ee0fd1-763c-4aa9-a09a-de1c91eadfac"
]
},
{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_bet",
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- "urn:72932eea-675b-445a-a566-6bae2b98f4d2"
+ "urn:060115b8-449f-4a4a-8cb5-b5ed45d61f56",
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]
},
{
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+ "@id": "urn:8577bb07-1c01-44d3-bb9d-7aaa8458e8cc",
"Label": "fslstats",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_bet -p 2 -p 98",
"Used": [
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+ "urn:0f8fdd76-c020-44cd-8b51-47396be17e01"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_bet -thr 74.4585571 -Tmin -bin mask -odt char",
"Used": [
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+ "urn:0f8fdd76-c020-44cd-8b51-47396be17e01"
]
},
{
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"Label": "fslstats",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslstats prefiltered_func_data_mcf -k mask -p 50",
"Used": [
- "urn:1e5111e7-554a-4475-a3bd-eedf60f7af39"
+ "urn:060115b8-449f-4a4a-8cb5-b5ed45d61f56"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths mask -dilF mask",
"Used": [
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+ "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_mcf -mas mask prefiltered_func_data_thresh",
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- "urn:72932eea-675b-445a-a566-6bae2b98f4d2"
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]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_thresh -Tmean mean_func",
"Used": [
- "urn:2b061de6-9339-4873-b556-40feb2d7bb4f"
+ "urn:017d5cbd-ff1f-4475-9735-a22b07004037"
]
},
{
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+ "@id": "urn:b23c9053-e877-4cff-a86f-0cb404e0234f",
"Label": "susan",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/susan prefiltered_func_data_thresh 445.8289035 2.54777070064 3 1 1 mean_func 445.8289035 prefiltered_func_data_smooth",
"Used": [
- "urn:2b061de6-9339-4873-b556-40feb2d7bb4f"
+ "urn:017d5cbd-ff1f-4475-9735-a22b07004037"
]
},
{
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+ "@id": "urn:a7e9f58c-017c-4461-98a4-cf15453dfee6",
"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mas mask prefiltered_func_data_smooth",
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- "urn:998920fc-bc8a-4ead-aac5-a44e39b2a4c0"
+ "urn:a06f1142-ca51-461c-a20f-80e2f40ffb15",
+ "urn:b4f63892-1788-4ba1-ade6-fcbe5bec44b8"
]
},
{
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+ "@id": "urn:5198f1aa-9245-41b1-91e1-49d022310f37",
"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_smooth -mul 16.8225970571 prefiltered_func_data_intnorm",
"Used": [
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+ "urn:b4f63892-1788-4ba1-ade6-fcbe5bec44b8"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -Tmean tempMean",
"Used": [
- "urn:8100e5db-f870-49c9-a8db-fdbc87ef7e8e"
+ "urn:566a4cd0-3a6b-4377-815b-2ba571321b52"
]
},
{
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"Label": "fslmaths",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_intnorm -bptf 15.0 -1 -add tempMean prefiltered_func_data_tempfilt",
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- "urn:b4155dba-057b-4b8a-9925-1c3911333ee4"
+ "urn:566a4cd0-3a6b-4377-815b-2ba571321b52",
+ "urn:88bd7bdd-d84f-40ba-8642-3b33286e3b08"
]
},
{
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+ "@id": "urn:f586b952-902c-42fb-8138-8f3c80d36894",
"Label": "imrm",
- "AssociatedWith": "urn:3a91568f-3bee-4245-9cdc-fd2740c30039",
+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/imrm tempMean",
"Used": [
- "urn:b4155dba-057b-4b8a-9925-1c3911333ee4"
+ "urn:88bd7bdd-d84f-40ba-8642-3b33286e3b08"
]
},
{
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"Label": "fslmaths",
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+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/fslmaths prefiltered_func_data_tempfilt filtered_func_data",
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+ "urn:96b1d1ae-8e5f-45b6-89c4-bf5532a8ae74"
]
},
{
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"Label": "fslmaths",
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]
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"Command": "/bin/rm -rf prefiltered_func_data*",
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]
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"Command": "mkdir -p custom_timing_files",
"Used": []
},
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"Used": [
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]
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{
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"Label": "Make directory",
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"Command": "mkdir -p custom_timing_files",
"Used": []
},
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"Used": [
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]
},
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"Label": "film_gls",
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"Used": []
},
{
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- "urn:d09ce11e-697a-4e13-bee2-7628d33893fd"
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]
},
{
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]
},
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"Label": "echo",
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"Used": []
},
{
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]
},
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"Label": "cluster2html",
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]
},
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]
},
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},
{
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]
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{
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"Label": "cp",
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"Command": "/bin/cp /usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif .ramp.gif",
"Used": [
- "urn:47e1138d-c62e-4541-b2d0-585c81198052"
+ "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70"
]
},
{
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+ "@id": "urn:863b4ba4-307a-4bf6-9f3a-6e5cb31669ea",
"Label": "Make directory",
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+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "mkdir -p tsplot",
"Used": []
},
{
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+ "@id": "urn:7fd7e58c-3520-4c39-932b-2de13979c4b7",
"Label": "tsplot",
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+ "AssociatedWith": "urn:d7052af7-241a-44ce-99ce-8a5b42550975",
"Command": "/usr/local/packages/fsl-5.0.10/bin/tsplot . -f filtered_func_data -o tsplot",
"Used": []
}
],
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold",
"digest": {
@@ -554,25 +554,25 @@
}
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{
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"AtLocation": "prefiltered_func_data",
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"AtLocation": "example_func",
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/example_func.nii.gz",
"digest": {
@@ -580,7 +580,7 @@
}
},
{
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"digest": {
@@ -588,7 +588,7 @@
}
},
{
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"AtLocation": "/usr/local/packages/fsl-5.0.8/data/standard/MNI152_T1_2mm_brain",
"digest": {
@@ -596,31 +596,31 @@
}
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{
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat",
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"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/fsl_FWE_p005.feat/reg",
- "GeneratedBy": "urn:f4597fb7-fadd-471e-829c-1481a4122c40",
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"Label": "highres",
"AtLocation": "highres",
- "GeneratedBy": "urn:a7f23811-e909-45a2-9551-846e81269793",
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{
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"Label": "sub-01_T1w",
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"digest": {
@@ -628,13 +628,13 @@
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{
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"AtLocation": "example_func2highres.mat",
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@@ -642,16 +642,16 @@
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"AtLocation": "highres2example_func.mat",
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"AtLocation": "example_func2highres",
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@@ -659,250 +659,250 @@
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@@ -910,25 +910,25 @@
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@@ -936,7 +936,7 @@
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@@ -944,7 +944,7 @@
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@@ -952,7 +952,7 @@
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@@ -960,7 +960,7 @@
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@@ -968,7 +968,7 @@
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@@ -976,34 +976,34 @@
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@@ -1011,34 +1011,34 @@
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"Label": "mask_mask",
"AtLocation": "mask_mask",
"digest": {
@@ -1046,106 +1046,106 @@
}
},
{
- "@id": "urn:db3d1dcc-4074-462c-8169-ae9beed13792",
+ "@id": "urn:9fb33f03-76f5-46d7-970f-e644098dbcac",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:bbed6eaf-912f-44a5-ad69-bcdd07b5611c",
+ "GeneratedBy": "urn:f15dc3f1-5707-4d5e-af3f-7650223df45c",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:d3c5145f-774b-428e-834c-b7c6f59a6035",
+ "@id": "urn:0f8fdd76-c020-44cd-8b51-47396be17e01",
"Label": "prefiltered_func_data_bet",
"AtLocation": "prefiltered_func_data_bet",
- "GeneratedBy": "urn:9bf6596d-5bb9-4781-8357-feaaccd82518",
+ "GeneratedBy": "urn:4678ecbb-8466-49c4-84f4-5e092e99ada6",
"digest": {
"sha256": "c01f21947b38d9886528dec14edf23dfb55304b7da67569fe93902472b286cf4"
}
},
{
- "@id": "urn:e5d4ba8e-eedc-49e1-afda-963d466945a1",
+ "@id": "urn:5597e536-cc2e-4140-a887-f9cf062a7cc8",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:ff71fdd3-6130-454c-bb60-6e05689951d0",
+ "GeneratedBy": "urn:ef0c3f4e-4e67-4cfb-b6a4-e9c40b2dc7e9",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:ec4e23f3-d608-4e76-b1d0-afb393f4f5af",
+ "@id": "urn:fabf4f69-def8-49d7-9611-c11f35a72be7",
"Label": "mask",
"AtLocation": "mask",
- "GeneratedBy": "urn:c45aa579-f1e2-43b7-88c6-ac3538101b48",
+ "GeneratedBy": "urn:b68a203c-17bc-4181-9131-451583349b15",
"digest": {
"sha256": "949a652a7389482d85f92185aaed9c21b7f6b514e929b523456f45f68c3ab14f"
}
},
{
- "@id": "urn:2b061de6-9339-4873-b556-40feb2d7bb4f",
+ "@id": "urn:017d5cbd-ff1f-4475-9735-a22b07004037",
"Label": "prefiltered_func_data_thresh",
"AtLocation": "prefiltered_func_data_thresh",
- "GeneratedBy": "urn:9747a8ff-1f5f-4e82-9c77-9925d9afb4bf",
+ "GeneratedBy": "urn:628b15c9-964e-46ad-8a6a-82fcee469f97",
"digest": {
"sha256": "c5c015a8df079b497bbce596808cbbdc09fb39411f490244de192dfa72d33640"
}
},
{
- "@id": "urn:cefdfa11-917c-4d55-870b-b181f657575f",
+ "@id": "urn:2a7e8f4f-dc2a-4a36-9279-78f92698bd2d",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:09d9c8f9-372f-4df5-9eec-3925b086aff3",
+ "GeneratedBy": "urn:c539699d-a880-484f-9bd4-c583ac826a98",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:998920fc-bc8a-4ead-aac5-a44e39b2a4c0",
+ "@id": "urn:b4f63892-1788-4ba1-ade6-fcbe5bec44b8",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:931c0fca-72bc-4596-a994-9a18b2f928b5",
+ "GeneratedBy": "urn:b23c9053-e877-4cff-a86f-0cb404e0234f",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:390eec17-c797-4abc-82ba-6403ead30662",
+ "@id": "urn:ff437011-9364-42c4-a64d-7a8b7a8562eb",
"Label": "prefiltered_func_data_smooth",
"AtLocation": "prefiltered_func_data_smooth",
- "GeneratedBy": "urn:c13342ec-7aed-4f95-904a-ce7f33f1f427",
+ "GeneratedBy": "urn:a7e9f58c-017c-4461-98a4-cf15453dfee6",
"digest": {
"sha256": "2a4901d885fce0b083c9f99364da8dcff184635e74ab011f53a68cfc6827b429"
}
},
{
- "@id": "urn:8100e5db-f870-49c9-a8db-fdbc87ef7e8e",
+ "@id": "urn:566a4cd0-3a6b-4377-815b-2ba571321b52",
"Label": "prefiltered_func_data_intnorm",
"AtLocation": "prefiltered_func_data_intnorm",
- "GeneratedBy": "urn:c3241f9a-4b0c-49b5-984d-184a6f3759cc",
+ "GeneratedBy": "urn:5198f1aa-9245-41b1-91e1-49d022310f37",
"digest": {
"sha256": "0698a276f6f0fdccfb06033926d333a176503a09aaa87b78384fbffbf1c54dee"
}
},
{
- "@id": "urn:b4155dba-057b-4b8a-9925-1c3911333ee4",
+ "@id": "urn:88bd7bdd-d84f-40ba-8642-3b33286e3b08",
"Label": "tempMean",
"AtLocation": "tempMean",
- "GeneratedBy": "urn:70915a37-30ca-4cc8-89ac-1b4313150671",
+ "GeneratedBy": "urn:4d43a36a-2f9a-4350-aa97-f0cdd03fc576",
"digest": {
"sha256": "1a01513c76bc17516b60df315a1922789ce79d72e66e105fbf2723df9cb1b038"
}
},
{
- "@id": "urn:b8758907-f1ed-454e-985c-d0ec7bbd892f",
+ "@id": "urn:2e25efab-eb2c-43de-b4d4-f013727a6bac",
"Label": "15.0",
"AtLocation": "15.0",
- "GeneratedBy": "urn:a9c533e0-0460-4990-bc3e-52138db556f2",
+ "GeneratedBy": "urn:414ccb5f-fd54-428e-9967-4c795f82cf42",
"digest": {
"sha256": "552db91328a881034f16ec50203ba34d4af448f52c616eb28db6c07aa575a286"
}
},
{
- "@id": "urn:97a56b57-4ac3-43c8-a6e1-bf20b58206dd",
+ "@id": "urn:96b1d1ae-8e5f-45b6-89c4-bf5532a8ae74",
"Label": "prefiltered_func_data_tempfilt",
"AtLocation": "prefiltered_func_data_tempfilt",
"digest": {
@@ -1153,25 +1153,25 @@
}
},
{
- "@id": "urn:6e9de955-cc00-45bc-8b70-e5eff209ba8a",
+ "@id": "urn:ed65319b-bef9-45d6-9ef4-1d7df77a0226",
"Label": "filtered_func_data",
"AtLocation": "filtered_func_data",
- "GeneratedBy": "urn:527f0565-2044-4b55-832c-3a09aa4f78ee",
+ "GeneratedBy": "urn:618abbfe-0696-4bc2-9baf-0a6b4493c230",
"digest": {
"sha256": "2a1854e3b48a54f88e063191e25159015a0afbd300d18a1cfda37b4b68a1ee69"
}
},
{
- "@id": "urn:8c453e99-08d2-4dc0-be26-4e3d7142869f",
+ "@id": "urn:891d4254-5573-4c46-9512-d88fb1ed57dd",
"Label": "mean_func",
"AtLocation": "mean_func",
- "GeneratedBy": "urn:01813183-0b7e-4d7a-9d01-a64ac607b9d1",
+ "GeneratedBy": "urn:9fb85f2d-fa9e-4326-b9d4-ef68a8b2cb4a",
"digest": {
"sha256": "5629950501d629b6a15792e71751c4e17494fcd62e0f2b2ee8a3bc106735786e"
}
},
{
- "@id": "urn:259ba45e-774a-49f8-857b-82f0fe731dd6",
+ "@id": "urn:8942bc5b-9a39-43d0-8c94-4c3e9f5e1506",
"Label": "prefiltered_func_data*",
"AtLocation": "prefiltered_func_data*",
"digest": {
@@ -1179,16 +1179,16 @@
}
},
{
- "@id": "urn:52ac7507-1b78-451b-8d71-a8134799b096",
+ "@id": "urn:fa048c67-a097-4f41-9f60-c89251545103",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:abf735c9-2667-495b-9fa1-321a42d9e42b",
+ "GeneratedBy": "urn:1cbd903f-9c67-4046-8bb4-7f88a62e7436",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:28ba5f12-1365-4bbb-ab4a-159bd0b33b34",
+ "@id": "urn:537668d1-e7fc-4fcb-8426-530e32022b51",
"Label": "sub-01_tone_counting.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting.txt",
"digest": {
@@ -1196,22 +1196,22 @@
}
},
{
- "@id": "urn:c6a0afd0-daa5-4243-aa57-e91e9b546865",
+ "@id": "urn:1ebb651d-2df4-4ac7-92f1-f0b9bad15e7b",
"Label": "ev1.txt",
"AtLocation": "custom_timing_files/ev1.txt",
- "GeneratedBy": "urn:4ba9541e-ec77-485c-bc03-5344cbfa840c"
+ "GeneratedBy": "urn:291a1eb3-7456-4ee0-b51d-558295a0aa9f"
},
{
- "@id": "urn:e276d06e-84be-4349-8afb-33c503367cc2",
+ "@id": "urn:459fe5cc-61f1-4f5f-acc6-d95602f22bfe",
"Label": "custom_timing_files",
"AtLocation": "custom_timing_files",
- "GeneratedBy": "urn:7403f17c-c790-471e-8b6d-55d5650cb385",
+ "GeneratedBy": "urn:42366a41-e48f-452f-a56a-4f2c4fb82d0b",
"digest": {
"sha256": "1d7e19792328d5040f2f9fb3c15d59de90fc771785f81c67039a043bd5f2ed20"
}
},
{
- "@id": "urn:8c4107d0-f88c-4a4c-9357-6e1e19ad1201",
+ "@id": "urn:0617f869-1d93-49de-8802-eebcca654cec",
"Label": "sub-01_tone_counting_probe.txt",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/FSL/ONSETS/sub-01_tone_counting_probe.txt",
"digest": {
@@ -1219,13 +1219,13 @@
}
},
{
- "@id": "urn:108825b6-48c2-46ba-a0d2-5aaacfc59220",
+ "@id": "urn:d2ebc0e6-bed8-4914-951b-d486a8a6b19d",
"Label": "ev2.txt",
"AtLocation": "custom_timing_files/ev2.txt",
- "GeneratedBy": "urn:a8be1d24-6de4-45b2-92ad-dc44be445319"
+ "GeneratedBy": "urn:5b6ece1d-f451-442f-a3c6-c9f484150172"
},
{
- "@id": "urn:d09ce11e-697a-4e13-bee2-7628d33893fd",
+ "@id": "urn:c7abed1c-541a-416f-a69b-7d91ad6de028",
"Label": "res4d",
"AtLocation": "stats/res4d",
"digest": {
@@ -1233,16 +1233,16 @@
}
},
{
- "@id": "urn:95c94be2-273b-4c7d-8a39-1ce112181183",
+ "@id": "urn:94ee237c-3ace-498a-bde4-6dc285a62fc1",
"Label": "smoothness",
"AtLocation": "stats/smoothness",
- "GeneratedBy": "urn:b83677f5-b62b-4acd-96b5-716f9da67ac6",
+ "GeneratedBy": "urn:75e04324-713b-4e74-9e24-6ff65cdf32c7",
"digest": {
"sha256": "67b0aaf95a257beff60d331b56265034807ca51e67e2d312d481d5835ef0b1d0"
}
},
{
- "@id": "urn:0bc910a4-11f0-409b-a806-fc0893a40976",
+ "@id": "urn:e2444068-c742-4dd1-84c7-0641984fb6d9",
"Label": "zstat1",
"AtLocation": "stats/zstat1",
"digest": {
@@ -1250,16 +1250,16 @@
}
},
{
- "@id": "urn:ab4d3e7f-fd6c-4189-a5dd-b726f1e3eaab",
+ "@id": "urn:d20ce534-d9dd-4432-befb-e4af83255cad",
"Label": "thresh_zstat1",
"AtLocation": "thresh_zstat1",
- "GeneratedBy": "urn:69fcfb15-c77c-40c4-a487-3ad726504cfb",
+ "GeneratedBy": "urn:2988ce82-4171-40d3-83f1-a52e190aeeb3",
"digest": {
"sha256": "662e7ba670e124d15bb3cc18b818868f76604578034b524c8882f35fc5db413f"
}
},
{
- "@id": "urn:9713c577-48d4-4ce2-9732-3e5b2cf78e79",
+ "@id": "urn:e1f4504e-a931-4560-b135-c4b165528bc3",
"Label": "cope1",
"AtLocation": "stats/cope1",
"digest": {
@@ -1267,25 +1267,25 @@
}
},
{
- "@id": "urn:918fcb03-359d-488c-bb96-5b75f21afc6b",
+ "@id": "urn:d6c4bcf4-12c5-438c-9367-b4d2d5946dfe",
"Label": "cluster_mask_zstat1",
"AtLocation": "cluster_mask_zstat1",
- "GeneratedBy": "urn:3e718433-e2b5-434d-a596-249413698da1",
+ "GeneratedBy": "urn:ae0d63b9-8eea-4635-a229-46d0e077f4f6",
"digest": {
"sha256": "b28c170e33d2917cac55183786616a9e976e5e7f30dc7c8666341f12ed6d0277"
}
},
{
- "@id": "urn:f8a81771-0ea9-47d0-8c3e-b3482efcb7a4",
+ "@id": "urn:8b99de74-04a3-4a04-ab08-a2af09fa3473",
"Label": "cope1",
"AtLocation": "stats/cope1",
- "GeneratedBy": "urn:3e718433-e2b5-434d-a596-249413698da1",
+ "GeneratedBy": "urn:ae0d63b9-8eea-4635-a229-46d0e077f4f6",
"digest": {
"sha256": "bf3b603569da6dbe3d6f0e8667d346f3ac943c9d01d2fc9743ce17abeb1547fb"
}
},
{
- "@id": "urn:e36979a0-f0bf-44cd-aadc-8b80d1ca6d10",
+ "@id": "urn:1b7afc2f-569a-4de1-b8e4-aa3e690095ca",
"Label": "cluster_zstat1",
"AtLocation": "cluster_zstat1",
"digest": {
@@ -1293,25 +1293,25 @@
}
},
{
- "@id": "urn:8796fa10-3cd2-44da-80b5-3e07ffc7eb8b",
+ "@id": "urn:1c63a241-1fd2-41ec-99f2-041b3914e2c5",
"Label": "rendered_thresh_zstat1",
"AtLocation": "rendered_thresh_zstat1",
- "GeneratedBy": "urn:5bbeda84-ea59-4602-8539-b4825125464d",
+ "GeneratedBy": "urn:0f4a4e05-e37b-4628-96fe-b0474b7d5184",
"digest": {
"sha256": "de5b9d44d95f4252f491eb45c76a0ae2b4d2c75b58664fc0df7d9153810c0bf6"
}
},
{
- "@id": "urn:6b2dccb0-069c-4d61-91cb-9885fcb4a556",
+ "@id": "urn:ae169208-f61b-4a71-a1f2-33e0b026a76c",
"Label": "rendered_thresh_zstat1.png",
"AtLocation": "rendered_thresh_zstat1.png",
- "GeneratedBy": "urn:bb40fcd5-09a3-4b42-93b4-ed8ed7ee95dd",
+ "GeneratedBy": "urn:09188984-37c7-42dd-882b-24f9abaaaaea",
"digest": {
"sha256": "15d6a8bf7a902df8c5feeb7468a3d0caacf9eb3067c0840c2f4763f5e2301527"
}
},
{
- "@id": "urn:47e1138d-c62e-4541-b2d0-585c81198052",
+ "@id": "urn:a51452a7-71ed-46f1-b3f9-63b70b3cfd70",
"Label": "ramp.gif",
"AtLocation": "/usr/local/packages/fsl-5.0.10/etc/luts/ramp.gif",
"digest": {
@@ -1319,28 +1319,28 @@
}
},
{
- "@id": "urn:34938128-0ef3-4618-8817-c35f21e124a4",
+ "@id": "urn:063be7f7-a32c-4d48-b5a4-fbe6cecd07c3",
"Label": ".ramp.gif",
"AtLocation": ".ramp.gif",
- "GeneratedBy": "urn:06372779-6792-4e37-84d1-cd68357b7aed",
+ "GeneratedBy": "urn:55491742-f275-45e3-b023-a7f53aaae248",
"digest": {
"sha256": "93f4284ccb854d5a41401d9360a13223017b67479cb289a33d83836922e028a4"
}
},
{
- "@id": "urn:39ea58bb-83ea-4c9e-8050-7adcf255c33d",
+ "@id": "urn:2d5ccef6-0f80-48b9-925a-36720b12df94",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:19459e8e-1991-490b-b90f-a18c3dc7528b",
+ "GeneratedBy": "urn:863b4ba4-307a-4bf6-9f3a-6e5cb31669ea",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
},
{
- "@id": "urn:3b785f19-73bf-4c34-a038-7a9b4396a169",
+ "@id": "urn:434ccaa0-1c21-4718-9ca3-4659154e28cd",
"Label": "tsplot",
"AtLocation": "tsplot",
- "GeneratedBy": "urn:1dcfe420-527d-4cc2-8411-9c1433b5fdff",
+ "GeneratedBy": "urn:7fd7e58c-3520-4c39-932b-2de13979c4b7",
"digest": {
"sha256": "2a74042f4edf02288edf16961307f741651efb4346e102a04b7603e781d1625e"
}
diff --git a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png
index 72bb138e4..4ecc0528f 100644
Binary files a/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png and b/examples/from_parsers/fsl/fsl_thr_voxelfwep05_report_log.png differ
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
index 58e6618b6..fd44f36af 100644
--- a/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
+++ b/examples/from_parsers/spm/spm_2_t_test_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "@id": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:7271accf-6874-4774-8e77-f2c8317f2b9b",
+ "@id": "urn:a9c4648d-41a0-4fe4-90e6-41b5f0a72d3e",
"Label": "Move file",
"Used": [
- "urn:1d1b3389-23b1-48cb-9e01-94d17230ada3"
+ "urn:826557c4-b724-4e3c-bc51-cd7035d9eea8"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:acc7bdb5-8fac-4151-8026-d741958f047d",
+ "@id": "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e",
"Label": "Move file",
"Used": [
- "urn:5a59dd20-8346-4538-8661-9396d02224d7"
+ "urn:c9b41c2e-95ef-41ff-ab0e-6ebafe11329d"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:4dc466e1-b429-43bb-b880-add7232b7347",
+ "@id": "urn:927af817-f93a-489f-a7f9-8042ef2bd242",
"Label": "Gunzip",
"Used": [
- "urn:f33a292b-a905-408f-ba76-441a2058a27b"
+ "urn:2714f869-ac76-4842-8998-8d005cbe8b00"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:dda87c51-4f5a-49b0-928d-a53c9b3c47f6",
+ "@id": "urn:c6b77905-a877-4bf7-bb02-8b2c581b45a6",
"Label": "Gunzip",
"Used": [
- "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c"
+ "urn:8bc12560-688d-456f-909d-dc9eda67b073"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:3625a84c-5333-49e0-86c1-737bfc8d7f7a",
+ "@id": "urn:76125b99-5fb8-4a46-9b93-8ff9cd4e3e70",
"Label": "Realign",
"Used": [
- "urn:c3acf82f-0adc-4874-bd69-b28b507542c7"
+ "urn:835d8881-a887-40b8-9960-a4fc64ada68c"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:19cea046-4b73-4065-8d07-f2ab4cd05577",
+ "@id": "urn:12fad9c5-48eb-46f2-8071-7d08b1fb1098",
"Label": "Coregister",
"Used": [
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8",
- "urn:b5c075e3-f245-4bc9-8cc4-d55eec21091e"
+ "urn:34dbf791-6f89-4a89-aee7-1908de2b5835",
+ "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "@id": "urn:63dd083a-b6c0-4169-bdc1-5b4c478ae687",
"Label": "Segment",
"Used": [
- "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8"
+ "urn:34dbf791-6f89-4a89-aee7-1908de2b5835"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:920dddce-28c6-421c-882c-9a68550b6b34",
+ "@id": "urn:fcbb6d50-3a39-441e-8ef0-33ce03204491",
"Label": "Normalize",
"Used": [
- "urn:b5c075e3-f245-4bc9-8cc4-d55eec21091e",
- "urn:d254e790-3eb0-457a-a728-94483f898737"
+ "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf",
+ "urn:cdf01b16-5de4-40b6-9a04-768396aa5a90"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:12748a32-4f2a-4755-966a-c3bf5f628803",
+ "@id": "urn:8500e20b-129d-4b7e-b98d-7ae07cb72fe0",
"Label": "Normalize",
"Used": [
- "urn:d254e790-3eb0-457a-a728-94483f898737"
+ "urn:cdf01b16-5de4-40b6-9a04-768396aa5a90"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:7437f41a-5203-4d70-ac17-53d387d4947b",
+ "@id": "urn:87df8dbe-2e41-469e-8d14-659937a28e3b",
"Label": "Smooth",
"Used": [
- "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee"
+ "urn:6fa4a3dc-b817-41d3-855c-7932de8c100a"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:aca48b64-0f58-44c1-bf54-eb7e9089f5b9",
+ "@id": "urn:3878d997-9e11-4659-8125-0da6e3e3551b",
"Label": "Stat Design",
"Used": [
- "urn:31571f6d-d8ca-4c66-a64a-c2a2a88753d4",
- "urn:3f64e75a-698c-4349-9f6a-7bd538d135df"
+ "urn:c7b12f74-8c20-4dd8-9a5c-254c67cbf054",
+ "urn:e890a08f-17db-4033-95ea-b7cf9d1b867a"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_2_T_test'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:7d6a5166-4869-456a-a070-411d9eaf76b3",
+ "@id": "urn:1a0cb55a-5189-4fdb-9433-3e72793bd1b5",
"Label": "Estimate stat.",
"Used": [
- "urn:924f0baf-a156-4e39-835b-4b9974948de2"
+ "urn:4e8eb6a1-96ac-4d65-8d34-d2db225432c4"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:5c0e3a05-6e09-4bc9-bb52-e8c4c019ce22",
+ "@id": "urn:72e5bfd9-a294-46c1-b247-b738f3b081c0",
"Label": "Estimate contrast",
"Used": [
- "urn:7a6d6abf-77ee-4c02-a123-ba97020ff74c"
+ "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:71f1ade3-2b62-4c18-a187-26d24d3a7f1a",
+ "@id": "urn:a68d5032-c2be-4a84-ab5d-fbde9e657d5f",
"Label": "Threshold",
"Used": [
- "urn:9d7031f9-b790-4f40-b4db-a36f7f1cdd18"
+ "urn:33ae67f5-2af6-4277-998e-aa229e2f8b26"
],
- "AssociatedWith": "urn:e10b80dc-2736-45e6-b5cb-3754b829f806",
+ "AssociatedWith": "urn:c48fddaa-6cf5-4453-b931-ef29776dbaad",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,7 +268,7 @@
],
"Entities": [
{
- "@id": "urn:1d1b3389-23b1-48cb-9e01-94d17230ada3",
+ "@id": "urn:826557c4-b724-4e3c-bc51-cd7035d9eea8",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -276,7 +276,7 @@
}
},
{
- "@id": "urn:5a59dd20-8346-4538-8661-9396d02224d7",
+ "@id": "urn:c9b41c2e-95ef-41ff-ab0e-6ebafe11329d",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -284,57 +284,57 @@
}
},
{
- "@id": "urn:f33a292b-a905-408f-ba76-441a2058a27b",
+ "@id": "urn:2714f869-ac76-4842-8998-8d005cbe8b00",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:7271accf-6874-4774-8e77-f2c8317f2b9b"
+ "GeneratedBy": "urn:a9c4648d-41a0-4fe4-90e6-41b5f0a72d3e"
},
{
- "@id": "urn:95b6a627-a7cb-4607-b603-d359f8b3c75c",
+ "@id": "urn:8bc12560-688d-456f-909d-dc9eda67b073",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:acc7bdb5-8fac-4151-8026-d741958f047d"
+ "GeneratedBy": "urn:dcb7674a-1e3c-411c-95d8-0e4fc5aab43e"
},
{
- "@id": "urn:c3acf82f-0adc-4874-bd69-b28b507542c7",
+ "@id": "urn:835d8881-a887-40b8-9960-a4fc64ada68c",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:4dc466e1-b429-43bb-b880-add7232b7347"
+ "GeneratedBy": "urn:927af817-f93a-489f-a7f9-8042ef2bd242"
},
{
- "@id": "urn:b5c075e3-f245-4bc9-8cc4-d55eec21091e",
+ "@id": "urn:bec98c26-9830-48d9-9ac8-1b988eb49dbf",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:3625a84c-5333-49e0-86c1-737bfc8d7f7a"
+ "GeneratedBy": "urn:76125b99-5fb8-4a46-9b93-8ff9cd4e3e70"
},
{
- "@id": "urn:b5bab357-1440-40f7-a07a-e81de6dee8b8",
+ "@id": "urn:34dbf791-6f89-4a89-aee7-1908de2b5835",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:dda87c51-4f5a-49b0-928d-a53c9b3c47f6"
+ "GeneratedBy": "urn:c6b77905-a877-4bf7-bb02-8b2c581b45a6"
},
{
- "@id": "urn:d254e790-3eb0-457a-a728-94483f898737",
+ "@id": "urn:cdf01b16-5de4-40b6-9a04-768396aa5a90",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "GeneratedBy": "urn:63dd083a-b6c0-4169-bdc1-5b4c478ae687",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:1a0a3bff-cc42-4522-8a1b-0ec281a16e51",
+ "@id": "urn:8ebafb08-97b1-4df0-bcd0-c9dbac423ea5",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:7cd59bc5-33fb-4897-b2bb-5cfee20798ee",
+ "GeneratedBy": "urn:63dd083a-b6c0-4169-bdc1-5b4c478ae687",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:a4f12a49-cdd0-4f79-8ec4-1e30561765ee",
+ "@id": "urn:6fa4a3dc-b817-41d3-855c-7932de8c100a",
"Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:920dddce-28c6-421c-882c-9a68550b6b34"
+ "GeneratedBy": "urn:fcbb6d50-3a39-441e-8ef0-33ce03204491"
},
{
- "@id": "urn:3f64e75a-698c-4349-9f6a-7bd538d135df",
+ "@id": "urn:e890a08f-17db-4033-95ea-b7cf9d1b867a",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -342,24 +342,24 @@
}
},
{
- "@id": "urn:31571f6d-d8ca-4c66-a64a-c2a2a88753d4",
+ "@id": "urn:c7b12f74-8c20-4dd8-9a5c-254c67cbf054",
"Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:7437f41a-5203-4d70-ac17-53d387d4947b"
+ "GeneratedBy": "urn:87df8dbe-2e41-469e-8d14-659937a28e3b"
},
{
- "@id": "urn:924f0baf-a156-4e39-835b-4b9974948de2",
+ "@id": "urn:4e8eb6a1-96ac-4d65-8d34-d2db225432c4",
"Label": "SPM.mat",
- "GeneratedBy": "urn:aca48b64-0f58-44c1-bf54-eb7e9089f5b9"
+ "GeneratedBy": "urn:3878d997-9e11-4659-8125-0da6e3e3551b"
},
{
- "@id": "urn:7a6d6abf-77ee-4c02-a123-ba97020ff74c",
+ "@id": "urn:ce6239a0-e326-47c3-b7d0-1ee3963c36b4",
"Label": "SPM.mat",
- "GeneratedBy": "urn:7d6a5166-4869-456a-a070-411d9eaf76b3"
+ "GeneratedBy": "urn:1a0cb55a-5189-4fdb-9433-3e72793bd1b5"
},
{
- "@id": "urn:9d7031f9-b790-4f40-b4db-a36f7f1cdd18",
+ "@id": "urn:33ae67f5-2af6-4277-998e-aa229e2f8b26",
"Label": "SPM.mat",
- "GeneratedBy": "urn:5c0e3a05-6e09-4bc9-bb52-e8c4c019ce22"
+ "GeneratedBy": "urn:72e5bfd9-a294-46c1-b247-b738f3b081c0"
}
]
}
diff --git a/examples/from_parsers/spm/spm_2_t_test_batch.png b/examples/from_parsers/spm/spm_2_t_test_batch.png
index 7716f528f..374c20d84 100644
Binary files a/examples/from_parsers/spm/spm_2_t_test_batch.png and b/examples/from_parsers/spm/spm_2_t_test_batch.png differ
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
index deb111d9b..f5a90f358 100644
--- a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
+++ b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "@id": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:6a389401-d37b-4c0e-89e2-a748ed2a46af",
+ "@id": "urn:6861a623-9c0f-4e38-a22e-5c2ca462fefb",
"Label": "Move file",
"Used": [
- "urn:360c6e24-8ef1-4e78-a20c-4f1e6ebabc67"
+ "urn:0793c7ec-0feb-4aa0-bfb0-f2c1a23e3df6"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:0132a039-6f29-43c3-95e5-c1f46d2f6919",
+ "@id": "urn:935da944-c6e7-430f-9fd4-6b451d957275",
"Label": "Move file",
"Used": [
- "urn:96d45e7e-9830-4d18-bab2-b0968b5f6d40"
+ "urn:56324442-e0d7-4e0a-a988-0b3618c3a03e"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:e7fa77d8-7c17-453f-bf44-06a83aa361fb",
+ "@id": "urn:3c5556a5-3f9b-487c-8fb1-83537d211fe6",
"Label": "Gunzip",
"Used": [
- "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610"
+ "urn:64dd7975-86f9-4f68-af87-ef3e6a3149c4"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:35351fd9-63f9-465b-8b5f-9d5214224587",
+ "@id": "urn:48eb8fc4-4dde-4276-913a-35e1c1dcd0e2",
"Label": "Gunzip",
"Used": [
- "urn:4405e61e-5f17-478e-8619-f860c4f23e39"
+ "urn:1b1ff05f-85fe-4337-80e1-7a9b9cde64fc"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:1d237c07-a52d-4a05-81d5-bbabc95bf4d5",
+ "@id": "urn:14f4eefc-3419-4c20-b7f1-518348efbefb",
"Label": "Realign",
"Used": [
- "urn:03d5f94b-379d-43ba-82a1-346e22e37619"
+ "urn:592a3b92-acfc-4483-a533-fe9b09f9012d"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:cc63cbf1-a938-4f36-94b0-28d7334c06ff",
+ "@id": "urn:1ee453c4-5765-48b9-8227-12962cdb6860",
"Label": "Coregister",
"Used": [
- "urn:2420bc5d-17a3-48d3-9182-fcca102bd8bf",
- "urn:8270d8d8-058e-45d1-bcc6-2073d90606e5"
+ "urn:34c2680b-4c77-468f-9b0a-94210ada4c1f",
+ "urn:a30e819a-5b66-4fb4-ada6-e07513b0c982"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:d5c97dfd-bc9a-4c8f-bd4f-fa5162003600",
+ "@id": "urn:48d1fa50-189a-4908-baba-601a43a8f22d",
"Label": "Segment",
"Used": [
- "urn:2420bc5d-17a3-48d3-9182-fcca102bd8bf"
+ "urn:34c2680b-4c77-468f-9b0a-94210ada4c1f"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:1bea0f51-9adc-43ee-8606-9199fe51d37c",
+ "@id": "urn:054e71ab-2edf-478c-802e-c7e68a254970",
"Label": "Normalize",
"Used": [
- "urn:8270d8d8-058e-45d1-bcc6-2073d90606e5",
- "urn:f4931a39-0143-4666-b2d0-ea5a028c7585"
+ "urn:a30e819a-5b66-4fb4-ada6-e07513b0c982",
+ "urn:ef48de35-484e-4f6e-bccc-353b7247adc5"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:90f71712-65b6-4afd-9375-13f368a3ae90",
+ "@id": "urn:76a2a86f-3b5d-43d4-a38a-337f94d822dd",
"Label": "Normalize",
"Used": [
- "urn:f4931a39-0143-4666-b2d0-ea5a028c7585"
+ "urn:ef48de35-484e-4f6e-bccc-353b7247adc5"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:06099155-3078-41fa-b2dd-38b491373a17",
+ "@id": "urn:7a33b535-f02d-40b4-9e48-b6e94aeee80b",
"Label": "Smooth",
"Used": [
- "urn:d2d3e2a4-d1c8-4526-981d-515d6e512abc"
+ "urn:fdcb6c32-a4be-4021-b672-192113a2f992"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:b38636c2-8db1-4744-9952-28a75ff3368d",
+ "@id": "urn:3fe1918e-0921-403c-aff5-bd68b8f11bf4",
"Label": "Stat Design",
"Used": [
- "urn:f3d0fe4f-37ea-4f4c-a67b-d761a2d2c64e",
- "urn:76cf5f17-a795-4078-8068-c9e841f985ec"
+ "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
+ "urn:f88935b4-f79e-4b80-98b6-0842df6f8e9c"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 1];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_HRF_informed_basis'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:5930e704-0004-4552-aea9-a0eeceb4c5fd",
+ "@id": "urn:1abb6b74-47f8-4ecd-bf39-ce9eb36d5274",
"Label": "Estimate stat.",
"Used": [
- "urn:c6e14ecb-e59d-4623-9d39-1adedd84a242"
+ "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:d1ae6edb-eb2d-4090-8a91-27b487473beb",
+ "@id": "urn:ca984797-be7e-42b0-9135-ca32141717b4",
"Label": "Estimate contrast",
"Used": [
- "urn:fbee7fb9-d4f2-4e42-a7f6-b373c25c08be"
+ "urn:c381eab2-82cf-4d7e-bd79-c2b030ef9e99"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:0bb1792b-9b25-46e4-b72e-c2be6f624712",
+ "@id": "urn:ba4263cb-024a-40f0-8b09-48834d5a2245",
"Label": "Threshold",
"Used": [
- "urn:5ecaa27a-d8dc-48bf-acb6-e3c9283ad0b8"
+ "urn:fde13367-6de1-4a55-9b52-eba74f0cd730"
],
- "AssociatedWith": "urn:64836f0e-e8b3-40d6-9247-a8e347c4ccdc",
+ "AssociatedWith": "urn:055eaf97-6c38-407b-afaf-83c13f4f416a",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:360c6e24-8ef1-4e78-a20c-4f1e6ebabc67",
+ "@id": "urn:0793c7ec-0feb-4aa0-bfb0-f2c1a23e3df6",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:96d45e7e-9830-4d18-bab2-b0968b5f6d40",
+ "@id": "urn:56324442-e0d7-4e0a-a988-0b3618c3a03e",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:8e3dccf2-4041-43a7-ae8e-c6693ee12610",
+ "@id": "urn:64dd7975-86f9-4f68-af87-ef3e6a3149c4",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:6a389401-d37b-4c0e-89e2-a748ed2a46af"
+ "GeneratedBy": "urn:6861a623-9c0f-4e38-a22e-5c2ca462fefb"
},
{
- "@id": "urn:4405e61e-5f17-478e-8619-f860c4f23e39",
+ "@id": "urn:1b1ff05f-85fe-4337-80e1-7a9b9cde64fc",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:0132a039-6f29-43c3-95e5-c1f46d2f6919"
+ "GeneratedBy": "urn:935da944-c6e7-430f-9fd4-6b451d957275"
},
{
- "@id": "urn:03d5f94b-379d-43ba-82a1-346e22e37619",
+ "@id": "urn:592a3b92-acfc-4483-a533-fe9b09f9012d",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:e7fa77d8-7c17-453f-bf44-06a83aa361fb"
+ "GeneratedBy": "urn:3c5556a5-3f9b-487c-8fb1-83537d211fe6"
},
{
- "@id": "urn:8270d8d8-058e-45d1-bcc6-2073d90606e5",
+ "@id": "urn:a30e819a-5b66-4fb4-ada6-e07513b0c982",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:1d237c07-a52d-4a05-81d5-bbabc95bf4d5"
+ "GeneratedBy": "urn:14f4eefc-3419-4c20-b7f1-518348efbefb"
},
{
- "@id": "urn:2420bc5d-17a3-48d3-9182-fcca102bd8bf",
+ "@id": "urn:34c2680b-4c77-468f-9b0a-94210ada4c1f",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:35351fd9-63f9-465b-8b5f-9d5214224587"
+ "GeneratedBy": "urn:48eb8fc4-4dde-4276-913a-35e1c1dcd0e2"
},
{
- "@id": "urn:f4931a39-0143-4666-b2d0-ea5a028c7585",
+ "@id": "urn:ef48de35-484e-4f6e-bccc-353b7247adc5",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:d5c97dfd-bc9a-4c8f-bd4f-fa5162003600",
+ "GeneratedBy": "urn:48d1fa50-189a-4908-baba-601a43a8f22d",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:53cb7ce5-86d5-486f-b549-3d7bc5744529",
+ "@id": "urn:5e64a756-8f63-4ddf-97fd-1852bbaa7597",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:d5c97dfd-bc9a-4c8f-bd4f-fa5162003600",
+ "GeneratedBy": "urn:48d1fa50-189a-4908-baba-601a43a8f22d",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:d2d3e2a4-d1c8-4526-981d-515d6e512abc",
+ "@id": "urn:fdcb6c32-a4be-4021-b672-192113a2f992",
"Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:1bea0f51-9adc-43ee-8606-9199fe51d37c"
+ "GeneratedBy": "urn:054e71ab-2edf-478c-802e-c7e68a254970"
},
{
- "@id": "urn:76cf5f17-a795-4078-8068-c9e841f985ec",
+ "@id": "urn:f88935b4-f79e-4b80-98b6-0842df6f8e9c",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:f3d0fe4f-37ea-4f4c-a67b-d761a2d2c64e",
+ "@id": "urn:b892fe98-5562-4bfd-9917-df93c8ea7c93",
"Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:06099155-3078-41fa-b2dd-38b491373a17"
+ "GeneratedBy": "urn:7a33b535-f02d-40b4-9e48-b6e94aeee80b"
},
{
- "@id": "urn:c6e14ecb-e59d-4623-9d39-1adedd84a242",
+ "@id": "urn:ad48371d-a0aa-40e9-87c1-3d835c7d9bc4",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b38636c2-8db1-4744-9952-28a75ff3368d"
+ "GeneratedBy": "urn:3fe1918e-0921-403c-aff5-bd68b8f11bf4"
},
{
- "@id": "urn:fbee7fb9-d4f2-4e42-a7f6-b373c25c08be",
+ "@id": "urn:c381eab2-82cf-4d7e-bd79-c2b030ef9e99",
"Label": "SPM.mat",
- "GeneratedBy": "urn:5930e704-0004-4552-aea9-a0eeceb4c5fd"
+ "GeneratedBy": "urn:1abb6b74-47f8-4ecd-bf39-ce9eb36d5274"
},
{
- "@id": "urn:5ecaa27a-d8dc-48bf-acb6-e3c9283ad0b8",
+ "@id": "urn:fde13367-6de1-4a55-9b52-eba74f0cd730",
"Label": "SPM.mat",
- "GeneratedBy": "urn:d1ae6edb-eb2d-4090-8a91-27b487473beb"
+ "GeneratedBy": "urn:ca984797-be7e-42b0-9135-ca32141717b4"
}
]
}
diff --git a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png
index 4b1853b4b..3965541e7 100644
Binary files a/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png and b/examples/from_parsers/spm/spm_HRF_informed_basis_batch.png differ
diff --git a/examples/from_parsers/spm/spm_con_f_batch.jsonld b/examples/from_parsers/spm/spm_con_f_batch.jsonld
index dcbb0137d..146099ff4 100644
--- a/examples/from_parsers/spm/spm_con_f_batch.jsonld
+++ b/examples/from_parsers/spm/spm_con_f_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "@id": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:9ab5110c-2de7-4074-8985-e7f7624951ff",
+ "@id": "urn:e0b8e2c6-9b28-45cb-8b45-721cdee3dcc0",
"Label": "Move file",
"Used": [
- "urn:3a4ffa60-001e-4864-aabd-3fa1bda050cb"
+ "urn:b5eac9fd-9254-4683-accf-f45cc6caaa64"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:a795b30c-e2ac-4510-8f49-b5d49d5a2666",
+ "@id": "urn:a49dacf2-01e0-4a32-aa85-02ab54a8d3b9",
"Label": "Move file",
"Used": [
- "urn:73f49fa2-a12e-4869-9bfd-c898044cd642"
+ "urn:73cd9e98-c666-404b-ae9b-7ac11c80b23f"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:1ee7bfb1-a896-4325-bde8-0aee923af16e",
+ "@id": "urn:c55fd982-cc22-464f-b285-58e9263ad25a",
"Label": "Gunzip",
"Used": [
- "urn:28f3ad86-7bbc-4bad-935d-7d4416682ba1"
+ "urn:6f086e2c-b943-4856-a4e4-b79e5ce78fb0"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:9bbaf345-c3e8-47fd-a68f-a115deca9946",
+ "@id": "urn:5255d402-08a6-4dd0-aefa-d239d213fce0",
"Label": "Gunzip",
"Used": [
- "urn:b431f690-cccb-41b1-9946-d52280b64525"
+ "urn:b591798c-d607-4b73-9ffd-0e7d6e22f4bb"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:66df70be-6cf3-4590-b1fe-898c0378e681",
+ "@id": "urn:f82cd723-49bf-43c0-a2d9-438e84b33318",
"Label": "Realign",
"Used": [
- "urn:a9ebcc48-ff9b-43ff-a6e2-e563f373103c"
+ "urn:2777a5ba-b8f6-4bb8-8a26-ff00ab683a62"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:b256c6cc-10b0-4f1b-a9a6-4fedf605381c",
+ "@id": "urn:d500e66c-aacc-4dde-8d83-ba94a5898c5b",
"Label": "Coregister",
"Used": [
- "urn:3712e048-0291-4277-83db-2089489d7987",
- "urn:76e92e1e-d7b6-44bc-ba6f-020b033a4523"
+ "urn:62a462c1-c20a-4255-b51a-4b0d02ff5a35",
+ "urn:e6997f21-9f7f-4f04-8936-c6985a945567"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:c490c359-1750-4d0e-9787-223cd2eb9efa",
+ "@id": "urn:23be68f7-c7f8-4eb2-b641-133be843e323",
"Label": "Segment",
"Used": [
- "urn:76e92e1e-d7b6-44bc-ba6f-020b033a4523"
+ "urn:e6997f21-9f7f-4f04-8936-c6985a945567"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:3fe69852-da91-41b2-b340-855464860260",
+ "@id": "urn:11f7d34b-6364-461b-af8e-ce7c7f9de369",
"Label": "Normalize",
"Used": [
- "urn:3712e048-0291-4277-83db-2089489d7987",
- "urn:682b3ad7-d506-48e4-924b-4aebb0a78f3c"
+ "urn:0df9b60d-731f-4e80-8d0b-bd8d32e8516b",
+ "urn:62a462c1-c20a-4255-b51a-4b0d02ff5a35"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:17d2cc88-4bae-4444-9530-b8c84f76341b",
+ "@id": "urn:0d815f16-c415-42d7-aab4-08caece2120f",
"Label": "Normalize",
"Used": [
- "urn:682b3ad7-d506-48e4-924b-4aebb0a78f3c"
+ "urn:0df9b60d-731f-4e80-8d0b-bd8d32e8516b"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:4c93db26-2d28-4a0a-ae59-ad5223a53e78",
+ "@id": "urn:08595e41-b6d0-4515-b786-e782353f3718",
"Label": "Smooth",
"Used": [
- "urn:f2a705dd-336d-40f8-bccc-2e62a0d1defb"
+ "urn:66375eb5-3649-457d-a56b-f5e53f3e3cf7"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:e4f4fc74-1ff9-4ecb-b55d-1dbdc28d771a",
+ "@id": "urn:18b0a656-3c03-498e-b5c1-fa41f1592e42",
"Label": "Stat Design",
"Used": [
- "urn:f8600926-68f6-46c9-bf0e-93641c333839",
- "urn:5e9a57b8-7d11-4db6-b1f9-8dea85ffd7de"
+ "urn:57001d88-00d9-4253-9041-85ab5a01963a",
+ "urn:9ffffff2-cbde-492e-826e-c36fa45269c4"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_f_test'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:ead1b8a3-9a6c-4821-b8b5-c47b5913f8b4",
+ "@id": "urn:fb9c408c-80e0-4ff0-b375-4886297f18bf",
"Label": "Estimate stat.",
"Used": [
- "urn:ab7c113a-12d1-4e0a-b4bf-bb15c9087274"
+ "urn:6dd32c60-529c-4e5e-b6d5-67ab04a4796f"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:92942894-91d4-46da-a851-212428e5ffd6",
+ "@id": "urn:bd48635b-88cf-43db-8e3d-0c149fc6cbbb",
"Label": "Estimate contrast",
"Used": [
- "urn:8f37612b-f99e-4cbe-8b56-6eec4e0cb0a5"
+ "urn:26abca2c-13dd-49f6-8680-caa46c170d5f"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.fcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:13201da7-d050-4ca2-bee2-a1986bb0104d",
+ "@id": "urn:4cb49b45-2fc1-44d0-b942-81ef74816b9e",
"Label": "Threshold",
"Used": [
- "urn:82715994-f108-4d17-ba20-8b5e1fe14ac3"
+ "urn:c141d9b9-99a2-4453-ac73-a8fd148700f6"
],
- "AssociatedWith": "urn:13a4d608-cdc4-4bb7-913a-ef1580a4804d",
+ "AssociatedWith": "urn:7bd5dc94-90f0-4d26-b304-d5ecea6af65e",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:3a4ffa60-001e-4864-aabd-3fa1bda050cb",
+ "@id": "urn:b5eac9fd-9254-4683-accf-f45cc6caaa64",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:73f49fa2-a12e-4869-9bfd-c898044cd642",
+ "@id": "urn:73cd9e98-c666-404b-ae9b-7ac11c80b23f",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:28f3ad86-7bbc-4bad-935d-7d4416682ba1",
+ "@id": "urn:6f086e2c-b943-4856-a4e4-b79e5ce78fb0",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:9ab5110c-2de7-4074-8985-e7f7624951ff"
+ "GeneratedBy": "urn:e0b8e2c6-9b28-45cb-8b45-721cdee3dcc0"
},
{
- "@id": "urn:b431f690-cccb-41b1-9946-d52280b64525",
+ "@id": "urn:b591798c-d607-4b73-9ffd-0e7d6e22f4bb",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:a795b30c-e2ac-4510-8f49-b5d49d5a2666"
+ "GeneratedBy": "urn:a49dacf2-01e0-4a32-aa85-02ab54a8d3b9"
},
{
- "@id": "urn:a9ebcc48-ff9b-43ff-a6e2-e563f373103c",
+ "@id": "urn:2777a5ba-b8f6-4bb8-8a26-ff00ab683a62",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:1ee7bfb1-a896-4325-bde8-0aee923af16e"
+ "GeneratedBy": "urn:c55fd982-cc22-464f-b285-58e9263ad25a"
},
{
- "@id": "urn:3712e048-0291-4277-83db-2089489d7987",
+ "@id": "urn:62a462c1-c20a-4255-b51a-4b0d02ff5a35",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:66df70be-6cf3-4590-b1fe-898c0378e681"
+ "GeneratedBy": "urn:f82cd723-49bf-43c0-a2d9-438e84b33318"
},
{
- "@id": "urn:76e92e1e-d7b6-44bc-ba6f-020b033a4523",
+ "@id": "urn:e6997f21-9f7f-4f04-8936-c6985a945567",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:9bbaf345-c3e8-47fd-a68f-a115deca9946"
+ "GeneratedBy": "urn:5255d402-08a6-4dd0-aefa-d239d213fce0"
},
{
- "@id": "urn:682b3ad7-d506-48e4-924b-4aebb0a78f3c",
+ "@id": "urn:0df9b60d-731f-4e80-8d0b-bd8d32e8516b",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:c490c359-1750-4d0e-9787-223cd2eb9efa",
+ "GeneratedBy": "urn:23be68f7-c7f8-4eb2-b641-133be843e323",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:e55cc102-2c9b-412f-872d-4338f24b718f",
+ "@id": "urn:d5163407-701a-404f-9edd-ef1427791617",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:c490c359-1750-4d0e-9787-223cd2eb9efa",
+ "GeneratedBy": "urn:23be68f7-c7f8-4eb2-b641-133be843e323",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:f2a705dd-336d-40f8-bccc-2e62a0d1defb",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:3fe69852-da91-41b2-b340-855464860260"
+ "@id": "urn:66375eb5-3649-457d-a56b-f5e53f3e3cf7",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:11f7d34b-6364-461b-af8e-ce7c7f9de369"
},
{
- "@id": "urn:5e9a57b8-7d11-4db6-b1f9-8dea85ffd7de",
+ "@id": "urn:9ffffff2-cbde-492e-826e-c36fa45269c4",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:f8600926-68f6-46c9-bf0e-93641c333839",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:4c93db26-2d28-4a0a-ae59-ad5223a53e78"
+ "@id": "urn:57001d88-00d9-4253-9041-85ab5a01963a",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:08595e41-b6d0-4515-b786-e782353f3718"
},
{
- "@id": "urn:ab7c113a-12d1-4e0a-b4bf-bb15c9087274",
+ "@id": "urn:6dd32c60-529c-4e5e-b6d5-67ab04a4796f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:e4f4fc74-1ff9-4ecb-b55d-1dbdc28d771a"
+ "GeneratedBy": "urn:18b0a656-3c03-498e-b5c1-fa41f1592e42"
},
{
- "@id": "urn:8f37612b-f99e-4cbe-8b56-6eec4e0cb0a5",
+ "@id": "urn:26abca2c-13dd-49f6-8680-caa46c170d5f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:ead1b8a3-9a6c-4821-b8b5-c47b5913f8b4"
+ "GeneratedBy": "urn:fb9c408c-80e0-4ff0-b375-4886297f18bf"
},
{
- "@id": "urn:82715994-f108-4d17-ba20-8b5e1fe14ac3",
+ "@id": "urn:c141d9b9-99a2-4453-ac73-a8fd148700f6",
"Label": "SPM.mat",
- "GeneratedBy": "urn:92942894-91d4-46da-a851-212428e5ffd6"
+ "GeneratedBy": "urn:bd48635b-88cf-43db-8e3d-0c149fc6cbbb"
}
]
}
diff --git a/examples/from_parsers/spm/spm_con_f_batch.png b/examples/from_parsers/spm/spm_con_f_batch.png
index 2fdff4d45..0256a25e4 100644
Binary files a/examples/from_parsers/spm/spm_con_f_batch.png and b/examples/from_parsers/spm/spm_con_f_batch.png differ
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
index b91956ef2..b5f9fcd59 100644
--- a/examples/from_parsers/spm/spm_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_conjunction_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "@id": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:305ec05b-5014-44e6-984a-2ea39883ade6",
+ "@id": "urn:95b80c3c-7b6a-40ff-97b5-9e1b96f0bfb7",
"Label": "Move file",
"Used": [
- "urn:fa8342fe-9330-4fbe-8c69-740405630269"
+ "urn:9636addd-4ce7-45df-a999-e6e6136f6bd5"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:8f20272a-5850-41f9-8c75-e24c8dcb1a93",
+ "@id": "urn:9784fc8e-7627-4dbb-8abc-886296d00f0e",
"Label": "Move file",
"Used": [
- "urn:8b0df28d-d3ef-4a15-9789-745572110d2a"
+ "urn:1a01b370-3827-4cae-a220-12911e53e9c2"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:f1ae068f-bd6c-4f5e-990f-bc158d798aa4",
+ "@id": "urn:00752b92-e109-448b-997f-b3ea8196cd92",
"Label": "Gunzip",
"Used": [
- "urn:efbf63f3-1453-44d7-943f-5ad271b15594"
+ "urn:f4788744-9fd7-46ff-ab58-b82a497af808"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:1ab1395a-bd77-4c9c-97e0-6e01726808ce",
+ "@id": "urn:65fc4b87-9264-42a7-9b71-53ce3afb9822",
"Label": "Gunzip",
"Used": [
- "urn:9c1ff056-0888-4199-b1a4-4c11252dcc8f"
+ "urn:5c4343d6-8bff-477b-9505-6886037bf8fa"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:8d19bcea-aa4e-45f1-9578-7d62a781c5d9",
+ "@id": "urn:c68b3c77-38d0-407c-830b-967321f739a9",
"Label": "Realign",
"Used": [
- "urn:3474c8cd-db1d-499b-a758-30039fb6ad37"
+ "urn:9f50245f-1c7a-46b8-ad97-1b9ddd842bd1"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:f10a5ad8-0374-4fc2-ad92-70ddf88959c8",
+ "@id": "urn:9bc6ddb2-0e44-4319-9930-3448025da245",
"Label": "Coregister",
"Used": [
- "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
- "urn:c66ec06e-eab2-4719-91c5-e81f8f54c33f"
+ "urn:0f413d1b-22ea-42e5-9d8f-a8ed53c5e448",
+ "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:9dce6e79-71ef-43e8-997d-4841605ad7c3",
+ "@id": "urn:df900226-398d-422c-963e-eee25dd764b6",
"Label": "Segment",
"Used": [
- "urn:c66ec06e-eab2-4719-91c5-e81f8f54c33f"
+ "urn:0f413d1b-22ea-42e5-9d8f-a8ed53c5e448"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:67c1a9ac-c5ad-4a62-9f8c-1bc385fbd286",
+ "@id": "urn:0c1e9eef-fa09-4004-ba3d-9269e91e41ed",
"Label": "Normalize",
"Used": [
- "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
- "urn:fb5b492a-60c2-449b-8413-fd136b506cd7"
+ "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4",
+ "urn:cf553d10-a526-4f50-b4bf-2ab75e14e197"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:3fd6b10a-ad16-41ce-987c-d9b67e25d95e",
+ "@id": "urn:81217ec8-dd0d-414e-bb72-4f7b170531f9",
"Label": "Normalize",
"Used": [
- "urn:fb5b492a-60c2-449b-8413-fd136b506cd7"
+ "urn:cf553d10-a526-4f50-b4bf-2ab75e14e197"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:0723034d-fc73-4fc4-9deb-605b9add0ee7",
+ "@id": "urn:d7935d12-a9c6-4de2-b227-19088bf23c08",
"Label": "Smooth",
"Used": [
- "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97"
+ "urn:b74b2e69-5eae-469c-9329-47e283140a24"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:0134c831-73b9-47b6-80a6-41535abaf825",
+ "@id": "urn:805c6a5b-bfd8-490d-b82c-7ff27e623d49",
"Label": "Stat Design",
"Used": [
- "urn:64b3106f-d986-42e5-bea5-ad79de7eed00",
- "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a"
+ "urn:47f5a58a-0751-4784-97be-0a8a6cb33e01",
+ "urn:3c1543d8-4784-4ffc-991d-1d6fd4cfa75d"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_partial_conjunction'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:086568a2-e38c-44a5-ac87-7bbb46fb1215",
+ "@id": "urn:470b8ae8-b596-423a-b519-6bdc19f0efed",
"Label": "Estimate stat.",
"Used": [
- "urn:76f8224d-55bf-46a5-bc7f-2973c300c08f"
+ "urn:c352cad6-7335-4623-ba36-f09dfed46807"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15",
+ "@id": "urn:f567c240-e857-4d6f-a6f7-5ace565663fc",
"Label": "Estimate contrast",
"Used": [
- "urn:9f26b129-9763-4b04-860e-3f44465c99ad"
+ "urn:9ee7d045-60cc-4630-9ecb-3a0d2d2c9ce5"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:b5d49317-69e9-4232-b911-58eab6897675",
+ "@id": "urn:faa033ad-6397-4a90-9967-81e2735c7665",
"Label": "Threshold",
"Used": [
- "urn:91ccbfe0-c5ec-43f2-92a1-79ae778813a9"
+ "urn:39e7b263-5bae-4497-82b1-de55fdb34cf3"
],
- "AssociatedWith": "urn:22e1f72a-aab4-4f7e-a6f5-e198f6c0ceff",
+ "AssociatedWith": "urn:78841fc2-5796-4cc5-9c0e-afab1681ff6b",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,7 +268,7 @@
],
"Entities": [
{
- "@id": "urn:fa8342fe-9330-4fbe-8c69-740405630269",
+ "@id": "urn:9636addd-4ce7-45df-a999-e6e6136f6bd5",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -276,7 +276,7 @@
}
},
{
- "@id": "urn:8b0df28d-d3ef-4a15-9789-745572110d2a",
+ "@id": "urn:1a01b370-3827-4cae-a220-12911e53e9c2",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -284,57 +284,57 @@
}
},
{
- "@id": "urn:efbf63f3-1453-44d7-943f-5ad271b15594",
+ "@id": "urn:f4788744-9fd7-46ff-ab58-b82a497af808",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:305ec05b-5014-44e6-984a-2ea39883ade6"
+ "GeneratedBy": "urn:95b80c3c-7b6a-40ff-97b5-9e1b96f0bfb7"
},
{
- "@id": "urn:9c1ff056-0888-4199-b1a4-4c11252dcc8f",
+ "@id": "urn:5c4343d6-8bff-477b-9505-6886037bf8fa",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:8f20272a-5850-41f9-8c75-e24c8dcb1a93"
+ "GeneratedBy": "urn:9784fc8e-7627-4dbb-8abc-886296d00f0e"
},
{
- "@id": "urn:3474c8cd-db1d-499b-a758-30039fb6ad37",
+ "@id": "urn:9f50245f-1c7a-46b8-ad97-1b9ddd842bd1",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:f1ae068f-bd6c-4f5e-990f-bc158d798aa4"
+ "GeneratedBy": "urn:00752b92-e109-448b-997f-b3ea8196cd92"
},
{
- "@id": "urn:714cd3ec-0190-4792-93f3-8c566734b8a4",
+ "@id": "urn:30c8cd54-1653-4cff-86ea-7ad669b107a4",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8d19bcea-aa4e-45f1-9578-7d62a781c5d9"
+ "GeneratedBy": "urn:c68b3c77-38d0-407c-830b-967321f739a9"
},
{
- "@id": "urn:c66ec06e-eab2-4719-91c5-e81f8f54c33f",
+ "@id": "urn:0f413d1b-22ea-42e5-9d8f-a8ed53c5e448",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:1ab1395a-bd77-4c9c-97e0-6e01726808ce"
+ "GeneratedBy": "urn:65fc4b87-9264-42a7-9b71-53ce3afb9822"
},
{
- "@id": "urn:fb5b492a-60c2-449b-8413-fd136b506cd7",
+ "@id": "urn:cf553d10-a526-4f50-b4bf-2ab75e14e197",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:9dce6e79-71ef-43e8-997d-4841605ad7c3",
+ "GeneratedBy": "urn:df900226-398d-422c-963e-eee25dd764b6",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:f1ebdf2e-24f8-49fd-8cf4-c135b087159d",
+ "@id": "urn:2b597991-b55c-470b-93e4-7495b66a06e7",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:9dce6e79-71ef-43e8-997d-4841605ad7c3",
+ "GeneratedBy": "urn:df900226-398d-422c-963e-eee25dd764b6",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:9f72ed22-2e83-4615-b7d0-34dd51fb3a97",
+ "@id": "urn:b74b2e69-5eae-469c-9329-47e283140a24",
"Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:67c1a9ac-c5ad-4a62-9f8c-1bc385fbd286"
+ "GeneratedBy": "urn:0c1e9eef-fa09-4004-ba3d-9269e91e41ed"
},
{
- "@id": "urn:e648781f-7a62-4523-8c8c-24cc9bfea61a",
+ "@id": "urn:3c1543d8-4784-4ffc-991d-1d6fd4cfa75d",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -342,24 +342,24 @@
}
},
{
- "@id": "urn:64b3106f-d986-42e5-bea5-ad79de7eed00",
+ "@id": "urn:47f5a58a-0751-4784-97be-0a8a6cb33e01",
"Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:0723034d-fc73-4fc4-9deb-605b9add0ee7"
+ "GeneratedBy": "urn:d7935d12-a9c6-4de2-b227-19088bf23c08"
},
{
- "@id": "urn:76f8224d-55bf-46a5-bc7f-2973c300c08f",
+ "@id": "urn:c352cad6-7335-4623-ba36-f09dfed46807",
"Label": "SPM.mat",
- "GeneratedBy": "urn:0134c831-73b9-47b6-80a6-41535abaf825"
+ "GeneratedBy": "urn:805c6a5b-bfd8-490d-b82c-7ff27e623d49"
},
{
- "@id": "urn:9f26b129-9763-4b04-860e-3f44465c99ad",
+ "@id": "urn:9ee7d045-60cc-4630-9ecb-3a0d2d2c9ce5",
"Label": "SPM.mat",
- "GeneratedBy": "urn:086568a2-e38c-44a5-ac87-7bbb46fb1215"
+ "GeneratedBy": "urn:470b8ae8-b596-423a-b519-6bdc19f0efed"
},
{
- "@id": "urn:91ccbfe0-c5ec-43f2-92a1-79ae778813a9",
+ "@id": "urn:39e7b263-5bae-4497-82b1-de55fdb34cf3",
"Label": "SPM.mat",
- "GeneratedBy": "urn:8ae4d11f-5d8d-474d-b00b-f7e5c882df15"
+ "GeneratedBy": "urn:f567c240-e857-4d6f-a6f7-5ace565663fc"
}
]
}
diff --git a/examples/from_parsers/spm/spm_conjunction_batch.png b/examples/from_parsers/spm/spm_conjunction_batch.png
index 95a6af086..81204cf12 100644
Binary files a/examples/from_parsers/spm/spm_conjunction_batch.png and b/examples/from_parsers/spm/spm_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
index 53d127a0b..19ba3974d 100644
--- a/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_contrast_mask_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "@id": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:644ce011-3d1e-4984-ad9c-f5771f000747",
+ "@id": "urn:b9dd4585-53b2-46d3-86ef-605a4028c435",
"Label": "Move file",
"Used": [
- "urn:beaf7a4a-26f6-4baf-a898-33fed1de6dd1"
+ "urn:0a2bd5ea-a64e-42a0-ae31-150e7a1257b4"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:aec7fb9b-2ee8-4f2d-b523-9da2972acaab",
+ "@id": "urn:fad38cb7-5e1a-4f82-ac2d-4f0cc81b0b2a",
"Label": "Move file",
"Used": [
- "urn:20343da6-1dbe-4abe-861a-b3c8749af810"
+ "urn:cf18c935-d808-4855-94c8-ab1e8af5e711"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:a5959023-1022-4359-806f-b2d2fa6bce85",
+ "@id": "urn:4ece4936-b75e-4cdf-a4fa-c1748c3364db",
"Label": "Gunzip",
"Used": [
- "urn:32250610-6808-46b2-8175-f03e3be56a9a"
+ "urn:972af39b-8673-4ab8-a38f-f2424bc248af"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:0daa00f1-fd07-4481-a724-16ce22dd13cf",
+ "@id": "urn:d3e9b075-7f99-4789-a358-bfc920fed3c3",
"Label": "Gunzip",
"Used": [
- "urn:75d1ea2b-1272-4eb8-aad1-cb8e455ce9f0"
+ "urn:eefeb4b9-0344-4121-aee1-626e816354fc"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:b9d00692-dc98-4bf8-b0e2-d7c35a873be5",
+ "@id": "urn:d9c5d9f6-d211-47e7-993d-ca16b373b789",
"Label": "Realign",
"Used": [
- "urn:1b96acb1-26b2-42db-a786-caf863b571e7"
+ "urn:51a344a6-d5d1-479d-802c-4912345b4574"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:72e8ec45-e14e-4035-b432-ccb27ed7ab2f",
+ "@id": "urn:b25b166c-87b5-473b-a60f-ad6c25f3622e",
"Label": "Coregister",
"Used": [
- "urn:b4269c4f-f3a9-4fde-ba7c-9e73f98efa77",
- "urn:ff2dd0ff-ce32-4d9d-aac4-3af1f285e5ba"
+ "urn:1435c1bd-2e36-477a-b417-5f57093bedde",
+ "urn:22ef0778-033a-4fc5-871a-2d082718833a"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:1f63bf46-8dde-4d8f-8199-b6b9ea05798c",
+ "@id": "urn:8a3f7a24-c685-4532-be83-851ae63ca6ad",
"Label": "Segment",
"Used": [
- "urn:ff2dd0ff-ce32-4d9d-aac4-3af1f285e5ba"
+ "urn:1435c1bd-2e36-477a-b417-5f57093bedde"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:4d4a2763-06ec-4da4-91fc-e50f4ef7373d",
+ "@id": "urn:0f920aab-f8e2-487a-b2c8-77fdd14ff21c",
"Label": "Normalize",
"Used": [
- "urn:b4269c4f-f3a9-4fde-ba7c-9e73f98efa77",
- "urn:dcbb3e88-d6dd-4ce7-81f0-f836944dfb88"
+ "urn:22ef0778-033a-4fc5-871a-2d082718833a",
+ "urn:aa250c9a-a324-4cbb-bd5b-2eb21542af2a"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:712dbdb6-fac4-47f8-bb62-8b88c2a43a94",
+ "@id": "urn:aa69b8f4-4148-47a4-a8fa-9dfb4d9aae01",
"Label": "Normalize",
"Used": [
- "urn:dcbb3e88-d6dd-4ce7-81f0-f836944dfb88"
+ "urn:aa250c9a-a324-4cbb-bd5b-2eb21542af2a"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:ed09bfc0-4e0f-4033-bdc5-2697ab125380",
+ "@id": "urn:944ad4a8-6abe-44bb-835f-307b53b5e187",
"Label": "Smooth",
"Used": [
- "urn:8482b2ed-8b32-48db-8ea7-3d86c6427ac2"
+ "urn:b1b7f674-9292-490a-9b80-8d2a29faf9d4"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:558037a1-cb9f-4066-92ce-2310858450e1",
+ "@id": "urn:3a2c9ee8-541c-4bc9-8e5b-13a00b8688c7",
"Label": "Stat Design",
"Used": [
- "urn:3ee13e32-1c59-4bee-b8d6-3486ed62edbb",
- "urn:e12b1d9b-dced-4e3a-923b-d879b6c3d501"
+ "urn:346f2f07-2990-484f-9e23-d74ce972f99a",
+ "urn:246c334f-7c51-4acd-9d77-7d54242fd2d7"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:befcb32b-1565-4ced-83d3-a9528d221226",
+ "@id": "urn:a1f10b4f-25b3-4000-b3f6-31730c142bdc",
"Label": "Estimate stat.",
"Used": [
- "urn:327caea3-5cef-4821-a4fe-f2306d78ad61"
+ "urn:549cda09-ef87-4910-a306-2c99b47b18e2"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:8f8f67e0-f527-4ed5-b657-afd90db8078b",
+ "@id": "urn:20c82882-8ba2-4c91-9eb1-ab785bfec6fb",
"Label": "Estimate contrast",
"Used": [
- "urn:d7fe2c97-549c-4ea7-973e-9928f6e71901"
+ "urn:b1e7295b-8203-48e0-ad4e-03135f3e8d6c"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:36bfbdaa-5cb9-4458-a584-6dd5dcfdfbce",
+ "@id": "urn:adee1c78-e6cf-4a0e-9264-2ceaceb54ee0",
"Label": "Threshold",
"Used": [
- "urn:97a8160f-bb2a-462b-817e-8fea22ad5497"
+ "urn:b96fb921-457b-4883-9be8-b07579a040e0"
],
- "AssociatedWith": "urn:6d2a953f-fdaf-4c5a-a514-5012e2683234",
+ "AssociatedWith": "urn:ae29f890-cf49-4621-9cbe-6eeeab313c8e",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.contrasts = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.mask.contrast.mtype = 0;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -270,7 +270,7 @@
],
"Entities": [
{
- "@id": "urn:beaf7a4a-26f6-4baf-a898-33fed1de6dd1",
+ "@id": "urn:0a2bd5ea-a64e-42a0-ae31-150e7a1257b4",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -278,7 +278,7 @@
}
},
{
- "@id": "urn:20343da6-1dbe-4abe-861a-b3c8749af810",
+ "@id": "urn:cf18c935-d808-4855-94c8-ab1e8af5e711",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -286,57 +286,57 @@
}
},
{
- "@id": "urn:32250610-6808-46b2-8175-f03e3be56a9a",
+ "@id": "urn:972af39b-8673-4ab8-a38f-f2424bc248af",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:644ce011-3d1e-4984-ad9c-f5771f000747"
+ "GeneratedBy": "urn:b9dd4585-53b2-46d3-86ef-605a4028c435"
},
{
- "@id": "urn:75d1ea2b-1272-4eb8-aad1-cb8e455ce9f0",
+ "@id": "urn:eefeb4b9-0344-4121-aee1-626e816354fc",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:aec7fb9b-2ee8-4f2d-b523-9da2972acaab"
+ "GeneratedBy": "urn:fad38cb7-5e1a-4f82-ac2d-4f0cc81b0b2a"
},
{
- "@id": "urn:1b96acb1-26b2-42db-a786-caf863b571e7",
+ "@id": "urn:51a344a6-d5d1-479d-802c-4912345b4574",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:a5959023-1022-4359-806f-b2d2fa6bce85"
+ "GeneratedBy": "urn:4ece4936-b75e-4cdf-a4fa-c1748c3364db"
},
{
- "@id": "urn:b4269c4f-f3a9-4fde-ba7c-9e73f98efa77",
+ "@id": "urn:22ef0778-033a-4fc5-871a-2d082718833a",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:b9d00692-dc98-4bf8-b0e2-d7c35a873be5"
+ "GeneratedBy": "urn:d9c5d9f6-d211-47e7-993d-ca16b373b789"
},
{
- "@id": "urn:ff2dd0ff-ce32-4d9d-aac4-3af1f285e5ba",
+ "@id": "urn:1435c1bd-2e36-477a-b417-5f57093bedde",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:0daa00f1-fd07-4481-a724-16ce22dd13cf"
+ "GeneratedBy": "urn:d3e9b075-7f99-4789-a358-bfc920fed3c3"
},
{
- "@id": "urn:dcbb3e88-d6dd-4ce7-81f0-f836944dfb88",
+ "@id": "urn:aa250c9a-a324-4cbb-bd5b-2eb21542af2a",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:1f63bf46-8dde-4d8f-8199-b6b9ea05798c",
+ "GeneratedBy": "urn:8a3f7a24-c685-4532-be83-851ae63ca6ad",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:162b1d46-bf30-462d-be37-9e63f1bbdc34",
+ "@id": "urn:25ae9bf9-095e-447e-a614-2c4608c5a78a",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:1f63bf46-8dde-4d8f-8199-b6b9ea05798c",
+ "GeneratedBy": "urn:8a3f7a24-c685-4532-be83-851ae63ca6ad",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:8482b2ed-8b32-48db-8ea7-3d86c6427ac2",
+ "@id": "urn:b1b7f674-9292-490a-9b80-8d2a29faf9d4",
"Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:4d4a2763-06ec-4da4-91fc-e50f4ef7373d"
+ "GeneratedBy": "urn:0f920aab-f8e2-487a-b2c8-77fdd14ff21c"
},
{
- "@id": "urn:e12b1d9b-dced-4e3a-923b-d879b6c3d501",
+ "@id": "urn:246c334f-7c51-4acd-9d77-7d54242fd2d7",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -344,24 +344,24 @@
}
},
{
- "@id": "urn:3ee13e32-1c59-4bee-b8d6-3486ed62edbb",
+ "@id": "urn:346f2f07-2990-484f-9e23-d74ce972f99a",
"Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:ed09bfc0-4e0f-4033-bdc5-2697ab125380"
+ "GeneratedBy": "urn:944ad4a8-6abe-44bb-835f-307b53b5e187"
},
{
- "@id": "urn:327caea3-5cef-4821-a4fe-f2306d78ad61",
+ "@id": "urn:549cda09-ef87-4910-a306-2c99b47b18e2",
"Label": "SPM.mat",
- "GeneratedBy": "urn:558037a1-cb9f-4066-92ce-2310858450e1"
+ "GeneratedBy": "urn:3a2c9ee8-541c-4bc9-8e5b-13a00b8688c7"
},
{
- "@id": "urn:d7fe2c97-549c-4ea7-973e-9928f6e71901",
+ "@id": "urn:b1e7295b-8203-48e0-ad4e-03135f3e8d6c",
"Label": "SPM.mat",
- "GeneratedBy": "urn:befcb32b-1565-4ced-83d3-a9528d221226"
+ "GeneratedBy": "urn:a1f10b4f-25b3-4000-b3f6-31730c142bdc"
},
{
- "@id": "urn:97a8160f-bb2a-462b-817e-8fea22ad5497",
+ "@id": "urn:b96fb921-457b-4883-9be8-b07579a040e0",
"Label": "SPM.mat",
- "GeneratedBy": "urn:8f8f67e0-f527-4ed5-b657-afd90db8078b"
+ "GeneratedBy": "urn:20c82882-8ba2-4c91-9eb1-ab785bfec6fb"
}
]
}
diff --git a/examples/from_parsers/spm/spm_contrast_mask_batch.png b/examples/from_parsers/spm/spm_contrast_mask_batch.png
index 0fb8c08f4..3e8e68b50 100644
Binary files a/examples/from_parsers/spm/spm_contrast_mask_batch.png and b/examples/from_parsers/spm/spm_contrast_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_covariate_batch.jsonld b/examples/from_parsers/spm/spm_covariate_batch.jsonld
index a46c6d948..549c3cc9f 100644
--- a/examples/from_parsers/spm/spm_covariate_batch.jsonld
+++ b/examples/from_parsers/spm/spm_covariate_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "@id": "urn:6ed758a4-a952-4c72-8d80-3b26c317be7a",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,24 +13,24 @@
],
"Activities": [
{
- "@id": "urn:7ad4dcb0-cec7-4d82-ab67-1da97d0a6e4e",
+ "@id": "urn:4a5dea9f-6bdf-4711-9173-e4b12cde29a0",
"Label": "stats.factorial_design",
"Used": [
- "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
- "urn:9fe42f85-752e-4fee-8973-6463a374f383",
- "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
- "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
- "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21",
- "urn:e3afcce5-5eab-469d-a72b-caa4bf38c61d",
- "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b",
- "urn:b3b270f2-332e-408c-9217-66156ffa79ff",
- "urn:b3ad7f23-b5b1-495b-bd54-c81324facbbf",
- "urn:a73f4c88-b010-423c-a66f-891d32b30cc8",
- "urn:45ff77e8-eb82-4175-80d0-f95a34bedc2d",
- "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
- "urn:7b8a0aed-a199-45c6-9984-691a3b9342b0"
+ "urn:0eb0f6b1-0ccb-4560-ac74-fe45af46a58e",
+ "urn:a79bff62-4ee1-4d65-98da-116a57aa3f55",
+ "urn:835bafaa-c616-48e8-b40d-7fb9d3c2d3a3",
+ "urn:a18588f4-df77-4829-8460-3556c295d412",
+ "urn:c75f3793-ca85-4574-8a96-672272ecca70",
+ "urn:b0a3cb2e-f8c9-4140-bb6e-375dbe8a71f3",
+ "urn:ebca06a5-6084-4d81-90c4-3a4f6991a90d",
+ "urn:14e6bb01-26e9-4060-98c5-b0a23501fba5",
+ "urn:57c85ca9-05dd-4f03-b0ea-a6f28b13b1d9",
+ "urn:0f7dcc16-674e-4c5c-b23d-eb183b3d75b1",
+ "urn:5d0a7512-806e-4183-a0d2-a32c710120e5",
+ "urn:1180ec80-cd33-484a-a50e-f69f9498ef73",
+ "urn:7ab4fccc-8b12-41ff-9bf3-24a5c9e6adcc"
],
- "AssociatedWith": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "AssociatedWith": "urn:6ed758a4-a952-4c72-8d80-3b26c317be7a",
"Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov.c = [1 2 3 4 5 6 7 8 9 10 11 12 13];\nmatlabbatch{1}.spm.stats.factorial_design.cov.cname = 'Subject ID Covariate';\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCFI = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov.iCC = 1;\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Con1/Covariate'}",
@@ -48,12 +48,12 @@
}
},
{
- "@id": "urn:6cc92bfd-ba05-4178-9439-f356bb45800e",
+ "@id": "urn:70e729c9-db06-459c-955c-37465b487ff4",
"Label": "Estimate stat.",
"Used": [
- "urn:1b5ca7ef-1b1c-417d-9180-6a48d5f2fcb6"
+ "urn:a31ea3d9-4c28-48eb-8885-2f4d2fb8a62a"
],
- "AssociatedWith": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "AssociatedWith": "urn:6ed758a4-a952-4c72-8d80-3b26c317be7a",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -61,12 +61,12 @@
}
},
{
- "@id": "urn:5f912f03-d39f-41da-8581-476057afa5b2",
+ "@id": "urn:a2836735-4d3b-45d7-8aa6-2414149e2686",
"Label": "Estimate contrast",
"Used": [
- "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315"
+ "urn:53cd4a1b-2c9f-47d9-ab78-307d86656924"
],
- "AssociatedWith": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "AssociatedWith": "urn:6ed758a4-a952-4c72-8d80-3b26c317be7a",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain covariate';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'mr vs plain covariate'",
@@ -76,12 +76,12 @@
}
},
{
- "@id": "urn:1e091424-d3b1-4596-b5e1-2b5167927fa1",
+ "@id": "urn:495b1d53-fc03-4a92-a295-05cc097f1f0c",
"Label": "Threshold",
"Used": [
- "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf"
+ "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a"
],
- "AssociatedWith": "urn:035743bc-1100-484b-94c6-b43764e0cd18",
+ "AssociatedWith": "urn:6ed758a4-a952-4c72-8d80-3b26c317be7a",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -99,7 +99,7 @@
],
"Entities": [
{
- "@id": "urn:fe7f40a7-0fb0-4d06-bbd9-2b2eac246769",
+ "@id": "urn:0eb0f6b1-0ccb-4560-ac74-fe45af46a58e",
"Label": "Sub01_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub01/con_0001.nii",
"digest": {
@@ -107,7 +107,7 @@
}
},
{
- "@id": "urn:9fe42f85-752e-4fee-8973-6463a374f383",
+ "@id": "urn:a79bff62-4ee1-4d65-98da-116a57aa3f55",
"Label": "Sub02_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub02/con_0001.nii",
"digest": {
@@ -115,7 +115,7 @@
}
},
{
- "@id": "urn:bb39b855-9542-4c73-800c-28d70f33d72f",
+ "@id": "urn:835bafaa-c616-48e8-b40d-7fb9d3c2d3a3",
"Label": "Sub03_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub03/con_0001.nii",
"digest": {
@@ -123,7 +123,7 @@
}
},
{
- "@id": "urn:a9e915bc-4251-4ce4-aae6-e019c0098d4a",
+ "@id": "urn:a18588f4-df77-4829-8460-3556c295d412",
"Label": "Sub04_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub04/con_0001.nii",
"digest": {
@@ -131,7 +131,7 @@
}
},
{
- "@id": "urn:a3a0a820-1bda-451a-9a7a-8efcde1f9e21",
+ "@id": "urn:c75f3793-ca85-4574-8a96-672272ecca70",
"Label": "Sub05_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub05/con_0001.nii",
"digest": {
@@ -139,7 +139,7 @@
}
},
{
- "@id": "urn:e3afcce5-5eab-469d-a72b-caa4bf38c61d",
+ "@id": "urn:b0a3cb2e-f8c9-4140-bb6e-375dbe8a71f3",
"Label": "Sub06_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub06/con_0001.nii",
"digest": {
@@ -147,7 +147,7 @@
}
},
{
- "@id": "urn:af3a6a6e-ab3b-495f-9d79-975b4fac173b",
+ "@id": "urn:ebca06a5-6084-4d81-90c4-3a4f6991a90d",
"Label": "Sub07_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub07/con_0001.nii",
"digest": {
@@ -155,7 +155,7 @@
}
},
{
- "@id": "urn:b3b270f2-332e-408c-9217-66156ffa79ff",
+ "@id": "urn:14e6bb01-26e9-4060-98c5-b0a23501fba5",
"Label": "Sub08_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub08/con_0001.nii",
"digest": {
@@ -163,7 +163,7 @@
}
},
{
- "@id": "urn:b3ad7f23-b5b1-495b-bd54-c81324facbbf",
+ "@id": "urn:57c85ca9-05dd-4f03-b0ea-a6f28b13b1d9",
"Label": "Sub09_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub09/con_0001.nii",
"digest": {
@@ -171,7 +171,7 @@
}
},
{
- "@id": "urn:a73f4c88-b010-423c-a66f-891d32b30cc8",
+ "@id": "urn:0f7dcc16-674e-4c5c-b23d-eb183b3d75b1",
"Label": "Sub10_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub10/con_0001.nii",
"digest": {
@@ -179,7 +179,7 @@
}
},
{
- "@id": "urn:45ff77e8-eb82-4175-80d0-f95a34bedc2d",
+ "@id": "urn:5d0a7512-806e-4183-a0d2-a32c710120e5",
"Label": "Sub11_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub11/con_0001.nii",
"digest": {
@@ -187,7 +187,7 @@
}
},
{
- "@id": "urn:fe7823e7-a7a4-4991-8938-14e7d736a233",
+ "@id": "urn:1180ec80-cd33-484a-a50e-f69f9498ef73",
"Label": "Sub12_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub12/con_0001.nii",
"digest": {
@@ -195,7 +195,7 @@
}
},
{
- "@id": "urn:7b8a0aed-a199-45c6-9984-691a3b9342b0",
+ "@id": "urn:7ab4fccc-8b12-41ff-9bf3-24a5c9e6adcc",
"Label": "Sub13_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/Data/ds000052/RESULTS/Sub13/con_0001.nii",
"digest": {
@@ -203,19 +203,19 @@
}
},
{
- "@id": "urn:1b5ca7ef-1b1c-417d-9180-6a48d5f2fcb6",
+ "@id": "urn:a31ea3d9-4c28-48eb-8885-2f4d2fb8a62a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:7ad4dcb0-cec7-4d82-ab67-1da97d0a6e4e"
+ "GeneratedBy": "urn:4a5dea9f-6bdf-4711-9173-e4b12cde29a0"
},
{
- "@id": "urn:e455fbcd-8b0e-476b-964a-230f3fb1f315",
+ "@id": "urn:53cd4a1b-2c9f-47d9-ab78-307d86656924",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6cc92bfd-ba05-4178-9439-f356bb45800e"
+ "GeneratedBy": "urn:70e729c9-db06-459c-955c-37465b487ff4"
},
{
- "@id": "urn:b591dfe1-e4c6-4e46-9d53-c59c3a00c8bf",
+ "@id": "urn:f921fdf0-acde-4ee9-bd00-c633b56c947a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:5f912f03-d39f-41da-8581-476057afa5b2"
+ "GeneratedBy": "urn:a2836735-4d3b-45d7-8aa6-2414149e2686"
}
]
}
diff --git a/examples/from_parsers/spm/spm_covariate_batch.png b/examples/from_parsers/spm/spm_covariate_batch.png
index 53ef0d994..4fea88112 100644
Binary files a/examples/from_parsers/spm/spm_covariate_batch.png and b/examples/from_parsers/spm/spm_covariate_batch.png differ
diff --git a/examples/from_parsers/spm/spm_default_batch.jsonld b/examples/from_parsers/spm/spm_default_batch.jsonld
index 9cab68574..364d77cb9 100644
--- a/examples/from_parsers/spm/spm_default_batch.jsonld
+++ b/examples/from_parsers/spm/spm_default_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "@id": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:9a8a0caf-982f-4090-b178-7415ef5842b0",
+ "@id": "urn:f2382eed-c3ed-4d76-a432-94fcaae0bfcc",
"Label": "Move file",
"Used": [
- "urn:b97f8a1e-186a-4b15-bab1-ee845c16352d"
+ "urn:e9bf6240-19c0-42ac-a1b0-1ce5e68c2a2d"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:b4d4a49d-8698-4991-92f7-6ded6f8f4ab8",
+ "@id": "urn:d993fcfd-8fa4-405e-906a-3df84fda0fb4",
"Label": "Move file",
"Used": [
- "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481"
+ "urn:ed57bc97-cb5e-45ab-a3de-7c80b54d3a8a"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:5fb06023-e8e1-439e-9746-ceaedfd29f11",
+ "@id": "urn:261dc1bd-062a-45f8-aaf6-940102b64247",
"Label": "Gunzip",
"Used": [
- "urn:0b8198b6-4d60-44c0-9caa-24b1b282aced"
+ "urn:b51f6a09-3f73-4fb2-85a4-d4686faec93e"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:7abc0423-3682-48cf-8806-fee1a3fb186c",
+ "@id": "urn:e27ae9b4-0f62-4c4e-9c20-049a703eee03",
"Label": "Gunzip",
"Used": [
- "urn:ceb18837-f089-46e0-8d15-f53ebe8394c7"
+ "urn:f82e1fae-57f1-43e5-a4c0-9ffc534c0060"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:22e2af84-1f98-4cf6-b486-bf0a79a98a8b",
+ "@id": "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540",
"Label": "Realign",
"Used": [
- "urn:01b68f11-7d17-4160-ba1b-f1fbd37d9835"
+ "urn:774e8f06-f15d-4e68-a1f8-a836aea358c8"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:41b4dd62-a1d6-471a-9459-b7c3d9e66545",
+ "@id": "urn:e0483247-a008-491a-8bb4-5b7c9e14dc17",
"Label": "Coregister",
"Used": [
- "urn:33d1e994-20d3-4a55-b264-9c6eae9e8172",
- "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3"
+ "urn:618fc7f8-1c11-4b09-85db-22ba7d0e74a6",
+ "urn:a9e05bff-7f86-441f-aea4-2b1431340600"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:6db2c440-a1c5-4be4-be37-c75b9faba368",
+ "@id": "urn:f015120b-6635-4636-8f4e-0bc4e2972782",
"Label": "Segment",
"Used": [
- "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3"
+ "urn:a9e05bff-7f86-441f-aea4-2b1431340600"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:8dc86011-0121-48e3-945d-edfafd138b17",
+ "@id": "urn:6125eeaa-3720-4cc7-b376-1b8818e8ab18",
"Label": "Normalize",
"Used": [
- "urn:33d1e994-20d3-4a55-b264-9c6eae9e8172",
- "urn:d9236ad7-4bbc-4dad-ad64-95059a111499"
+ "urn:514b91e5-0436-42ce-8c57-e5b70a35d201",
+ "urn:618fc7f8-1c11-4b09-85db-22ba7d0e74a6"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:cb8bda64-2c63-42e4-8f16-df3a7449ba41",
+ "@id": "urn:f150c860-a320-4b6a-bffb-3296f4a0d6df",
"Label": "Normalize",
"Used": [
- "urn:d9236ad7-4bbc-4dad-ad64-95059a111499"
+ "urn:514b91e5-0436-42ce-8c57-e5b70a35d201"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:b01d3376-c72d-48d5-8d9b-624e86c64704",
+ "@id": "urn:0b33d168-0899-4fa2-b3aa-87ae050f04f7",
"Label": "Smooth",
"Used": [
- "urn:58675ac0-241a-40e0-8600-1775c2221c7b"
+ "urn:00d0dd9b-49a6-4edb-942a-98bf60c00693"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:05033224-1bed-4f2e-904f-113e6309a493",
+ "@id": "urn:ee8b07e3-4017-444c-9bac-3be692a993d1",
"Label": "Stat Design",
"Used": [
- "urn:9279f452-aed7-4fdd-b6c0-56f597dd3384",
- "urn:ac224873-aa4f-43e1-bce8-57961761c3b5"
+ "urn:33d18bc3-e882-4fba-bf30-f7b91218f422",
+ "urn:b88a65a1-2916-49de-be5d-06517bcb7976"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_p0001'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:cc9700cd-65ba-4289-bd45-05989e9f1060",
+ "@id": "urn:0a585478-d1f8-42a3-835f-4ee727f66c02",
"Label": "Estimate stat.",
"Used": [
- "urn:e3fada0d-7fcf-4eb8-9901-c8a9e6d0cb11"
+ "urn:8f306cc1-f996-42e7-9d77-2467d960872b"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:71389023-8336-415b-898f-3cea608e577f",
+ "@id": "urn:566bad3a-0d1d-4981-a676-8b044f761589",
"Label": "Estimate contrast",
"Used": [
- "urn:610c8f66-d08d-4279-8b6a-ea432da642c9"
+ "urn:667100fe-1645-4dd0-9b7f-2c28142a449a"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:4ba80317-1444-4c5a-a247-982471301cb6",
+ "@id": "urn:e627c9be-9e10-4f74-aa24-583b88f495a7",
"Label": "Threshold",
"Used": [
- "urn:15a73dc4-e916-465e-a7f7-1cdfe5c68626"
+ "urn:ee3cd2fb-999e-4a2c-b4f7-13eadd9a792c"
],
- "AssociatedWith": "urn:c9b78aca-d364-47a2-b0a0-a38de2ecc994",
+ "AssociatedWith": "urn:a0570dc0-3e1c-4223-8846-d876f85c4147",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:b97f8a1e-186a-4b15-bab1-ee845c16352d",
+ "@id": "urn:e9bf6240-19c0-42ac-a1b0-1ce5e68c2a2d",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:150a7ce4-f3d0-43dd-81a6-637409ba5481",
+ "@id": "urn:ed57bc97-cb5e-45ab-a3de-7c80b54d3a8a",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:0b8198b6-4d60-44c0-9caa-24b1b282aced",
+ "@id": "urn:b51f6a09-3f73-4fb2-85a4-d4686faec93e",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:9a8a0caf-982f-4090-b178-7415ef5842b0"
+ "GeneratedBy": "urn:f2382eed-c3ed-4d76-a432-94fcaae0bfcc"
},
{
- "@id": "urn:ceb18837-f089-46e0-8d15-f53ebe8394c7",
+ "@id": "urn:f82e1fae-57f1-43e5-a4c0-9ffc534c0060",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:b4d4a49d-8698-4991-92f7-6ded6f8f4ab8"
+ "GeneratedBy": "urn:d993fcfd-8fa4-405e-906a-3df84fda0fb4"
},
{
- "@id": "urn:01b68f11-7d17-4160-ba1b-f1fbd37d9835",
+ "@id": "urn:774e8f06-f15d-4e68-a1f8-a836aea358c8",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:5fb06023-e8e1-439e-9746-ceaedfd29f11"
+ "GeneratedBy": "urn:261dc1bd-062a-45f8-aaf6-940102b64247"
},
{
- "@id": "urn:33d1e994-20d3-4a55-b264-9c6eae9e8172",
+ "@id": "urn:618fc7f8-1c11-4b09-85db-22ba7d0e74a6",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:22e2af84-1f98-4cf6-b486-bf0a79a98a8b"
+ "GeneratedBy": "urn:d4632aff-3cc6-4d05-9e3d-3a245046d540"
},
{
- "@id": "urn:420cd2a7-49c9-4fcb-a221-45d7da289ec3",
+ "@id": "urn:a9e05bff-7f86-441f-aea4-2b1431340600",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:7abc0423-3682-48cf-8806-fee1a3fb186c"
+ "GeneratedBy": "urn:e27ae9b4-0f62-4c4e-9c20-049a703eee03"
},
{
- "@id": "urn:d9236ad7-4bbc-4dad-ad64-95059a111499",
+ "@id": "urn:514b91e5-0436-42ce-8c57-e5b70a35d201",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:6db2c440-a1c5-4be4-be37-c75b9faba368",
+ "GeneratedBy": "urn:f015120b-6635-4636-8f4e-0bc4e2972782",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:ff48f871-b123-4c72-b715-2253a677865a",
+ "@id": "urn:bb6ab84c-76ed-43cc-a8fd-e3605bb6abbe",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:6db2c440-a1c5-4be4-be37-c75b9faba368",
+ "GeneratedBy": "urn:f015120b-6635-4636-8f4e-0bc4e2972782",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:58675ac0-241a-40e0-8600-1775c2221c7b",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8dc86011-0121-48e3-945d-edfafd138b17"
+ "@id": "urn:00d0dd9b-49a6-4edb-942a-98bf60c00693",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:6125eeaa-3720-4cc7-b376-1b8818e8ab18"
},
{
- "@id": "urn:ac224873-aa4f-43e1-bce8-57961761c3b5",
+ "@id": "urn:b88a65a1-2916-49de-be5d-06517bcb7976",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:9279f452-aed7-4fdd-b6c0-56f597dd3384",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:b01d3376-c72d-48d5-8d9b-624e86c64704"
+ "@id": "urn:33d18bc3-e882-4fba-bf30-f7b91218f422",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:0b33d168-0899-4fa2-b3aa-87ae050f04f7"
},
{
- "@id": "urn:e3fada0d-7fcf-4eb8-9901-c8a9e6d0cb11",
+ "@id": "urn:8f306cc1-f996-42e7-9d77-2467d960872b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:05033224-1bed-4f2e-904f-113e6309a493"
+ "GeneratedBy": "urn:ee8b07e3-4017-444c-9bac-3be692a993d1"
},
{
- "@id": "urn:610c8f66-d08d-4279-8b6a-ea432da642c9",
+ "@id": "urn:667100fe-1645-4dd0-9b7f-2c28142a449a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:cc9700cd-65ba-4289-bd45-05989e9f1060"
+ "GeneratedBy": "urn:0a585478-d1f8-42a3-835f-4ee727f66c02"
},
{
- "@id": "urn:15a73dc4-e916-465e-a7f7-1cdfe5c68626",
+ "@id": "urn:ee3cd2fb-999e-4a2c-b4f7-13eadd9a792c",
"Label": "SPM.mat",
- "GeneratedBy": "urn:71389023-8336-415b-898f-3cea608e577f"
+ "GeneratedBy": "urn:566bad3a-0d1d-4981-a676-8b044f761589"
}
]
}
diff --git a/examples/from_parsers/spm/spm_default_batch.png b/examples/from_parsers/spm/spm_default_batch.png
index 31e9e91ab..35e7e079c 100644
Binary files a/examples/from_parsers/spm/spm_default_batch.png and b/examples/from_parsers/spm/spm_default_batch.png differ
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
index 244d49f82..c59106fdd 100644
--- a/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
+++ b/examples/from_parsers/spm/spm_explicit_mask_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "@id": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:6ec6582b-5a64-41b9-b74a-d118936b0284",
+ "@id": "urn:8adeaab1-5051-4afe-ab60-3ae3cdffae8e",
"Label": "Move file",
"Used": [
- "urn:514fce8a-8ed3-4f25-8595-068414f01b0c"
+ "urn:55071848-721d-4f1b-a087-898f26dbedeb"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:cd3e9e9a-6f09-400c-9eef-126515d808a8",
+ "@id": "urn:3488314f-c550-4532-8db8-90bcec24624f",
"Label": "Move file",
"Used": [
- "urn:876c515d-0b2c-4896-a395-f5208dbee953"
+ "urn:18b46de4-cda4-45c6-8b8c-a772424da1c8"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:ad185281-72cb-4c30-9556-4af3978bbe83",
+ "@id": "urn:b9777891-96c9-4d17-bc32-87980e3082c4",
"Label": "Gunzip",
"Used": [
- "urn:4ea6317a-4ae1-4f30-b5a2-4e01539d929e"
+ "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:287cbf00-f101-4375-ad78-e61d0f8c648f",
+ "@id": "urn:fb4e2311-201d-4500-bfed-86410f92c0fe",
"Label": "Gunzip",
"Used": [
- "urn:c4a84cc8-b43e-4379-8adc-83c8d4b5727e"
+ "urn:01153fae-af6f-4928-9d6a-e2e7663f5e0a"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:5a20644f-8235-42e5-b56f-e86bb7753ecd",
+ "@id": "urn:aa937459-3615-478b-9878-ca3f30fbd2db",
"Label": "Realign",
"Used": [
- "urn:77b26c36-1727-41bd-92d1-903d0fd511c9"
+ "urn:38783393-8687-499e-af74-4c389b7a07f8"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:37121a7c-b567-4f85-a500-bb3562563a9d",
+ "@id": "urn:fe4ece1f-7b99-4e67-a08b-391381b191b2",
"Label": "Coregister",
"Used": [
- "urn:5b603fd4-6998-4e64-b80b-e8c5d0c4544a",
- "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f"
+ "urn:ae9f3ec1-ab33-409a-8f91-a998a39193a1",
+ "urn:dee1e7d2-c686-4cbf-b6a8-e0b9a487316d"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "@id": "urn:94ada5b6-7c58-4d21-ace8-a7427a655b89",
"Label": "Segment",
"Used": [
- "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f"
+ "urn:ae9f3ec1-ab33-409a-8f91-a998a39193a1"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:d604d4b1-3ba4-4569-a3e2-e89c6cb6b835",
+ "@id": "urn:a5aa38fd-d304-44a9-92b2-14f06c963626",
"Label": "Normalize",
"Used": [
- "urn:281f3d24-626f-4c05-b06f-01ed8c009bdc",
- "urn:5b603fd4-6998-4e64-b80b-e8c5d0c4544a"
+ "urn:dee1e7d2-c686-4cbf-b6a8-e0b9a487316d",
+ "urn:ff9d2e07-fb6b-455d-9b57-97f81076b8f6"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:25126a8b-b6aa-45e0-b05b-aaddcb7793c8",
+ "@id": "urn:6158b642-a0ac-4038-948f-738eaa9fd738",
"Label": "Normalize",
"Used": [
- "urn:281f3d24-626f-4c05-b06f-01ed8c009bdc"
+ "urn:ff9d2e07-fb6b-455d-9b57-97f81076b8f6"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:f429e94a-e5cc-4796-835d-4fc7ba1917d1",
+ "@id": "urn:03155384-991a-4f87-b1f4-b56ea90b5ccb",
"Label": "Smooth",
"Used": [
- "urn:d15366f1-fcfc-4689-94f3-936e235b3bdd"
+ "urn:11f36d42-9679-47b3-9b39-4a651b5ec2cd"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,14 +186,14 @@
}
},
{
- "@id": "urn:8d91aa22-22f8-4ea2-9ca5-42d0f4643f4f",
+ "@id": "urn:4ac9e1cd-fcae-4c2e-87eb-e57eb4263733",
"Label": "Stat Design",
"Used": [
- "urn:52c07d8f-2a53-4bf0-bf9e-c5a1656c9deb",
- "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
- "urn:affc4ea6-1cd3-4deb-bf21-c01b7d788de1"
+ "urn:7687e560-68ce-415d-abaa-18a1c6b032df",
+ "urn:dc81bcc2-7d97-408d-91ba-5edf765cf2c7",
+ "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii,1'};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_explicit_mask'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:9e439a85-3103-4992-96af-be574019827e",
+ "@id": "urn:23f0145c-5038-48f3-923d-9dc25d3fba95",
"Label": "Estimate stat.",
"Used": [
- "urn:947fc159-4080-408c-90d8-9c082ab4f5db"
+ "urn:e491e8a4-7a73-446f-a215-8fd224c0788f"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:16e3f814-261e-426c-ac40-a4112a65d10d",
+ "@id": "urn:9d0204dd-562e-4760-ae27-0eabbfb6c2e7",
"Label": "Estimate contrast",
"Used": [
- "urn:5ca8b30b-941d-4623-abe9-cd9d43ac941c"
+ "urn:b96555f7-c09a-4102-82ac-6680fdd6e15f"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:170a2642-1f39-449a-b52c-43a3f96332f4",
+ "@id": "urn:66e9a593-4c31-41b9-95f3-d37201741051",
"Label": "Threshold",
"Used": [
- "urn:8d4a17dd-0272-4c84-abd0-49fe8c41c0ee"
+ "urn:7bd9021a-8ece-4eae-8527-15966a3238e0"
],
- "AssociatedWith": "urn:e64b9468-e646-4716-a449-e734edd20283",
+ "AssociatedWith": "urn:5153bb2a-e317-45d6-b735-34a7e7e4ed70",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:514fce8a-8ed3-4f25-8595-068414f01b0c",
+ "@id": "urn:55071848-721d-4f1b-a087-898f26dbedeb",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:876c515d-0b2c-4896-a395-f5208dbee953",
+ "@id": "urn:18b46de4-cda4-45c6-8b8c-a772424da1c8",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:4ea6317a-4ae1-4f30-b5a2-4e01539d929e",
+ "@id": "urn:9b8d1d9b-abd7-4aa3-969f-7bfe9ca49bf9",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:6ec6582b-5a64-41b9-b74a-d118936b0284"
+ "GeneratedBy": "urn:8adeaab1-5051-4afe-ab60-3ae3cdffae8e"
},
{
- "@id": "urn:c4a84cc8-b43e-4379-8adc-83c8d4b5727e",
+ "@id": "urn:01153fae-af6f-4928-9d6a-e2e7663f5e0a",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:cd3e9e9a-6f09-400c-9eef-126515d808a8"
+ "GeneratedBy": "urn:3488314f-c550-4532-8db8-90bcec24624f"
},
{
- "@id": "urn:77b26c36-1727-41bd-92d1-903d0fd511c9",
+ "@id": "urn:38783393-8687-499e-af74-4c389b7a07f8",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:ad185281-72cb-4c30-9556-4af3978bbe83"
+ "GeneratedBy": "urn:b9777891-96c9-4d17-bc32-87980e3082c4"
},
{
- "@id": "urn:5b603fd4-6998-4e64-b80b-e8c5d0c4544a",
+ "@id": "urn:dee1e7d2-c686-4cbf-b6a8-e0b9a487316d",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:5a20644f-8235-42e5-b56f-e86bb7753ecd"
+ "GeneratedBy": "urn:aa937459-3615-478b-9878-ca3f30fbd2db"
},
{
- "@id": "urn:863f1088-36af-4ae7-8a09-4c5ee8c5559f",
+ "@id": "urn:ae9f3ec1-ab33-409a-8f91-a998a39193a1",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:287cbf00-f101-4375-ad78-e61d0f8c648f"
+ "GeneratedBy": "urn:fb4e2311-201d-4500-bfed-86410f92c0fe"
},
{
- "@id": "urn:281f3d24-626f-4c05-b06f-01ed8c009bdc",
+ "@id": "urn:ff9d2e07-fb6b-455d-9b57-97f81076b8f6",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "GeneratedBy": "urn:94ada5b6-7c58-4d21-ace8-a7427a655b89",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:70348754-5a48-4403-b347-fc5192079828",
+ "@id": "urn:02bac1d5-5bff-45e9-af9e-bd8cb8544e48",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:580b968d-c1ef-4ea6-a72c-b4a7646d5ee4",
+ "GeneratedBy": "urn:94ada5b6-7c58-4d21-ace8-a7427a655b89",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:d15366f1-fcfc-4689-94f3-936e235b3bdd",
- "Label": "wsegment1",
- "GeneratedBy": "urn:d604d4b1-3ba4-4569-a3e2-e89c6cb6b835"
+ "@id": "urn:11f36d42-9679-47b3-9b39-4a651b5ec2cd",
+ "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:a5aa38fd-d304-44a9-92b2-14f06c963626"
},
{
- "@id": "urn:8a207674-153d-4980-85d2-dbcc92f688d2",
+ "@id": "urn:dc81bcc2-7d97-408d-91ba-5edf765cf2c7",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,7 +339,7 @@
}
},
{
- "@id": "urn:affc4ea6-1cd3-4deb-bf21-c01b7d788de1",
+ "@id": "urn:aef87910-bf4c-4baf-b74b-862b0f9916e6",
"Label": "spm_contrast_mask_mask.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_contrast_mask/mask.nii",
"digest": {
@@ -347,24 +347,24 @@
}
},
{
- "@id": "urn:52c07d8f-2a53-4bf0-bf9e-c5a1656c9deb",
- "Label": "swsegment1",
- "GeneratedBy": "urn:f429e94a-e5cc-4796-835d-4fc7ba1917d1"
+ "@id": "urn:7687e560-68ce-415d-abaa-18a1c6b032df",
+ "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:03155384-991a-4f87-b1f4-b56ea90b5ccb"
},
{
- "@id": "urn:947fc159-4080-408c-90d8-9c082ab4f5db",
+ "@id": "urn:e491e8a4-7a73-446f-a215-8fd224c0788f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:8d91aa22-22f8-4ea2-9ca5-42d0f4643f4f"
+ "GeneratedBy": "urn:4ac9e1cd-fcae-4c2e-87eb-e57eb4263733"
},
{
- "@id": "urn:5ca8b30b-941d-4623-abe9-cd9d43ac941c",
+ "@id": "urn:b96555f7-c09a-4102-82ac-6680fdd6e15f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:9e439a85-3103-4992-96af-be574019827e"
+ "GeneratedBy": "urn:23f0145c-5038-48f3-923d-9dc25d3fba95"
},
{
- "@id": "urn:8d4a17dd-0272-4c84-abd0-49fe8c41c0ee",
+ "@id": "urn:7bd9021a-8ece-4eae-8527-15966a3238e0",
"Label": "SPM.mat",
- "GeneratedBy": "urn:16e3f814-261e-426c-ac40-a4112a65d10d"
+ "GeneratedBy": "urn:9d0204dd-562e-4760-ae27-0eabbfb6c2e7"
}
]
}
diff --git a/examples/from_parsers/spm/spm_explicit_mask_batch.png b/examples/from_parsers/spm/spm_explicit_mask_batch.png
index 976c7ea4f..7aa6196f5 100644
Binary files a/examples/from_parsers/spm/spm_explicit_mask_batch.png and b/examples/from_parsers/spm/spm_explicit_mask_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.jsonld b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
index 5745ee46b..6293a7374 100644
--- a/examples/from_parsers/spm/spm_group_ols_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_ols_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "@id": "urn:59104013-7df9-4454-925f-bdb123c22844",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,25 +13,25 @@
],
"Activities": [
{
- "@id": "urn:c4b41eb0-6e4c-466e-907d-9ae326422bdb",
+ "@id": "urn:63557888-6f6f-4d2a-81a1-932de748541d",
"Label": "stats.factorial_design",
"Used": [
- "urn:0139ed04-010d-414f-8907-5d6163b567ea",
- "urn:cd76fc5a-b376-4723-bac8-111eaaa24083",
- "urn:793001e3-092c-46bb-b006-638851f60f1e",
- "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
- "urn:51085d5c-9272-48b6-8298-868f86ac98e5",
- "urn:3e6964e1-0ce4-4cae-b165-83f556a2a6e4",
- "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
- "urn:6310131e-c904-4128-a310-bcd85a930896",
- "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
- "urn:11447d06-8a2a-4344-baaa-cf78666297e9",
- "urn:e743a0bb-478d-4238-aedf-b1620721c88b",
- "urn:322ef859-6275-4576-b46c-c4b1de5333f5",
- "urn:a65b8d80-0bd7-4490-b8d2-6dbe12682ca9",
- "urn:6670247b-4942-4a7a-a1fa-31c4d3f24695"
+ "urn:2313510a-a7a7-457f-8c2c-53a655cf260c",
+ "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a",
+ "urn:192e03df-9cbd-4758-a519-d36f7449d11e",
+ "urn:7564cc1a-4e3d-4126-ba65-335ca4eb7193",
+ "urn:6095f7d1-7e5e-483d-bf1a-5a4838cc9152",
+ "urn:9d7819db-957f-415a-890b-f1b8d9dbd88c",
+ "urn:48149b18-b685-420c-aa12-600700527a8b",
+ "urn:4abf85b0-30e5-4e03-92bb-35fd73da6f1d",
+ "urn:e65f3ff3-df11-4c71-98a9-d653b6e20e63",
+ "urn:5a8ac39b-1335-4c41-889f-60783a5e2b84",
+ "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434",
+ "urn:54a4c888-fa93-41c0-873a-cc43fff460c0",
+ "urn:17f60b95-1e29-42f6-9f58-15348ca2b014",
+ "urn:a781eafc-1231-45aa-8acf-0aff50490664"
],
- "AssociatedWith": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "AssociatedWith": "urn:59104013-7df9-4454-925f-bdb123c22844",
"Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'};\nmatlabbatch{1}.spm.stats.factorial_design.des.t1.scans = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_t_test'}",
@@ -46,12 +46,12 @@
}
},
{
- "@id": "urn:9ab1f065-b1b1-4d54-a405-59ef938a5da1",
+ "@id": "urn:3689a407-0661-43c1-b0a4-bd37850fd700",
"Label": "Estimate stat.",
"Used": [
- "urn:58295d4c-36e1-499e-8a3a-181a424b6142"
+ "urn:f21f492c-1ded-461d-a8ba-11cf5b61aacf"
],
- "AssociatedWith": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "AssociatedWith": "urn:59104013-7df9-4454-925f-bdb123c22844",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -59,12 +59,12 @@
}
},
{
- "@id": "urn:b1cfd1b0-2ccc-4359-b62c-14e43afb5b18",
+ "@id": "urn:46d2d540-a591-40b0-85f4-6d99a9fd34cb",
"Label": "Estimate contrast",
"Used": [
- "urn:3dc068ee-1ef5-4ee5-bb1b-e1c8b3c87c91"
+ "urn:0019adae-0fa4-4e8f-8824-8ecb74ced688"
],
- "AssociatedWith": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "AssociatedWith": "urn:59104013-7df9-4454-925f-bdb123c22844",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'con-01';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'con-01'",
@@ -74,12 +74,12 @@
}
},
{
- "@id": "urn:00eac208-4c30-4d3c-9282-5d94b806e027",
+ "@id": "urn:19f90103-0415-4e89-9031-04bc863b9076",
"Label": "Threshold",
"Used": [
- "urn:9d1898a7-03e2-445f-8756-faeb5bec2948"
+ "urn:5d377cc5-43ba-4030-91de-b34c5c5d5523"
],
- "AssociatedWith": "urn:325a2bfd-6837-4b92-822d-3b697d0883a6",
+ "AssociatedWith": "urn:59104013-7df9-4454-925f-bdb123c22844",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 120;\nmatlabbatch{4}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -97,7 +97,7 @@
],
"Entities": [
{
- "@id": "urn:0139ed04-010d-414f-8907-5d6163b567ea",
+ "@id": "urn:2313510a-a7a7-457f-8c2c-53a655cf260c",
"Label": "sub-01_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/con_0001.nii",
"digest": {
@@ -105,7 +105,7 @@
}
},
{
- "@id": "urn:cd76fc5a-b376-4723-bac8-111eaaa24083",
+ "@id": "urn:a63a5415-2d86-4ea7-995b-f862b8f47f9a",
"Label": "sub-02_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/con_0001.nii",
"digest": {
@@ -113,7 +113,7 @@
}
},
{
- "@id": "urn:793001e3-092c-46bb-b006-638851f60f1e",
+ "@id": "urn:192e03df-9cbd-4758-a519-d36f7449d11e",
"Label": "sub-03_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/con_0001.nii",
"digest": {
@@ -121,7 +121,7 @@
}
},
{
- "@id": "urn:695fc232-c43b-47af-9cef-3c948b5bfcff",
+ "@id": "urn:7564cc1a-4e3d-4126-ba65-335ca4eb7193",
"Label": "sub-04_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/con_0001.nii",
"digest": {
@@ -129,7 +129,7 @@
}
},
{
- "@id": "urn:51085d5c-9272-48b6-8298-868f86ac98e5",
+ "@id": "urn:6095f7d1-7e5e-483d-bf1a-5a4838cc9152",
"Label": "sub-05_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/con_0001.nii",
"digest": {
@@ -137,7 +137,7 @@
}
},
{
- "@id": "urn:3e6964e1-0ce4-4cae-b165-83f556a2a6e4",
+ "@id": "urn:9d7819db-957f-415a-890b-f1b8d9dbd88c",
"Label": "sub-06_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/con_0001.nii",
"digest": {
@@ -145,7 +145,7 @@
}
},
{
- "@id": "urn:90ae9a95-aa81-4c49-a5ba-b7a37d554b7f",
+ "@id": "urn:48149b18-b685-420c-aa12-600700527a8b",
"Label": "sub-07_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/con_0001.nii",
"digest": {
@@ -153,7 +153,7 @@
}
},
{
- "@id": "urn:6310131e-c904-4128-a310-bcd85a930896",
+ "@id": "urn:4abf85b0-30e5-4e03-92bb-35fd73da6f1d",
"Label": "sub-08_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/con_0001.nii",
"digest": {
@@ -161,7 +161,7 @@
}
},
{
- "@id": "urn:6029fd2b-6341-4c78-9c8f-ed8b23999598",
+ "@id": "urn:e65f3ff3-df11-4c71-98a9-d653b6e20e63",
"Label": "sub-09_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/con_0001.nii",
"digest": {
@@ -169,7 +169,7 @@
}
},
{
- "@id": "urn:11447d06-8a2a-4344-baaa-cf78666297e9",
+ "@id": "urn:5a8ac39b-1335-4c41-889f-60783a5e2b84",
"Label": "sub-10_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/con_0001.nii",
"digest": {
@@ -177,7 +177,7 @@
}
},
{
- "@id": "urn:e743a0bb-478d-4238-aedf-b1620721c88b",
+ "@id": "urn:d9466a6c-9b6f-4bf0-9164-e9ea186ea434",
"Label": "sub-11_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/con_0001.nii",
"digest": {
@@ -185,7 +185,7 @@
}
},
{
- "@id": "urn:322ef859-6275-4576-b46c-c4b1de5333f5",
+ "@id": "urn:54a4c888-fa93-41c0-873a-cc43fff460c0",
"Label": "sub-12_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/con_0001.nii",
"digest": {
@@ -193,7 +193,7 @@
}
},
{
- "@id": "urn:a65b8d80-0bd7-4490-b8d2-6dbe12682ca9",
+ "@id": "urn:17f60b95-1e29-42f6-9f58-15348ca2b014",
"Label": "sub-13_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/con_0001.nii",
"digest": {
@@ -201,7 +201,7 @@
}
},
{
- "@id": "urn:6670247b-4942-4a7a-a1fa-31c4d3f24695",
+ "@id": "urn:a781eafc-1231-45aa-8acf-0aff50490664",
"Label": "sub-14_con_0001.nii",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/con_0001.nii",
"digest": {
@@ -209,19 +209,19 @@
}
},
{
- "@id": "urn:58295d4c-36e1-499e-8a3a-181a424b6142",
+ "@id": "urn:f21f492c-1ded-461d-a8ba-11cf5b61aacf",
"Label": "SPM.mat",
- "GeneratedBy": "urn:c4b41eb0-6e4c-466e-907d-9ae326422bdb"
+ "GeneratedBy": "urn:63557888-6f6f-4d2a-81a1-932de748541d"
},
{
- "@id": "urn:3dc068ee-1ef5-4ee5-bb1b-e1c8b3c87c91",
+ "@id": "urn:0019adae-0fa4-4e8f-8824-8ecb74ced688",
"Label": "SPM.mat",
- "GeneratedBy": "urn:9ab1f065-b1b1-4d54-a405-59ef938a5da1"
+ "GeneratedBy": "urn:3689a407-0661-43c1-b0a4-bd37850fd700"
},
{
- "@id": "urn:9d1898a7-03e2-445f-8756-faeb5bec2948",
+ "@id": "urn:5d377cc5-43ba-4030-91de-b34c5c5d5523",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b1cfd1b0-2ccc-4359-b62c-14e43afb5b18"
+ "GeneratedBy": "urn:46d2d540-a591-40b0-85f4-6d99a9fd34cb"
}
]
}
diff --git a/examples/from_parsers/spm/spm_group_ols_batch.png b/examples/from_parsers/spm/spm_group_ols_batch.png
index b3fe6f175..40d26f0cc 100644
Binary files a/examples/from_parsers/spm/spm_group_ols_batch.png and b/examples/from_parsers/spm/spm_group_ols_batch.png differ
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.jsonld b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
index 899402ddd..ac95ef995 100644
--- a/examples/from_parsers/spm/spm_group_wls_batch.jsonld
+++ b/examples/from_parsers/spm/spm_group_wls_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "@id": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,37 +13,37 @@
],
"Activities": [
{
- "@id": "urn:1170e700-aa59-4aa0-997b-b8f4e38a73d6",
+ "@id": "urn:807971b5-90d4-4741-a69f-8931c3c5e746",
"Label": "stats.mfx.ffx",
"Used": [
- "urn:de7874b0-8d41-4d13-9f8a-d25dd58b7343",
- "urn:80c4a099-d6e8-436f-95e3-7200b12e2428",
- "urn:12c1865a-4e4e-43c6-9f86-75748ccc4b69",
- "urn:283f6a2c-60bd-4445-8863-64da92b4e7ec",
- "urn:2fc87508-3c73-46fa-8b6d-1ee5c8e516e5",
- "urn:fe07b655-f61a-42ab-997a-c3213afad432",
- "urn:cb76aa60-f974-4049-9756-cd45aff5f484",
- "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
- "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
- "urn:a73c178f-c270-4508-803e-75b75a75d3d5",
- "urn:20676c33-d8a3-4691-977a-ea452c18f373",
- "urn:aa96021b-cc85-47e0-afd1-a427861606f0",
- "urn:50667222-e5a1-489b-b422-5627eca72bc6",
- "urn:5149ab44-6c94-47ec-9d96-f8a8558e930b"
+ "urn:f01afec8-8551-4e82-a73e-7b0e7466afdd",
+ "urn:89d72914-4200-41f9-a756-1f0024506f14",
+ "urn:86b9e119-37bf-49fd-b850-0570cc53c3b8",
+ "urn:029ff773-b876-4565-854a-eafde9c7aaaa",
+ "urn:0a18f670-0cec-40ad-8458-5613c2aaf574",
+ "urn:4abe4996-f2c8-41cc-8561-e4ae6c3e9474",
+ "urn:32abc1e4-0bbf-4ef4-a8e9-c2f67a5eb11c",
+ "urn:a76bfa82-0ac8-4e80-ac42-ec944929459f",
+ "urn:fd12a58d-0911-428a-9049-3519c84b23d6",
+ "urn:f6fe1240-45ad-4a19-a07d-df7de9f3f96d",
+ "urn:186b2014-9458-4f2b-8d8a-31a9b39be1f5",
+ "urn:55b47535-6244-4008-b24c-b417f36f1a07",
+ "urn:c95a9c1f-ad08-4358-a423-8f333dd6e996",
+ "urn:8cb2cdce-390d-44a3-9b79-61baed152e49"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{1}.spm.stats.mfx.ffx.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'};\nmatlabbatch{1}.spm.stats.mfx.ffx.spmmat = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat','/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat',};",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_WLS_t_test'}"
}
},
{
- "@id": "urn:fc2beb3a-0ddd-4657-a687-4409efff62b4",
+ "@id": "urn:da9be219-1e1c-469d-9def-a0f6c1cd679f",
"Label": "Estimate stat.",
"Used": [
- "urn:d191a56c-9c39-409d-a7f3-89bf42f57cc6"
+ "urn:45e2bca9-7675-4ee6-8c57-7fcd33d51a0e"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('FFX Specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -51,24 +51,24 @@
}
},
{
- "@id": "urn:072360e9-f1eb-43eb-9fa1-b58a93ba009d",
+ "@id": "urn:613d4024-978b-4042-8677-856dcd153fdd",
"Label": "stats.mfx.spec",
"Used": [
- "urn:1dcfc72d-5ed6-4ff7-a613-c69991b5c517"
+ "urn:e2b94bbc-7b9d-42b4-a4a8-02abcdf4eafd"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{3}.spm.stats.mfx.spec.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.mfx.spec.contrast = [];",
"Parameters": {
"contrast": "[]"
}
},
{
- "@id": "urn:162eba86-ca6b-40ce-90b8-82fc8a8aee10",
+ "@id": "urn:3c406d97-e58a-4264-9ea1-cd9cc3009c32",
"Label": "Estimate stat.",
"Used": [
- "urn:d6cbc859-2b90-4245-a5fa-a7da66481e8f"
+ "urn:7bb84456-964c-4314-bb24-10f5018731ab"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{4}.spm.stats.fmri_est.spmmat(1) = cfg_dep('MFX Specification: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{4}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -76,12 +76,12 @@
}
},
{
- "@id": "urn:b50c1808-e500-4550-966a-e626b6b521f9",
+ "@id": "urn:8e237c8a-8985-456f-ba72-ae41b9f753a0",
"Label": "Estimate contrast",
"Used": [
- "urn:0f978606-b24a-49bb-bc30-6419c648087e"
+ "urn:86b35929-f1ee-473d-8639-edd3a207b228"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{5}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.name = 'con-01: Tone Counting vs Baseline';\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{5}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{5}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'con-01: Tone Counting vs Baseline'",
@@ -91,12 +91,12 @@
}
},
{
- "@id": "urn:be39d02a-940a-4437-9d22-c7f954010a48",
+ "@id": "urn:f7a8a677-377a-4757-bd2c-fde4fc3b1150",
"Label": "Threshold",
"Used": [
- "urn:b75e6167-a56b-47f0-b2b3-f704b2e3f1d1"
+ "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7"
],
- "AssociatedWith": "urn:cad734fe-8e50-4457-92ae-2951b1114e43",
+ "AssociatedWith": "urn:cc69fc0d-25e0-46fe-8712-4370967c20e5",
"Command": "matlabbatch{6}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{6}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{6}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{6}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{6}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{6}.spm.stats.results.conspec.extent = 2;\nmatlabbatch{6}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{6}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{6}.spm.stats.results.units = 1;\nmatlabbatch{6}.spm.stats.results.print = 'pdf';\nmatlabbatch{6}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -114,7 +114,7 @@
],
"Entities": [
{
- "@id": "urn:de7874b0-8d41-4d13-9f8a-d25dd58b7343",
+ "@id": "urn:f01afec8-8551-4e82-a73e-7b0e7466afdd",
"Label": "sub-01_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-01/SPM.mat",
"digest": {
@@ -122,7 +122,7 @@
}
},
{
- "@id": "urn:80c4a099-d6e8-436f-95e3-7200b12e2428",
+ "@id": "urn:89d72914-4200-41f9-a756-1f0024506f14",
"Label": "sub-02_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-02/SPM.mat",
"digest": {
@@ -130,7 +130,7 @@
}
},
{
- "@id": "urn:12c1865a-4e4e-43c6-9f86-75748ccc4b69",
+ "@id": "urn:86b9e119-37bf-49fd-b850-0570cc53c3b8",
"Label": "sub-03_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-03/SPM.mat",
"digest": {
@@ -138,7 +138,7 @@
}
},
{
- "@id": "urn:283f6a2c-60bd-4445-8863-64da92b4e7ec",
+ "@id": "urn:029ff773-b876-4565-854a-eafde9c7aaaa",
"Label": "sub-04_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-04/SPM.mat",
"digest": {
@@ -146,7 +146,7 @@
}
},
{
- "@id": "urn:2fc87508-3c73-46fa-8b6d-1ee5c8e516e5",
+ "@id": "urn:0a18f670-0cec-40ad-8458-5613c2aaf574",
"Label": "sub-06_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-06/SPM.mat",
"digest": {
@@ -154,7 +154,7 @@
}
},
{
- "@id": "urn:fe07b655-f61a-42ab-997a-c3213afad432",
+ "@id": "urn:4abe4996-f2c8-41cc-8561-e4ae6c3e9474",
"Label": "sub-07_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-07/SPM.mat",
"digest": {
@@ -162,7 +162,7 @@
}
},
{
- "@id": "urn:cb76aa60-f974-4049-9756-cd45aff5f484",
+ "@id": "urn:32abc1e4-0bbf-4ef4-a8e9-c2f67a5eb11c",
"Label": "sub-08_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-08/SPM.mat",
"digest": {
@@ -170,7 +170,7 @@
}
},
{
- "@id": "urn:4f3e80fa-50c7-4f8b-8415-92b4b77b380e",
+ "@id": "urn:a76bfa82-0ac8-4e80-ac42-ec944929459f",
"Label": "sub-09_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-09/SPM.mat",
"digest": {
@@ -178,7 +178,7 @@
}
},
{
- "@id": "urn:d3f5c0f9-c276-4ecf-b5e5-7842e1866af6",
+ "@id": "urn:fd12a58d-0911-428a-9049-3519c84b23d6",
"Label": "sub-10_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-10/SPM.mat",
"digest": {
@@ -186,7 +186,7 @@
}
},
{
- "@id": "urn:a73c178f-c270-4508-803e-75b75a75d3d5",
+ "@id": "urn:f6fe1240-45ad-4a19-a07d-df7de9f3f96d",
"Label": "sub-11_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-11/SPM.mat",
"digest": {
@@ -194,7 +194,7 @@
}
},
{
- "@id": "urn:20676c33-d8a3-4691-977a-ea452c18f373",
+ "@id": "urn:186b2014-9458-4f2b-8d8a-31a9b39be1f5",
"Label": "sub-12_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-12/SPM.mat",
"digest": {
@@ -202,7 +202,7 @@
}
},
{
- "@id": "urn:aa96021b-cc85-47e0-afd1-a427861606f0",
+ "@id": "urn:55b47535-6244-4008-b24c-b417f36f1a07",
"Label": "sub-13_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-13/SPM.mat",
"digest": {
@@ -210,7 +210,7 @@
}
},
{
- "@id": "urn:50667222-e5a1-489b-b422-5627eca72bc6",
+ "@id": "urn:c95a9c1f-ad08-4358-a423-8f333dd6e996",
"Label": "sub-14_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-14/SPM.mat",
"digest": {
@@ -218,7 +218,7 @@
}
},
{
- "@id": "urn:5149ab44-6c94-47ec-9d96-f8a8558e930b",
+ "@id": "urn:8cb2cdce-390d-44a3-9b79-61baed152e49",
"Label": "sub-05_SPM.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/LEVEL1/sub-05/SPM.mat",
"digest": {
@@ -226,29 +226,29 @@
}
},
{
- "@id": "urn:d191a56c-9c39-409d-a7f3-89bf42f57cc6",
+ "@id": "urn:45e2bca9-7675-4ee6-8c57-7fcd33d51a0e",
"Label": "SPM.mat",
- "GeneratedBy": "urn:1170e700-aa59-4aa0-997b-b8f4e38a73d6"
+ "GeneratedBy": "urn:807971b5-90d4-4741-a69f-8931c3c5e746"
},
{
- "@id": "urn:1dcfc72d-5ed6-4ff7-a613-c69991b5c517",
+ "@id": "urn:e2b94bbc-7b9d-42b4-a4a8-02abcdf4eafd",
"Label": "SPM.mat",
- "GeneratedBy": "urn:fc2beb3a-0ddd-4657-a687-4409efff62b4"
+ "GeneratedBy": "urn:da9be219-1e1c-469d-9def-a0f6c1cd679f"
},
{
- "@id": "urn:d6cbc859-2b90-4245-a5fa-a7da66481e8f",
+ "@id": "urn:7bb84456-964c-4314-bb24-10f5018731ab",
"Label": "SPM.mat",
- "GeneratedBy": "urn:072360e9-f1eb-43eb-9fa1-b58a93ba009d"
+ "GeneratedBy": "urn:613d4024-978b-4042-8677-856dcd153fdd"
},
{
- "@id": "urn:0f978606-b24a-49bb-bc30-6419c648087e",
+ "@id": "urn:86b35929-f1ee-473d-8639-edd3a207b228",
"Label": "SPM.mat",
- "GeneratedBy": "urn:162eba86-ca6b-40ce-90b8-82fc8a8aee10"
+ "GeneratedBy": "urn:3c406d97-e58a-4264-9ea1-cd9cc3009c32"
},
{
- "@id": "urn:b75e6167-a56b-47f0-b2b3-f704b2e3f1d1",
+ "@id": "urn:d41c4d7c-7f7f-4c9d-8db0-b3bb3e06f8a7",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b50c1808-e500-4550-966a-e626b6b521f9"
+ "GeneratedBy": "urn:8e237c8a-8985-456f-ba72-ae41b9f753a0"
}
]
}
diff --git a/examples/from_parsers/spm/spm_group_wls_batch.png b/examples/from_parsers/spm/spm_group_wls_batch.png
index 6b96edcaa..a259e4791 100644
Binary files a/examples/from_parsers/spm/spm_group_wls_batch.png and b/examples/from_parsers/spm/spm_group_wls_batch.png differ
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
index 93c8b2380..278286105 100644
--- a/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
+++ b/examples/from_parsers/spm/spm_hrf_fir_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "@id": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:083e7a48-1f1e-4a25-8049-d4b80641baae",
+ "@id": "urn:71bf85a6-3335-409a-a4bb-c2fa29231c14",
"Label": "Move file",
"Used": [
- "urn:105801bb-7b35-42d6-9ff2-4966a82149c5"
+ "urn:32ca811a-225c-43e8-a31c-2546ee3ada58"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:dc28ed67-83ae-483a-9eeb-de245979553a",
+ "@id": "urn:9be18a5c-3e3e-47aa-bac9-211eae7b613e",
"Label": "Move file",
"Used": [
- "urn:1ae8f36b-01cf-4052-ac85-d10dc0aa6524"
+ "urn:4ae04bd2-f829-465d-967b-51490c165efc"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:45579f06-fc67-4a72-a435-4a2bde6046c2",
+ "@id": "urn:9d012f66-8a8a-4b25-8006-061296d9b452",
"Label": "Gunzip",
"Used": [
- "urn:d6be4df1-d211-401a-8876-ee0cf6e05ac3"
+ "urn:73d43f31-95c3-4568-b492-5ca4371c4f13"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:bf51fb88-d326-4f30-be43-ab454615eef4",
+ "@id": "urn:9b12c597-55e3-4cc1-8d36-7229cbd4b64a",
"Label": "Gunzip",
"Used": [
- "urn:d1e447a7-bec3-421c-b7c3-9138d92c7206"
+ "urn:9d77733e-7a2d-451f-970e-c6292ca36386"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:b740cb2c-c571-42cb-92e6-030da5016c8f",
+ "@id": "urn:536112dd-62ec-4f7c-bad8-95c16e582d83",
"Label": "Realign",
"Used": [
- "urn:b6722269-67c1-45e2-a55d-94e6e075c7f4"
+ "urn:0e2032e9-ee9a-41f0-bd5b-53089bd62c12"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:33f25266-483a-4f84-b431-94d1e059dbfa",
+ "@id": "urn:53e45275-0dd2-4380-89b0-e06263477c86",
"Label": "Coregister",
"Used": [
- "urn:ae25f772-385e-4722-90fd-3d6bca543569",
- "urn:d188f22b-b723-47f5-b94e-a0060df4a500"
+ "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
+ "urn:8fe8a3f1-b285-4417-b942-d9a281060918"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266",
+ "@id": "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df",
"Label": "Segment",
"Used": [
- "urn:d188f22b-b723-47f5-b94e-a0060df4a500"
+ "urn:8fe8a3f1-b285-4417-b942-d9a281060918"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:a46ad4e6-5621-4686-b06f-2f4c85f6fded",
+ "@id": "urn:36bb8644-008c-45bd-8c8e-ce0fd687b486",
"Label": "Normalize",
"Used": [
- "urn:2a713eec-eb1a-4ace-9328-7e0d28524daa",
- "urn:ae25f772-385e-4722-90fd-3d6bca543569"
+ "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
+ "urn:19e57842-9830-4d40-b483-414e17fe13b2"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:afb009d3-f148-4a9d-b917-855c4c049aab",
+ "@id": "urn:068a56ed-fa24-4ab2-9781-d333a439bf94",
"Label": "Normalize",
"Used": [
- "urn:2a713eec-eb1a-4ace-9328-7e0d28524daa"
+ "urn:19e57842-9830-4d40-b483-414e17fe13b2"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:e4838222-2b8c-4e52-9bcb-14121cde4681",
+ "@id": "urn:e15e0c07-ad7d-4cf8-8615-461337751f00",
"Label": "Smooth",
"Used": [
- "urn:beff7ab6-7cd1-4cc4-a241-5a6e8d8024ef"
+ "urn:acd4e7d2-df0c-48fb-aa83-679b3df6591c"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:a2983d0b-37f1-46b8-8815-5532cf9dd9f4",
+ "@id": "urn:0a4cb941-af52-4ed0-883f-ad9d4e7b316c",
"Label": "Stat Design",
"Used": [
- "urn:abe0ec4f-41d6-4388-83b3-816399fb430b",
- "urn:6d9c0313-572b-46d4-acdc-537652e3b978"
+ "urn:8679d689-6609-4dd7-85a2-330a667c96e9",
+ "urn:5c190260-bee3-477a-956e-d0675ac7e19e"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.length = 20;\nmatlabbatch{11}.spm.stats.fmri_spec.bases.fir.order = 10;\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FIR_basis'}",
@@ -215,12 +215,12 @@
}
},
{
- "@id": "urn:3888ab93-e11b-43ed-a1f4-4829a093becf",
+ "@id": "urn:9d964c85-58a1-40e2-8ea1-06c596be6661",
"Label": "Estimate stat.",
"Used": [
- "urn:4663d55e-670a-44cf-94de-46cc8a947ede"
+ "urn:e9c625c6-6f1f-4f30-a2ca-393e566b1ad8"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -228,12 +228,12 @@
}
},
{
- "@id": "urn:ae83add3-6da7-4eae-8dfe-79cea4c4d1ac",
+ "@id": "urn:5d51bc01-580e-4fb9-a4b5-453ef634cd1a",
"Label": "Estimate contrast",
"Used": [
- "urn:b627d50b-31e2-462e-b4f6-a5e381e2a660"
+ "urn:32bbae9d-fb30-4902-bf42-a34d51ac5989"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.name = 'Tone Counting vs Baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.weights = [1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1];\nmatlabbatch{13}.spm.stats.con.consess{1}.fcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.fcon.name": "'Tone Counting vs Baseline'",
@@ -243,12 +243,12 @@
}
},
{
- "@id": "urn:98a3c2dc-d375-4d4b-b976-391124a62240",
+ "@id": "urn:f1197319-954d-477d-bb96-7dee72a45bd7",
"Label": "Threshold",
"Used": [
- "urn:3cd9afa2-db8f-4e97-8362-708061f8f699"
+ "urn:0e2f2522-9df7-4407-a50e-04e4fc9f4475"
],
- "AssociatedWith": "urn:634b8ef5-df07-4afc-8509-66a3973abbeb",
+ "AssociatedWith": "urn:63b1ead7-b09f-4f03-8bc6-1d1d547c045f",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -266,7 +266,7 @@
],
"Entities": [
{
- "@id": "urn:105801bb-7b35-42d6-9ff2-4966a82149c5",
+ "@id": "urn:32ca811a-225c-43e8-a31c-2546ee3ada58",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -274,7 +274,7 @@
}
},
{
- "@id": "urn:1ae8f36b-01cf-4052-ac85-d10dc0aa6524",
+ "@id": "urn:4ae04bd2-f829-465d-967b-51490c165efc",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -282,57 +282,57 @@
}
},
{
- "@id": "urn:d6be4df1-d211-401a-8876-ee0cf6e05ac3",
+ "@id": "urn:73d43f31-95c3-4568-b492-5ca4371c4f13",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:083e7a48-1f1e-4a25-8049-d4b80641baae"
+ "GeneratedBy": "urn:71bf85a6-3335-409a-a4bb-c2fa29231c14"
},
{
- "@id": "urn:d1e447a7-bec3-421c-b7c3-9138d92c7206",
+ "@id": "urn:9d77733e-7a2d-451f-970e-c6292ca36386",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:dc28ed67-83ae-483a-9eeb-de245979553a"
+ "GeneratedBy": "urn:9be18a5c-3e3e-47aa-bac9-211eae7b613e"
},
{
- "@id": "urn:b6722269-67c1-45e2-a55d-94e6e075c7f4",
+ "@id": "urn:0e2032e9-ee9a-41f0-bd5b-53089bd62c12",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:45579f06-fc67-4a72-a435-4a2bde6046c2"
+ "GeneratedBy": "urn:9d012f66-8a8a-4b25-8006-061296d9b452"
},
{
- "@id": "urn:ae25f772-385e-4722-90fd-3d6bca543569",
+ "@id": "urn:12dfa6ff-144e-4f66-9fd4-2409d56c120d",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:b740cb2c-c571-42cb-92e6-030da5016c8f"
+ "GeneratedBy": "urn:536112dd-62ec-4f7c-bad8-95c16e582d83"
},
{
- "@id": "urn:d188f22b-b723-47f5-b94e-a0060df4a500",
+ "@id": "urn:8fe8a3f1-b285-4417-b942-d9a281060918",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:bf51fb88-d326-4f30-be43-ab454615eef4"
+ "GeneratedBy": "urn:9b12c597-55e3-4cc1-8d36-7229cbd4b64a"
},
{
- "@id": "urn:2a713eec-eb1a-4ace-9328-7e0d28524daa",
+ "@id": "urn:19e57842-9830-4d40-b483-414e17fe13b2",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266",
+ "GeneratedBy": "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:fd1d4aff-2275-4cf2-a575-8ee7b01253b0",
+ "@id": "urn:ecb956c2-4afd-45b2-836a-a5deb9acec5b",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:1f888d36-8dc1-4dd9-aed3-6307c376c266",
+ "GeneratedBy": "urn:f4fa8ecb-fe15-40ca-92ed-74c9e1fe18df",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:beff7ab6-7cd1-4cc4-a241-5a6e8d8024ef",
- "Label": "wsegment1",
- "GeneratedBy": "urn:a46ad4e6-5621-4686-b06f-2f4c85f6fded"
+ "@id": "urn:acd4e7d2-df0c-48fb-aa83-679b3df6591c",
+ "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:36bb8644-008c-45bd-8c8e-ce0fd687b486"
},
{
- "@id": "urn:6d9c0313-572b-46d4-acdc-537652e3b978",
+ "@id": "urn:5c190260-bee3-477a-956e-d0675ac7e19e",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -340,24 +340,24 @@
}
},
{
- "@id": "urn:abe0ec4f-41d6-4388-83b3-816399fb430b",
- "Label": "swsegment1",
- "GeneratedBy": "urn:e4838222-2b8c-4e52-9bcb-14121cde4681"
+ "@id": "urn:8679d689-6609-4dd7-85a2-330a667c96e9",
+ "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:e15e0c07-ad7d-4cf8-8615-461337751f00"
},
{
- "@id": "urn:4663d55e-670a-44cf-94de-46cc8a947ede",
+ "@id": "urn:e9c625c6-6f1f-4f30-a2ca-393e566b1ad8",
"Label": "SPM.mat",
- "GeneratedBy": "urn:a2983d0b-37f1-46b8-8815-5532cf9dd9f4"
+ "GeneratedBy": "urn:0a4cb941-af52-4ed0-883f-ad9d4e7b316c"
},
{
- "@id": "urn:b627d50b-31e2-462e-b4f6-a5e381e2a660",
+ "@id": "urn:32bbae9d-fb30-4902-bf42-a34d51ac5989",
"Label": "SPM.mat",
- "GeneratedBy": "urn:3888ab93-e11b-43ed-a1f4-4829a093becf"
+ "GeneratedBy": "urn:9d964c85-58a1-40e2-8ea1-06c596be6661"
},
{
- "@id": "urn:3cd9afa2-db8f-4e97-8362-708061f8f699",
+ "@id": "urn:0e2f2522-9df7-4407-a50e-04e4fc9f4475",
"Label": "SPM.mat",
- "GeneratedBy": "urn:ae83add3-6da7-4eae-8dfe-79cea4c4d1ac"
+ "GeneratedBy": "urn:5d51bc01-580e-4fb9-a4b5-453ef634cd1a"
}
]
}
diff --git a/examples/from_parsers/spm/spm_hrf_fir_batch.png b/examples/from_parsers/spm/spm_hrf_fir_batch.png
index efd4d1461..49c37ff7a 100644
Binary files a/examples/from_parsers/spm/spm_hrf_fir_batch.png and b/examples/from_parsers/spm/spm_hrf_fir_batch.png differ
diff --git a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
index 8bd06a3a2..032d41b79 100644
--- a/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
+++ b/examples/from_parsers/spm/spm_non_sphericity_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "@id": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,10 +13,10 @@
],
"Activities": [
{
- "@id": "urn:b02e72d6-09fc-41b9-b8c1-24d50bab9a4a",
+ "@id": "urn:caf2279a-3820-496f-be73-ce7f46be7671",
"Label": "stats.factorial_design",
"Used": [],
- "AssociatedWith": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "AssociatedWith": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
"Command": "matlabbatch{1}.spm.stats.factorial_design.dir = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.name = 'Basis';\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.dept = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.variance = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.gmsca = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.fact.ancova = 0;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).levels = 1;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(1).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0001.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0001.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).levels = 2;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(2).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0005.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0005.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).levels = 3;\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.icell(3).scans = {'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub01/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub02/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub03/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub04/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub05/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub06/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub07/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub08/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub09/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub10/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub11/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub12/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub13/CanonicalHRF/con_0009.nii,1','/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Sub14/CanonicalHRF/con_0009.nii,1',};\nmatlabbatch{1}.spm.stats.factorial_design.des.fd.contrasts = 1;\nmatlabbatch{1}.spm.stats.factorial_design.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});\nmatlabbatch{1}.spm.stats.factorial_design.masking.tm.tm_none = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.im = 1;\nmatlabbatch{1}.spm.stats.factorial_design.masking.em = {''};\nmatlabbatch{1}.spm.stats.factorial_design.globalc.g_omit = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.gmsca.gmsca_no = 1;\nmatlabbatch{1}.spm.stats.factorial_design.globalm.glonorm = 1;",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/Testing/ds000006/RESULTS/Group/Informed'}",
@@ -44,12 +44,12 @@
}
},
{
- "@id": "urn:30e03dcc-204f-4159-afcc-fcd7efe4664d",
+ "@id": "urn:766de64a-5420-4b86-ad90-769f84993459",
"Label": "Estimate stat.",
"Used": [
- "urn:66596f41-21e7-4190-82a8-de0697b8d0c6"
+ "urn:cfec80c8-b4bb-46d9-a53b-5f045b4743fc"
],
- "AssociatedWith": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "AssociatedWith": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
"Command": "matlabbatch{2}.spm.stats.fmri_est.spmmat(1) = cfg_dep('Factorial design specification: SPM.mat File', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{2}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{2}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -57,12 +57,12 @@
}
},
{
- "@id": "urn:d56be92e-40d9-463a-9e7e-2b14886091df",
+ "@id": "urn:b1782bbc-0ad8-4cf5-a5ce-d586bc629dfa",
"Label": "Estimate contrast",
"Used": [
- "urn:8b77e7f5-fa5d-43fe-a8c3-caf66c861b43"
+ "urn:af33c7b9-c0cb-4b14-b3b8-f3834419057c"
],
- "AssociatedWith": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "AssociatedWith": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
"Command": "matlabbatch{3}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.name = 'mr vs plain informed basis';\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.weights = 1;\nmatlabbatch{3}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{3}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'mr vs plain informed basis'",
@@ -72,12 +72,12 @@
}
},
{
- "@id": "urn:df94604f-7f06-4143-9b98-e624dab2dc66",
+ "@id": "urn:87cf0f33-5bbd-4175-a409-80425fd78b0c",
"Label": "Threshold",
"Used": [
- "urn:b5bb999c-2c05-4151-8a2a-4fec1f086e87"
+ "urn:a34697f5-7ad9-481b-bbfe-69d17ec623ff"
],
- "AssociatedWith": "urn:5808802e-2ed8-4307-966b-e5ca05b9ce35",
+ "AssociatedWith": "urn:ef63cb18-25fb-485f-b5c1-5c528cb4080c",
"Command": "matlabbatch{4}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{4}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{4}.spm.stats.results.conspec.contrasts = 1;\nmatlabbatch{4}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{4}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{4}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{4}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{4}.spm.stats.results.units = 1;\nmatlabbatch{4}.spm.stats.results.print = 'pdf';\nmatlabbatch{4}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -94,19 +94,19 @@
],
"Entities": [
{
- "@id": "urn:66596f41-21e7-4190-82a8-de0697b8d0c6",
+ "@id": "urn:cfec80c8-b4bb-46d9-a53b-5f045b4743fc",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b02e72d6-09fc-41b9-b8c1-24d50bab9a4a"
+ "GeneratedBy": "urn:caf2279a-3820-496f-be73-ce7f46be7671"
},
{
- "@id": "urn:8b77e7f5-fa5d-43fe-a8c3-caf66c861b43",
+ "@id": "urn:af33c7b9-c0cb-4b14-b3b8-f3834419057c",
"Label": "SPM.mat",
- "GeneratedBy": "urn:30e03dcc-204f-4159-afcc-fcd7efe4664d"
+ "GeneratedBy": "urn:766de64a-5420-4b86-ad90-769f84993459"
},
{
- "@id": "urn:b5bb999c-2c05-4151-8a2a-4fec1f086e87",
+ "@id": "urn:a34697f5-7ad9-481b-bbfe-69d17ec623ff",
"Label": "SPM.mat",
- "GeneratedBy": "urn:d56be92e-40d9-463a-9e7e-2b14886091df"
+ "GeneratedBy": "urn:b1782bbc-0ad8-4cf5-a5ce-d586bc629dfa"
}
]
}
diff --git a/examples/from_parsers/spm/spm_non_sphericity_batch.png b/examples/from_parsers/spm/spm_non_sphericity_batch.png
index 5bcd620ca..fa331f50a 100644
Binary files a/examples/from_parsers/spm/spm_non_sphericity_batch.png and b/examples/from_parsers/spm/spm_non_sphericity_batch.png differ
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
index 18d129708..ad0d3d728 100644
--- a/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
+++ b/examples/from_parsers/spm/spm_partial_conjunction_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "@id": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:9fc79763-50ca-44d0-af53-ea663f18a6c9",
+ "@id": "urn:ee8550a1-3a25-4bd3-b41f-5f9db3c2b519",
"Label": "Move file",
"Used": [
- "urn:d816bf62-f91e-4d89-af7d-9078d2f8bc45"
+ "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:f268d524-4ea7-4ace-aa2e-80e6941b108d",
+ "@id": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7",
"Label": "Move file",
"Used": [
- "urn:a6e50cb0-3790-46cd-97c4-6108afc39afe"
+ "urn:7432af95-c46f-44b9-95d5-3ae073e9ad67"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:8abe0474-66d5-4e8d-b799-4ca935562832",
+ "@id": "urn:998c136b-89ab-434d-a383-742a8fe2cce7",
"Label": "Gunzip",
"Used": [
- "urn:247e6f18-0048-4538-afb0-c248e2ba36cf"
+ "urn:89c4e160-0920-4f79-8e68-1b551e450cfd"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:a05bcc8c-767e-4ef9-ad52-82fdcf352918",
+ "@id": "urn:5f19e94d-ef3e-4f08-a70a-fc0a4b04af0c",
"Label": "Gunzip",
"Used": [
- "urn:9c9633d5-e312-4218-beaf-ee48cdb1b684"
+ "urn:43ef2542-539e-48ab-a49a-8da522fc39f0"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:2f2e9df1-ab83-49ff-bf11-f4b440a61b43",
+ "@id": "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d",
"Label": "Realign",
"Used": [
- "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501"
+ "urn:5fef3b34-c5f1-40d0-9aea-2f73c630a76d"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:8a4b04a5-355c-436b-a9cd-d1ba1623a3de",
+ "@id": "urn:71f217d2-6168-49ce-b34a-2af8f784cbba",
"Label": "Coregister",
"Used": [
- "urn:32ee6bc3-7996-47c5-ba5d-ad3dae831538",
- "urn:63c66930-7e3d-4eee-a6b2-45f96119bb14"
+ "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "urn:5b5c87cc-97a8-4240-b775-75efd13b8593"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:0b11c98b-cb04-4ad6-943f-b7e64be5838a",
+ "@id": "urn:f19244b7-cdec-4f32-b146-f4960ae71b37",
"Label": "Segment",
"Used": [
- "urn:32ee6bc3-7996-47c5-ba5d-ad3dae831538"
+ "urn:5b5c87cc-97a8-4240-b775-75efd13b8593"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:617710f9-1f1a-416f-ae6b-d2994da8000b",
+ "@id": "urn:819c043e-ead2-4552-8e12-041ff73e323f",
"Label": "Normalize",
"Used": [
- "urn:63c66930-7e3d-4eee-a6b2-45f96119bb14",
- "urn:6f513969-f03e-43be-a09b-5dd6b976de3c"
+ "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
+ "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:9734bf62-20af-427c-a298-49437e993740",
+ "@id": "urn:1a23fb57-c14c-4da3-9204-95c4e584f280",
"Label": "Normalize",
"Used": [
- "urn:6f513969-f03e-43be-a09b-5dd6b976de3c"
+ "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:8f862f58-0135-443a-84b8-7d315d0751e5",
+ "@id": "urn:65818fda-55ce-49f1-8050-9d98c12d9a1f",
"Label": "Smooth",
"Used": [
- "urn:8683b331-474b-43db-938a-3fb2df8077ff"
+ "urn:b03f2346-70cd-49f6-a995-232920cbf408"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:dbb688bc-e370-4644-9913-9ae6f2e86ecb",
+ "@id": "urn:1f1dac39-5b79-476b-894e-a1676c4d2598",
"Label": "Stat Design",
"Used": [
- "urn:ebb912a3-bf02-4ba8-9363-a5e83909e65a",
- "urn:7cf453df-7e7b-4f99-8439-7859bdc17e52"
+ "urn:a658296a-11c4-4d87-ab0a-181e946b0a50",
+ "urn:476c572f-a2bc-434d-9299-303b612766fb"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_conjunction'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:66b30f36-6225-462e-8ad6-27c5ecd6af06",
+ "@id": "urn:96f5bf66-b838-41b0-9eb6-9bf8e0a1fd0a",
"Label": "Estimate stat.",
"Used": [
- "urn:49b19b62-af92-47fa-8c77-2337c2f05775"
+ "urn:3eb4f264-bd28-42b0-8b23-96b6e899eef6"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:67cafc9e-cf08-49e6-ab5b-e48caba9edf8",
+ "@id": "urn:c586e728-fcc7-4e86-b211-dfc2ab5d386c",
"Label": "Estimate contrast",
"Used": [
- "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a"
+ "urn:a8876dcf-5b2e-4d0f-9559-26f088731cff"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.name = 'tone counting probe vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.weights = [0 1];\nmatlabbatch{13}.spm.stats.con.consess{2}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -245,12 +245,12 @@
}
},
{
- "@id": "urn:f9d61dcc-d611-48da-8113-8e5d940d45bf",
+ "@id": "urn:6b9e5904-fd7d-4fd1-a40d-b84d8cd6e99b",
"Label": "Threshold",
"Used": [
- "urn:678f852c-890c-4abc-bf0a-1e737c5189bc"
+ "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da"
],
- "AssociatedWith": "urn:09ebc5dc-0466-4923-bd49-13831d041c86",
+ "AssociatedWith": "urn:5c9bd078-6db8-4b60-b5e2-aff1b54efc40",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = [1 2];\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 2;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -268,7 +268,7 @@
],
"Entities": [
{
- "@id": "urn:d816bf62-f91e-4d89-af7d-9078d2f8bc45",
+ "@id": "urn:2140f53b-4cd5-4241-a26a-b5784ee52d7c",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -276,7 +276,7 @@
}
},
{
- "@id": "urn:a6e50cb0-3790-46cd-97c4-6108afc39afe",
+ "@id": "urn:7432af95-c46f-44b9-95d5-3ae073e9ad67",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -284,57 +284,57 @@
}
},
{
- "@id": "urn:247e6f18-0048-4538-afb0-c248e2ba36cf",
+ "@id": "urn:89c4e160-0920-4f79-8e68-1b551e450cfd",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:9fc79763-50ca-44d0-af53-ea663f18a6c9"
+ "GeneratedBy": "urn:ee8550a1-3a25-4bd3-b41f-5f9db3c2b519"
},
{
- "@id": "urn:9c9633d5-e312-4218-beaf-ee48cdb1b684",
+ "@id": "urn:43ef2542-539e-48ab-a49a-8da522fc39f0",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:f268d524-4ea7-4ace-aa2e-80e6941b108d"
+ "GeneratedBy": "urn:260b6abf-d0ed-41b7-9357-f4dd9ad1d5c7"
},
{
- "@id": "urn:e6777837-2f7c-4cb1-ab0f-9ad45c985501",
+ "@id": "urn:5fef3b34-c5f1-40d0-9aea-2f73c630a76d",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8abe0474-66d5-4e8d-b799-4ca935562832"
+ "GeneratedBy": "urn:998c136b-89ab-434d-a383-742a8fe2cce7"
},
{
- "@id": "urn:63c66930-7e3d-4eee-a6b2-45f96119bb14",
+ "@id": "urn:4e8d8c44-d8ce-416c-affc-54c861d69d74",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:2f2e9df1-ab83-49ff-bf11-f4b440a61b43"
+ "GeneratedBy": "urn:324e8c1b-67a7-4216-8461-2cc4d2493a0d"
},
{
- "@id": "urn:32ee6bc3-7996-47c5-ba5d-ad3dae831538",
+ "@id": "urn:5b5c87cc-97a8-4240-b775-75efd13b8593",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:a05bcc8c-767e-4ef9-ad52-82fdcf352918"
+ "GeneratedBy": "urn:5f19e94d-ef3e-4f08-a70a-fc0a4b04af0c"
},
{
- "@id": "urn:6f513969-f03e-43be-a09b-5dd6b976de3c",
+ "@id": "urn:c5769ca5-ef3b-4107-a8bf-68949d5efc1d",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:0b11c98b-cb04-4ad6-943f-b7e64be5838a",
+ "GeneratedBy": "urn:f19244b7-cdec-4f32-b146-f4960ae71b37",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:a85d6e1c-9519-48a0-9494-5592eb2b8506",
+ "@id": "urn:eba8226f-0e46-44a0-8db3-f971ccf0da26",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:0b11c98b-cb04-4ad6-943f-b7e64be5838a",
+ "GeneratedBy": "urn:f19244b7-cdec-4f32-b146-f4960ae71b37",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:8683b331-474b-43db-938a-3fb2df8077ff",
+ "@id": "urn:b03f2346-70cd-49f6-a995-232920cbf408",
"Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:617710f9-1f1a-416f-ae6b-d2994da8000b"
+ "GeneratedBy": "urn:819c043e-ead2-4552-8e12-041ff73e323f"
},
{
- "@id": "urn:7cf453df-7e7b-4f99-8439-7859bdc17e52",
+ "@id": "urn:476c572f-a2bc-434d-9299-303b612766fb",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -342,24 +342,24 @@
}
},
{
- "@id": "urn:ebb912a3-bf02-4ba8-9363-a5e83909e65a",
+ "@id": "urn:a658296a-11c4-4d87-ab0a-181e946b0a50",
"Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8f862f58-0135-443a-84b8-7d315d0751e5"
+ "GeneratedBy": "urn:65818fda-55ce-49f1-8050-9d98c12d9a1f"
},
{
- "@id": "urn:49b19b62-af92-47fa-8c77-2337c2f05775",
+ "@id": "urn:3eb4f264-bd28-42b0-8b23-96b6e899eef6",
"Label": "SPM.mat",
- "GeneratedBy": "urn:dbb688bc-e370-4644-9913-9ae6f2e86ecb"
+ "GeneratedBy": "urn:1f1dac39-5b79-476b-894e-a1676c4d2598"
},
{
- "@id": "urn:2aafb6ce-d198-41d6-ab3e-16b28401a64a",
+ "@id": "urn:a8876dcf-5b2e-4d0f-9559-26f088731cff",
"Label": "SPM.mat",
- "GeneratedBy": "urn:66b30f36-6225-462e-8ad6-27c5ecd6af06"
+ "GeneratedBy": "urn:96f5bf66-b838-41b0-9eb6-9bf8e0a1fd0a"
},
{
- "@id": "urn:678f852c-890c-4abc-bf0a-1e737c5189bc",
+ "@id": "urn:6855557e-cac2-4c2c-8f4c-99dc46c313da",
"Label": "SPM.mat",
- "GeneratedBy": "urn:67cafc9e-cf08-49e6-ab5b-e48caba9edf8"
+ "GeneratedBy": "urn:c586e728-fcc7-4e86-b211-dfc2ab5d386c"
}
]
}
diff --git a/examples/from_parsers/spm/spm_partial_conjunction_batch.png b/examples/from_parsers/spm/spm_partial_conjunction_batch.png
index c8a071201..604bb6a66 100644
Binary files a/examples/from_parsers/spm/spm_partial_conjunction_batch.png and b/examples/from_parsers/spm/spm_partial_conjunction_batch.png differ
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
index e72b9bc54..edfd24573 100644
--- a/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
+++ b/examples/from_parsers/spm/spm_temporal_derivative_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "@id": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:9514e444-af9c-4649-b1e3-f2b7371e2ff3",
+ "@id": "urn:97410e53-4965-4ec1-8ab2-186b9801df5c",
"Label": "Move file",
"Used": [
- "urn:70787460-c0e9-4624-a974-df03ea059fd7"
+ "urn:7c6a5a4a-63e5-4786-b73c-f906e5120d91"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:a68a1574-7b09-437f-b75a-2c7214dbf8c6",
+ "@id": "urn:b2f24b4e-a723-44a7-bfeb-7434a9229cee",
"Label": "Move file",
"Used": [
- "urn:bbdd547f-1200-4863-9dda-efa4d1e55184"
+ "urn:1d6c2c35-9863-4bdf-b7fa-c197d57ea047"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:000439d2-1c29-420d-974e-96ebf05bc13c",
+ "@id": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb",
"Label": "Gunzip",
"Used": [
- "urn:02775417-0217-4d74-8e8a-e0541b4e1a0b"
+ "urn:8b7ebf9b-55a0-4a1d-b503-719151eebc50"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:0c6b3aeb-06f8-4e6b-b3ed-88acdbf9e0e6",
+ "@id": "urn:cc8f8d80-4f02-496d-9a4a-e0e2bfbe3189",
"Label": "Gunzip",
"Used": [
- "urn:2e107129-9700-4d13-a0b4-5ed8786d98ef"
+ "urn:0924054c-0c39-4d36-b059-e742e85e493d"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247",
+ "@id": "urn:74cebf5a-7236-4402-8dc4-8d5936bcc43c",
"Label": "Realign",
"Used": [
- "urn:cfc270b2-011d-4313-9bf2-42cf99099862"
+ "urn:3d1acc0f-aa48-46af-8bdb-36a6d9e4a8da"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:63697e02-287b-45a2-bb20-41e265601261",
+ "@id": "urn:8b3bbb39-0aea-4201-97f0-045c3f5022a9",
"Label": "Coregister",
"Used": [
- "urn:40eadda9-3a59-49a2-85e1-185be44acf98",
- "urn:d64426fc-7163-4fcf-ab12-74eda9c93e1d"
+ "urn:e9a73030-0006-4ef8-95e3-5834de3078f3",
+ "urn:fadd4862-4c4b-4a39-ba35-666f29181e2c"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:f63e0e3f-899b-4267-9ba8-15f26febbb07",
+ "@id": "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
"Label": "Segment",
"Used": [
- "urn:d64426fc-7163-4fcf-ab12-74eda9c93e1d"
+ "urn:fadd4862-4c4b-4a39-ba35-666f29181e2c"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:bcdad7b0-1900-445e-a58d-7cdbd0dd9cfc",
+ "@id": "urn:3e26d898-d64e-4301-8def-9765c710bcdf",
"Label": "Normalize",
"Used": [
- "urn:40eadda9-3a59-49a2-85e1-185be44acf98",
- "urn:eba38419-a546-4321-8e0a-8f3a41271a29"
+ "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01",
+ "urn:e9a73030-0006-4ef8-95e3-5834de3078f3"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:8b43fbba-524d-468c-87ea-c55ad1d6a24f",
+ "@id": "urn:d6a983fb-16fb-45a7-be11-a76b4e20cd8b",
"Label": "Normalize",
"Used": [
- "urn:eba38419-a546-4321-8e0a-8f3a41271a29"
+ "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:d8775774-929a-4f81-8fcb-6ba1f916e161",
+ "@id": "urn:1e662f78-13a4-474a-9645-9ee637aa9e4b",
"Label": "Smooth",
"Used": [
- "urn:e8191e7e-8505-4e9d-afc8-41e2324eb4dc"
+ "urn:b7a38a99-015b-4da7-abb8-e6579ba35172"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:53f02519-829b-4f61-9838-40048b816257",
+ "@id": "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53",
"Label": "Stat Design",
"Used": [
- "urn:379036c0-95c2-499c-aecc-8b2362a9a19f",
- "urn:8dc8374c-cbe1-47f8-9d6a-39ae8a5ebb34"
+ "urn:26a00968-1740-4b01-8330-41148ecff2f1",
+ "urn:e9aec74c-9fea-437a-8d93-0ae9789f2d8a"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [1 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_temporal_derivative'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:df826b1c-74a5-4f67-be42-d15657ccada8",
+ "@id": "urn:7c841b4f-a99a-48a0-8245-f7e4e890acb9",
"Label": "Estimate stat.",
"Used": [
- "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41"
+ "urn:42bc175e-636a-4d3f-8a84-ab0cec178f89"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:c6aa20f8-dfc4-434c-b06e-e6740edb0f2e",
+ "@id": "urn:cb078c97-7316-4480-a77e-abf7f6853c4e",
"Label": "Estimate contrast",
"Used": [
- "urn:5ec304ae-9211-417c-9b97-ef828474c68b"
+ "urn:5f05c7a5-2284-4cdf-b443-eaacdd73c3dc"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0 0 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:f89adc01-8d5d-425a-aff9-c4b6634b5ec2",
+ "@id": "urn:6b7b084a-b2b2-475f-920a-c985e82cda62",
"Label": "Threshold",
"Used": [
- "urn:cdeffd5b-2823-49f0-9667-028119716d19"
+ "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1"
],
- "AssociatedWith": "urn:bdf545f3-a058-4328-9ee9-0e77526c0c60",
+ "AssociatedWith": "urn:e438808b-da32-4b02-b7ad-36446653b4ae",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.none = 1;",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:70787460-c0e9-4624-a974-df03ea059fd7",
+ "@id": "urn:7c6a5a4a-63e5-4786-b73c-f906e5120d91",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:bbdd547f-1200-4863-9dda-efa4d1e55184",
+ "@id": "urn:1d6c2c35-9863-4bdf-b7fa-c197d57ea047",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:02775417-0217-4d74-8e8a-e0541b4e1a0b",
+ "@id": "urn:8b7ebf9b-55a0-4a1d-b503-719151eebc50",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:9514e444-af9c-4649-b1e3-f2b7371e2ff3"
+ "GeneratedBy": "urn:97410e53-4965-4ec1-8ab2-186b9801df5c"
},
{
- "@id": "urn:2e107129-9700-4d13-a0b4-5ed8786d98ef",
+ "@id": "urn:0924054c-0c39-4d36-b059-e742e85e493d",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:a68a1574-7b09-437f-b75a-2c7214dbf8c6"
+ "GeneratedBy": "urn:b2f24b4e-a723-44a7-bfeb-7434a9229cee"
},
{
- "@id": "urn:cfc270b2-011d-4313-9bf2-42cf99099862",
+ "@id": "urn:3d1acc0f-aa48-46af-8bdb-36a6d9e4a8da",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:000439d2-1c29-420d-974e-96ebf05bc13c"
+ "GeneratedBy": "urn:9c97f789-68aa-4cdc-aa0b-04d6151c43cb"
},
{
- "@id": "urn:40eadda9-3a59-49a2-85e1-185be44acf98",
+ "@id": "urn:e9a73030-0006-4ef8-95e3-5834de3078f3",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:eb67c517-fe9a-4f7c-b7b0-36247be03247"
+ "GeneratedBy": "urn:74cebf5a-7236-4402-8dc4-8d5936bcc43c"
},
{
- "@id": "urn:d64426fc-7163-4fcf-ab12-74eda9c93e1d",
+ "@id": "urn:fadd4862-4c4b-4a39-ba35-666f29181e2c",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:0c6b3aeb-06f8-4e6b-b3ed-88acdbf9e0e6"
+ "GeneratedBy": "urn:cc8f8d80-4f02-496d-9a4a-e0e2bfbe3189"
},
{
- "@id": "urn:eba38419-a546-4321-8e0a-8f3a41271a29",
+ "@id": "urn:d2c7c8ce-aa21-4a64-a01f-9425bfa93b01",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:f63e0e3f-899b-4267-9ba8-15f26febbb07",
+ "GeneratedBy": "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:79b5c51c-cfa6-40c1-9e81-1278998966c7",
+ "@id": "urn:7c045668-7bf9-44d6-8e7b-bfa797641a7b",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:f63e0e3f-899b-4267-9ba8-15f26febbb07",
+ "GeneratedBy": "urn:cb081815-8a6c-42f8-bb87-18c9e4cb7bc9",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:e8191e7e-8505-4e9d-afc8-41e2324eb4dc",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:bcdad7b0-1900-445e-a58d-7cdbd0dd9cfc"
+ "@id": "urn:b7a38a99-015b-4da7-abb8-e6579ba35172",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:3e26d898-d64e-4301-8def-9765c710bcdf"
},
{
- "@id": "urn:8dc8374c-cbe1-47f8-9d6a-39ae8a5ebb34",
+ "@id": "urn:e9aec74c-9fea-437a-8d93-0ae9789f2d8a",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:379036c0-95c2-499c-aecc-8b2362a9a19f",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d8775774-929a-4f81-8fcb-6ba1f916e161"
+ "@id": "urn:26a00968-1740-4b01-8330-41148ecff2f1",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:1e662f78-13a4-474a-9645-9ee637aa9e4b"
},
{
- "@id": "urn:938163b7-bf0d-40c8-8a24-9c77029d9a41",
+ "@id": "urn:42bc175e-636a-4d3f-8a84-ab0cec178f89",
"Label": "SPM.mat",
- "GeneratedBy": "urn:53f02519-829b-4f61-9838-40048b816257"
+ "GeneratedBy": "urn:c7e22265-242c-40b2-a6d4-3b6718af7d53"
},
{
- "@id": "urn:5ec304ae-9211-417c-9b97-ef828474c68b",
+ "@id": "urn:5f05c7a5-2284-4cdf-b443-eaacdd73c3dc",
"Label": "SPM.mat",
- "GeneratedBy": "urn:df826b1c-74a5-4f67-be42-d15657ccada8"
+ "GeneratedBy": "urn:7c841b4f-a99a-48a0-8245-f7e4e890acb9"
},
{
- "@id": "urn:cdeffd5b-2823-49f0-9667-028119716d19",
+ "@id": "urn:fa93e59f-1e2b-49fe-b6c1-2ea8c2665df1",
"Label": "SPM.mat",
- "GeneratedBy": "urn:c6aa20f8-dfc4-434c-b06e-e6740edb0f2e"
+ "GeneratedBy": "urn:cb078c97-7316-4480-a77e-abf7f6853c4e"
}
]
}
diff --git a/examples/from_parsers/spm/spm_temporal_derivative_batch.png b/examples/from_parsers/spm/spm_temporal_derivative_batch.png
index 3c9a16e2f..81916293e 100644
Binary files a/examples/from_parsers/spm/spm_temporal_derivative_batch.png and b/examples/from_parsers/spm/spm_temporal_derivative_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
index bd107878d..7bb35584c 100644
--- a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "@id": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20",
+ "@id": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7",
"Label": "Move file",
"Used": [
- "urn:1769375c-a644-4521-8e10-264cfa898796"
+ "urn:2112ebad-5343-4f17-b7b6-d84acc2618e4"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:a878b257-a9ba-4bcb-bec8-cff004db2580",
+ "@id": "urn:9dd4e0a3-87cb-4c2a-8ce1-6921569445e2",
"Label": "Move file",
"Used": [
- "urn:76ed4182-2eb5-43bc-85a5-03cd518dc93e"
+ "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:7d491214-e521-46a8-9f52-733c5d4835b5",
+ "@id": "urn:6b385db3-df78-45fb-8ca3-b2723d781363",
"Label": "Gunzip",
"Used": [
- "urn:0d96712d-754c-4811-b72f-475acab451eb"
+ "urn:e78bb29a-007b-491d-9e3c-a6001374ecca"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:c36375b8-841e-4bbd-a26e-921ddc5f074a",
+ "@id": "urn:562ffc54-25b5-458b-9a0d-19c47740a004",
"Label": "Gunzip",
"Used": [
- "urn:234b8167-b51f-4a3f-96a0-d7b22611b93b"
+ "urn:42d99646-29ac-48f5-a5c0-ecc93e09dd52"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:2b5a4047-ae13-4ad8-a91e-4bbedd00ee70",
+ "@id": "urn:15578984-fadf-4af5-8fc4-73962d165bfd",
"Label": "Realign",
"Used": [
- "urn:c0c5482a-7a18-4535-99df-1f2f4b42155f"
+ "urn:2366f9b3-3f7a-4ed2-b4a5-c91f73fdfa76"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:ad783a8d-3eff-4062-aaaa-b0da2153285b",
+ "@id": "urn:63c5707b-1fa7-4c34-9063-481dde955061",
"Label": "Coregister",
"Used": [
- "urn:ba73f7d7-f70a-4503-aafa-a70b10d74b93",
- "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
+ "urn:6f063688-2891-4c48-a796-36be5fde8862",
+ "urn:e0154622-ff40-45c9-95b0-d152011a123e"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:bc1a2433-b20b-499f-8b99-a202af1012f2",
+ "@id": "urn:bdcad4b4-738c-438d-bf8f-a3afa9085d98",
"Label": "Segment",
"Used": [
- "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3"
+ "urn:e0154622-ff40-45c9-95b0-d152011a123e"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:5b0ca4be-398b-4a17-bcfd-4979613d6409",
+ "@id": "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661",
"Label": "Normalize",
"Used": [
- "urn:300db58b-407a-44d5-a5bc-4ae178718157",
- "urn:ba73f7d7-f70a-4503-aafa-a70b10d74b93"
+ "urn:5718e82a-6a92-4d95-94ea-33eedbc07817",
+ "urn:6f063688-2891-4c48-a796-36be5fde8862"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:a1c94e5e-a659-4d81-a097-4534955c9cb6",
+ "@id": "urn:1e702c29-b4e1-41fa-bc95-23dfe6921348",
"Label": "Normalize",
"Used": [
- "urn:300db58b-407a-44d5-a5bc-4ae178718157"
+ "urn:5718e82a-6a92-4d95-94ea-33eedbc07817"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:1e21013c-20db-4252-9699-71e73b1cfd0e",
+ "@id": "urn:91e1e931-b451-49d1-9166-6fbc67b1335f",
"Label": "Smooth",
"Used": [
- "urn:3617818b-fc3c-4106-a1dc-5fd3c152eb59"
+ "urn:f68962ac-b1bf-4fc8-9194-ee95c76a54ac"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:c5da5238-d255-4788-8c65-a97fbad74c2e",
+ "@id": "urn:5a04266d-2945-46c5-9e01-ac3564a3bc81",
"Label": "Stat Design",
"Used": [
- "urn:c0b2dc25-6399-41b4-8c90-2115b9a9c877",
- "urn:2cf1aad2-75e7-427d-8859-f4a294b39611"
+ "urn:ea5183ba-9f9d-4703-8055-ad9ac1aaf1f0",
+ "urn:b6be9a53-13e4-4fdc-a78f-6e0ba8ae41d2"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_p005'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:298d54e4-1c6b-48c3-94f7-7d82fa1b91b7",
+ "@id": "urn:1560e13a-4274-41ec-adcf-6349a0bd9ad8",
"Label": "Estimate stat.",
"Used": [
- "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454"
+ "urn:d35acdb2-65ca-430b-977c-ec6062fccd3f"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:9cc3040c-923c-4223-bcdc-65e44e3724df",
+ "@id": "urn:6c448591-7c7a-4116-a49f-ffa219c38120",
"Label": "Estimate contrast",
"Used": [
- "urn:afb793a2-e11b-40df-bbab-7c55f13dce6f"
+ "urn:34ae4e39-b2ff-4522-936a-cc2b8c3a6e41"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:b983d8d0-a46d-4ad5-9e44-2803c2bba417",
+ "@id": "urn:d4e1ec48-2884-40d8-9e9d-1dbb2a02e5a6",
"Label": "Threshold",
"Used": [
- "urn:edb51084-4e7e-41bf-a92f-7012c0d532dd"
+ "urn:7bc01b6f-d058-4302-b0df-12b5722c8f9a"
],
- "AssociatedWith": "urn:15230b74-4ca6-46fd-b1af-f3fc88d9eaae",
+ "AssociatedWith": "urn:ec0e91e7-0d5a-4651-8771-0d8218963f1c",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 116;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:1769375c-a644-4521-8e10-264cfa898796",
+ "@id": "urn:2112ebad-5343-4f17-b7b6-d84acc2618e4",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:76ed4182-2eb5-43bc-85a5-03cd518dc93e",
+ "@id": "urn:7f3d1f14-a8c3-47f2-9af6-9b28a4bb791d",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:0d96712d-754c-4811-b72f-475acab451eb",
+ "@id": "urn:e78bb29a-007b-491d-9e3c-a6001374ecca",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:d2bdd17d-7e8f-4856-b026-90a880f4ba20"
+ "GeneratedBy": "urn:6c14e944-921d-43c2-b15c-4ede055a33b7"
},
{
- "@id": "urn:234b8167-b51f-4a3f-96a0-d7b22611b93b",
+ "@id": "urn:42d99646-29ac-48f5-a5c0-ecc93e09dd52",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:a878b257-a9ba-4bcb-bec8-cff004db2580"
+ "GeneratedBy": "urn:9dd4e0a3-87cb-4c2a-8ce1-6921569445e2"
},
{
- "@id": "urn:c0c5482a-7a18-4535-99df-1f2f4b42155f",
+ "@id": "urn:2366f9b3-3f7a-4ed2-b4a5-c91f73fdfa76",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:7d491214-e521-46a8-9f52-733c5d4835b5"
+ "GeneratedBy": "urn:6b385db3-df78-45fb-8ca3-b2723d781363"
},
{
- "@id": "urn:ba73f7d7-f70a-4503-aafa-a70b10d74b93",
+ "@id": "urn:6f063688-2891-4c48-a796-36be5fde8862",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:2b5a4047-ae13-4ad8-a91e-4bbedd00ee70"
+ "GeneratedBy": "urn:15578984-fadf-4af5-8fc4-73962d165bfd"
},
{
- "@id": "urn:ecb6bbdc-7c07-4bf7-aab1-114ab87660c3",
+ "@id": "urn:e0154622-ff40-45c9-95b0-d152011a123e",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:c36375b8-841e-4bbd-a26e-921ddc5f074a"
+ "GeneratedBy": "urn:562ffc54-25b5-458b-9a0d-19c47740a004"
},
{
- "@id": "urn:300db58b-407a-44d5-a5bc-4ae178718157",
+ "@id": "urn:5718e82a-6a92-4d95-94ea-33eedbc07817",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:bc1a2433-b20b-499f-8b99-a202af1012f2",
+ "GeneratedBy": "urn:bdcad4b4-738c-438d-bf8f-a3afa9085d98",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:27c64ef9-8a41-482c-80e9-1fef7e220907",
+ "@id": "urn:6a964585-80c4-4fd6-a4b9-3b69782a57cc",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:bc1a2433-b20b-499f-8b99-a202af1012f2",
+ "GeneratedBy": "urn:bdcad4b4-738c-438d-bf8f-a3afa9085d98",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:3617818b-fc3c-4106-a1dc-5fd3c152eb59",
+ "@id": "urn:f68962ac-b1bf-4fc8-9194-ee95c76a54ac",
"Label": "wsegment1",
- "GeneratedBy": "urn:5b0ca4be-398b-4a17-bcfd-4979613d6409"
+ "GeneratedBy": "urn:13b5dfe8-b7ac-4e01-a102-0ed6a57ef661"
},
{
- "@id": "urn:2cf1aad2-75e7-427d-8859-f4a294b39611",
+ "@id": "urn:b6be9a53-13e4-4fdc-a78f-6e0ba8ae41d2",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:c0b2dc25-6399-41b4-8c90-2115b9a9c877",
+ "@id": "urn:ea5183ba-9f9d-4703-8055-ad9ac1aaf1f0",
"Label": "swsegment1",
- "GeneratedBy": "urn:1e21013c-20db-4252-9699-71e73b1cfd0e"
+ "GeneratedBy": "urn:91e1e931-b451-49d1-9166-6fbc67b1335f"
},
{
- "@id": "urn:110ea3e4-213d-4c0f-b3d4-095ffe94e454",
+ "@id": "urn:d35acdb2-65ca-430b-977c-ec6062fccd3f",
"Label": "SPM.mat",
- "GeneratedBy": "urn:c5da5238-d255-4788-8c65-a97fbad74c2e"
+ "GeneratedBy": "urn:5a04266d-2945-46c5-9e01-ac3564a3bc81"
},
{
- "@id": "urn:afb793a2-e11b-40df-bbab-7c55f13dce6f",
+ "@id": "urn:34ae4e39-b2ff-4522-936a-cc2b8c3a6e41",
"Label": "SPM.mat",
- "GeneratedBy": "urn:298d54e4-1c6b-48c3-94f7-7d82fa1b91b7"
+ "GeneratedBy": "urn:1560e13a-4274-41ec-adcf-6349a0bd9ad8"
},
{
- "@id": "urn:edb51084-4e7e-41bf-a92f-7012c0d532dd",
+ "@id": "urn:7bc01b6f-d058-4302-b0df-12b5722c8f9a",
"Label": "SPM.mat",
- "GeneratedBy": "urn:9cc3040c-923c-4223-bcdc-65e44e3724df"
+ "GeneratedBy": "urn:6c448591-7c7a-4116-a49f-ffa219c38120"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png
index 8db423618..d321b3183 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_clustfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
index c33c1faeb..8fddda087 100644
--- a/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_clustunck10_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "@id": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:24494591-d5d7-4500-ad04-ae114c3334f9",
+ "@id": "urn:a7b6f5de-c2b2-49ed-b1f2-85cc15ba656d",
"Label": "Move file",
"Used": [
- "urn:9a733674-9bbb-4197-a3b3-6b052060bb4e"
+ "urn:c5b5bfe0-8a5e-42a0-a26c-0ca6a1f11bf8"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:2601600d-77ad-47b1-943f-527dce2f3c41",
+ "@id": "urn:61be7326-69b5-415e-a503-f694bba167a7",
"Label": "Move file",
"Used": [
- "urn:5818684f-eb4f-4926-ab68-239aef10f315"
+ "urn:72dc641b-3362-4d3b-ad48-4de534cc16f2"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:09b0869a-34b6-4e96-8b33-d3180f5c63ee",
+ "@id": "urn:8eadaf47-04dd-49a3-8554-1cc827514124",
"Label": "Gunzip",
"Used": [
- "urn:95b07d19-1268-4da8-aef5-714ebce7e815"
+ "urn:1893e68b-8760-487d-a672-661d89d67317"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:33ff81af-1444-46c3-a060-f926d0ced8ae",
+ "@id": "urn:1e1bc1b5-71fc-4694-8a0f-04858b7489a6",
"Label": "Gunzip",
"Used": [
- "urn:d4539ad2-b6b6-447b-b595-4c432dfba73a"
+ "urn:d183a43c-9467-43ef-b500-33cdff254012"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:90fb626f-4820-45e0-9abc-2fa1b442e8e4",
+ "@id": "urn:c9d8e8ff-1d2f-4924-bdfb-7d9994d48c73",
"Label": "Realign",
"Used": [
- "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04"
+ "urn:aa80a37f-3f74-4a58-9430-b8cc5642dd3b"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:68c80596-8a3a-41ec-abd1-1b5cb9f3908f",
+ "@id": "urn:5c99db67-dab4-4a16-8864-f735f817656f",
"Label": "Coregister",
"Used": [
- "urn:1abaf4b3-3b8b-47a5-9bef-ea9e15727931",
- "urn:48daa469-7980-4aef-8da7-ad179b504481"
+ "urn:15a47728-78c9-4ccc-8db9-c928c7fc4ae5",
+ "urn:e0d387ac-fcf6-44fc-8ada-630292a2d2b8"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:840c5d90-84c3-412a-ae8d-5b5b8af3c28a",
+ "@id": "urn:f715da09-7169-4935-8a19-0e64acad6228",
"Label": "Segment",
"Used": [
- "urn:1abaf4b3-3b8b-47a5-9bef-ea9e15727931"
+ "urn:15a47728-78c9-4ccc-8db9-c928c7fc4ae5"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:8ddb5caa-1d83-4fa7-81bc-bc33c94e9de0",
+ "@id": "urn:841327f1-5e7e-4483-acb6-fe061e15ab16",
"Label": "Normalize",
"Used": [
- "urn:162a1740-734c-4e43-8413-04fa22e9ac88",
- "urn:48daa469-7980-4aef-8da7-ad179b504481"
+ "urn:225dca91-f1db-4af3-923e-015c6cff0c3f",
+ "urn:e0d387ac-fcf6-44fc-8ada-630292a2d2b8"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:fcb04b90-a3a3-4c4d-b8db-b5c2e2f07f5d",
+ "@id": "urn:d9b57e2f-aeeb-4ce5-8ed6-c7a33b9cc8c9",
"Label": "Normalize",
"Used": [
- "urn:162a1740-734c-4e43-8413-04fa22e9ac88"
+ "urn:225dca91-f1db-4af3-923e-015c6cff0c3f"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:f48bc076-8f2e-47d0-b651-3a12200ba777",
+ "@id": "urn:391b6139-ccc6-4820-83d1-803d176f56c5",
"Label": "Smooth",
"Used": [
- "urn:63ad4bc7-4d97-46bc-b872-48b4e3cc971d"
+ "urn:008cf7fd-fd73-41c0-87f8-bb91d64c90ea"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:f59764b8-a925-44d9-8cc7-4e70fb2b3d1b",
+ "@id": "urn:9010c105-4fa2-4b9e-b829-552d9df111bd",
"Label": "Stat Design",
"Used": [
- "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
- "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237"
+ "urn:5d7bff8e-3649-4279-b652-65208d3038d8",
+ "urn:ce0367ad-797e-4e33-bcbf-d139eff4002d"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_cluster_k10'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:f0385465-4dbd-48ce-9470-433ea4f5b4ef",
+ "@id": "urn:1b43c2eb-1700-47e7-85b5-7ffe6978ebfa",
"Label": "Estimate stat.",
"Used": [
- "urn:a4cb1cd3-5946-4299-bda9-a293aea387b1"
+ "urn:931aa071-103b-4094-aebe-0874b1ee6b69"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:741a7638-5305-4e8c-b932-63bbac46e5b4",
+ "@id": "urn:de7ace33-d17f-4db4-985a-577e046b402c",
"Label": "Estimate contrast",
"Used": [
- "urn:c928a696-a036-4263-b227-10fed64c9e8e"
+ "urn:aed85e52-689e-4126-982f-f3922723d4bc"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:abc626d1-00a7-4658-8345-e262989b746d",
+ "@id": "urn:706293e7-948d-45eb-98f1-39e4e201f4eb",
"Label": "Threshold",
"Used": [
- "urn:e5b81464-47db-4542-8dc2-69a1ddd77020"
+ "urn:c6371710-d2ff-4ab7-a394-f9917321103e"
],
- "AssociatedWith": "urn:6187dbad-7f5e-4069-96d4-a5217ac853d3",
+ "AssociatedWith": "urn:b722df9c-540e-49b2-bf8a-2581b3fcdb28",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.001;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 10;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:9a733674-9bbb-4197-a3b3-6b052060bb4e",
+ "@id": "urn:c5b5bfe0-8a5e-42a0-a26c-0ca6a1f11bf8",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:5818684f-eb4f-4926-ab68-239aef10f315",
+ "@id": "urn:72dc641b-3362-4d3b-ad48-4de534cc16f2",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:95b07d19-1268-4da8-aef5-714ebce7e815",
+ "@id": "urn:1893e68b-8760-487d-a672-661d89d67317",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:24494591-d5d7-4500-ad04-ae114c3334f9"
+ "GeneratedBy": "urn:a7b6f5de-c2b2-49ed-b1f2-85cc15ba656d"
},
{
- "@id": "urn:d4539ad2-b6b6-447b-b595-4c432dfba73a",
+ "@id": "urn:d183a43c-9467-43ef-b500-33cdff254012",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:2601600d-77ad-47b1-943f-527dce2f3c41"
+ "GeneratedBy": "urn:61be7326-69b5-415e-a503-f694bba167a7"
},
{
- "@id": "urn:39fdeb1b-1b9e-48d6-967e-ba216bc07d04",
+ "@id": "urn:aa80a37f-3f74-4a58-9430-b8cc5642dd3b",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:09b0869a-34b6-4e96-8b33-d3180f5c63ee"
+ "GeneratedBy": "urn:8eadaf47-04dd-49a3-8554-1cc827514124"
},
{
- "@id": "urn:48daa469-7980-4aef-8da7-ad179b504481",
+ "@id": "urn:e0d387ac-fcf6-44fc-8ada-630292a2d2b8",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:90fb626f-4820-45e0-9abc-2fa1b442e8e4"
+ "GeneratedBy": "urn:c9d8e8ff-1d2f-4924-bdfb-7d9994d48c73"
},
{
- "@id": "urn:1abaf4b3-3b8b-47a5-9bef-ea9e15727931",
+ "@id": "urn:15a47728-78c9-4ccc-8db9-c928c7fc4ae5",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:33ff81af-1444-46c3-a060-f926d0ced8ae"
+ "GeneratedBy": "urn:1e1bc1b5-71fc-4694-8a0f-04858b7489a6"
},
{
- "@id": "urn:162a1740-734c-4e43-8413-04fa22e9ac88",
+ "@id": "urn:225dca91-f1db-4af3-923e-015c6cff0c3f",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:840c5d90-84c3-412a-ae8d-5b5b8af3c28a",
+ "GeneratedBy": "urn:f715da09-7169-4935-8a19-0e64acad6228",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:c72a767c-6c04-48a4-840f-8f8fce9c046f",
+ "@id": "urn:ff50cde1-de86-4145-82b6-32390e1d36da",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:840c5d90-84c3-412a-ae8d-5b5b8af3c28a",
+ "GeneratedBy": "urn:f715da09-7169-4935-8a19-0e64acad6228",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:63ad4bc7-4d97-46bc-b872-48b4e3cc971d",
+ "@id": "urn:008cf7fd-fd73-41c0-87f8-bb91d64c90ea",
"Label": "wsegment1",
- "GeneratedBy": "urn:8ddb5caa-1d83-4fa7-81bc-bc33c94e9de0"
+ "GeneratedBy": "urn:841327f1-5e7e-4483-acb6-fe061e15ab16"
},
{
- "@id": "urn:bfc94b09-104e-4f77-bc9c-6a254b2b3237",
+ "@id": "urn:ce0367ad-797e-4e33-bcbf-d139eff4002d",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:30934d7f-fa54-4dc4-92c2-0692dcc79bf8",
+ "@id": "urn:5d7bff8e-3649-4279-b652-65208d3038d8",
"Label": "swsegment1",
- "GeneratedBy": "urn:f48bc076-8f2e-47d0-b651-3a12200ba777"
+ "GeneratedBy": "urn:391b6139-ccc6-4820-83d1-803d176f56c5"
},
{
- "@id": "urn:a4cb1cd3-5946-4299-bda9-a293aea387b1",
+ "@id": "urn:931aa071-103b-4094-aebe-0874b1ee6b69",
"Label": "SPM.mat",
- "GeneratedBy": "urn:f59764b8-a925-44d9-8cc7-4e70fb2b3d1b"
+ "GeneratedBy": "urn:9010c105-4fa2-4b9e-b829-552d9df111bd"
},
{
- "@id": "urn:c928a696-a036-4263-b227-10fed64c9e8e",
+ "@id": "urn:aed85e52-689e-4126-982f-f3922723d4bc",
"Label": "SPM.mat",
- "GeneratedBy": "urn:f0385465-4dbd-48ce-9470-433ea4f5b4ef"
+ "GeneratedBy": "urn:1b43c2eb-1700-47e7-85b5-7ffe6978ebfa"
},
{
- "@id": "urn:e5b81464-47db-4542-8dc2-69a1ddd77020",
+ "@id": "urn:c6371710-d2ff-4ab7-a394-f9917321103e",
"Label": "SPM.mat",
- "GeneratedBy": "urn:741a7638-5305-4e8c-b932-63bbac46e5b4"
+ "GeneratedBy": "urn:de7ace33-d17f-4db4-985a-577e046b402c"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png
index c4fbb2bae..36f0c7c95 100644
Binary files a/examples/from_parsers/spm/spm_thr_clustunck10_batch.png and b/examples/from_parsers/spm/spm_thr_clustunck10_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
index 349c14b98..a8fb50fc6 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "@id": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:1e71f56b-d494-46ce-ba1b-e6e6a05abd1f",
+ "@id": "urn:7c11963b-3914-4ac8-a5fc-a935011ad6e9",
"Label": "Move file",
"Used": [
- "urn:f3a1b8eb-becf-4260-8526-cd7f14a93549"
+ "urn:a04913d6-f6ed-402b-b110-cf49ce78016a"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174",
+ "@id": "urn:b4169786-f8b4-4875-a20b-b4433c296029",
"Label": "Move file",
"Used": [
- "urn:f331cbfd-e6cb-4474-b9d2-f5093b12b4b7"
+ "urn:f7950dc3-735b-4be3-a659-65d79c66cc27"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:8e28756c-7915-4747-a230-d16d1b31fd66",
+ "@id": "urn:c09e350e-751b-4ef5-9a0f-48397e2fbe36",
"Label": "Gunzip",
"Used": [
- "urn:82ed7a10-62ca-4cdd-9124-cd33788aa5c7"
+ "urn:696ebbff-1fbb-4a38-8b97-78f2901d8167"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:e350024b-aa85-47b7-a4a4-239310870a5f",
+ "@id": "urn:c318e459-6636-41c0-baad-6553d27b820c",
"Label": "Gunzip",
"Used": [
- "urn:1f3ccb95-5c68-4eda-a0e2-23aef8d5c592"
+ "urn:d614eace-303b-4e36-aade-7a255d1426f6"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:d9166487-56b9-4a79-815c-e52de617b7d8",
+ "@id": "urn:35fd6ff1-968d-40ab-aaad-7cf131cab8cf",
"Label": "Realign",
"Used": [
- "urn:7be1cf76-746a-42a3-aa4f-a4ae45ef4735"
+ "urn:38b5d57d-2ccc-4626-a8f7-de90eae750e4"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:194a0e78-c788-4530-b7c0-0155f909d523",
+ "@id": "urn:36ff0b3c-ddbb-4e94-a6a3-56e2bfd7bb9d",
"Label": "Coregister",
"Used": [
- "urn:8923f9a6-0a25-4ceb-9abf-260fa1efec80",
- "urn:c04a985a-03ce-4123-916b-52f1738c5371"
+ "urn:1c32b8dc-a3cb-4ef0-9c8f-eb21e635e505",
+ "urn:8633c6ca-e187-4a73-8efa-926d8ca33d59"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
+ "@id": "urn:b3b5ba49-7388-4c3d-9bb8-bd7fc681ba7d",
"Label": "Segment",
"Used": [
- "urn:c04a985a-03ce-4123-916b-52f1738c5371"
+ "urn:1c32b8dc-a3cb-4ef0-9c8f-eb21e635e505"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:47ff32c1-ea81-41eb-aa5c-9e0cecfb40ce",
+ "@id": "urn:bfffb695-6bce-460d-9745-484236201700",
"Label": "Normalize",
"Used": [
- "urn:5a7858f6-1aa1-442f-8a48-e5b43e777f83",
- "urn:8923f9a6-0a25-4ceb-9abf-260fa1efec80"
+ "urn:8633c6ca-e187-4a73-8efa-926d8ca33d59",
+ "urn:dc9e4fe0-6cef-4a23-9009-138e1ebb75a7"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:c09831f3-2daa-4d46-8cc2-8d3a6d13e061",
+ "@id": "urn:46cf6b03-fe1d-4b26-9925-389bf65d67d2",
"Label": "Normalize",
"Used": [
- "urn:5a7858f6-1aa1-442f-8a48-e5b43e777f83"
+ "urn:dc9e4fe0-6cef-4a23-9009-138e1ebb75a7"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:a0828193-6c5d-4073-910f-4d6ef6b19f1a",
+ "@id": "urn:b66435cb-d795-4c33-b2e8-eeda2aab4832",
"Label": "Smooth",
"Used": [
- "urn:307ab064-d2fc-4591-bb45-46dd57cf2d2d"
+ "urn:e2b31149-680d-4526-ab18-abcf4b480c88"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239",
+ "@id": "urn:bf189218-ad14-4b5f-ba55-945ce218f2f7",
"Label": "Stat Design",
"Used": [
- "urn:6f8229a7-f228-4a5d-a39a-8d1fb380f779",
- "urn:8eebfcaf-f179-4ce4-83df-6d852735775d"
+ "urn:0f3dc826-1ad2-4563-a19a-aceadec0c483",
+ "urn:47d90f56-3811-4499-b673-1ef07bb242a9"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FDR_p005'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:6bf8a2e7-b254-4869-8156-8a248aa6d888",
+ "@id": "urn:77c710e3-0894-4482-b181-3c7abd3a69ce",
"Label": "Estimate stat.",
"Used": [
- "urn:ce469927-3e7f-4362-b6fc-0cca4d0aa043"
+ "urn:4d1dd6f4-b4e4-40c8-b95f-5ec76e8bd89b"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:b24277ee-2b84-4d0b-b76e-53234bf3a1ca",
+ "@id": "urn:b51eb436-940b-4b1b-9e47-f995a797d1cf",
"Label": "Estimate contrast",
"Used": [
- "urn:4125e09e-1e8f-485f-a75a-200cf5ed26c0"
+ "urn:cac6aef4-2dc3-4335-861e-a393fffa2d09"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:0f4d54c0-a22d-4e21-8302-30a73e21a790",
+ "@id": "urn:eab0d8bc-2fe3-4c10-b167-28e88bc93fe3",
"Label": "Threshold",
"Used": [
- "urn:64845e67-36b3-45b7-a4bb-2e3a3460a920"
+ "urn:0636ee2d-a3a6-4f30-87fa-789e47259146"
],
- "AssociatedWith": "urn:fc6df78f-dcf6-493f-9d17-9b7821a4991b",
+ "AssociatedWith": "urn:404a4d15-ee67-4dd8-ab02-993a22e6d405",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FDR';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:f3a1b8eb-becf-4260-8526-cd7f14a93549",
+ "@id": "urn:a04913d6-f6ed-402b-b110-cf49ce78016a",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:f331cbfd-e6cb-4474-b9d2-f5093b12b4b7",
+ "@id": "urn:f7950dc3-735b-4be3-a659-65d79c66cc27",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:82ed7a10-62ca-4cdd-9124-cd33788aa5c7",
+ "@id": "urn:696ebbff-1fbb-4a38-8b97-78f2901d8167",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:1e71f56b-d494-46ce-ba1b-e6e6a05abd1f"
+ "GeneratedBy": "urn:7c11963b-3914-4ac8-a5fc-a935011ad6e9"
},
{
- "@id": "urn:1f3ccb95-5c68-4eda-a0e2-23aef8d5c592",
+ "@id": "urn:d614eace-303b-4e36-aade-7a255d1426f6",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:94f1e1b4-8e76-41fb-9f3b-d60517272174"
+ "GeneratedBy": "urn:b4169786-f8b4-4875-a20b-b4433c296029"
},
{
- "@id": "urn:7be1cf76-746a-42a3-aa4f-a4ae45ef4735",
+ "@id": "urn:38b5d57d-2ccc-4626-a8f7-de90eae750e4",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:8e28756c-7915-4747-a230-d16d1b31fd66"
+ "GeneratedBy": "urn:c09e350e-751b-4ef5-9a0f-48397e2fbe36"
},
{
- "@id": "urn:8923f9a6-0a25-4ceb-9abf-260fa1efec80",
+ "@id": "urn:8633c6ca-e187-4a73-8efa-926d8ca33d59",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d9166487-56b9-4a79-815c-e52de617b7d8"
+ "GeneratedBy": "urn:35fd6ff1-968d-40ab-aaad-7cf131cab8cf"
},
{
- "@id": "urn:c04a985a-03ce-4123-916b-52f1738c5371",
+ "@id": "urn:1c32b8dc-a3cb-4ef0-9c8f-eb21e635e505",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:e350024b-aa85-47b7-a4a4-239310870a5f"
+ "GeneratedBy": "urn:c318e459-6636-41c0-baad-6553d27b820c"
},
{
- "@id": "urn:5a7858f6-1aa1-442f-8a48-e5b43e777f83",
+ "@id": "urn:dc9e4fe0-6cef-4a23-9009-138e1ebb75a7",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
+ "GeneratedBy": "urn:b3b5ba49-7388-4c3d-9bb8-bd7fc681ba7d",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:ef22e358-c84a-4ca8-b3e2-005482fd2886",
+ "@id": "urn:40286f70-3d33-483c-bfc2-3432761e3c7f",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:33ed9bcb-6059-4783-88f7-1aa00fe0a5c0",
+ "GeneratedBy": "urn:b3b5ba49-7388-4c3d-9bb8-bd7fc681ba7d",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:307ab064-d2fc-4591-bb45-46dd57cf2d2d",
- "Label": "wsegment1",
- "GeneratedBy": "urn:47ff32c1-ea81-41eb-aa5c-9e0cecfb40ce"
+ "@id": "urn:e2b31149-680d-4526-ab18-abcf4b480c88",
+ "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:bfffb695-6bce-460d-9745-484236201700"
},
{
- "@id": "urn:8eebfcaf-f179-4ce4-83df-6d852735775d",
+ "@id": "urn:47d90f56-3811-4499-b673-1ef07bb242a9",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:6f8229a7-f228-4a5d-a39a-8d1fb380f779",
- "Label": "swsegment1",
- "GeneratedBy": "urn:a0828193-6c5d-4073-910f-4d6ef6b19f1a"
+ "@id": "urn:0f3dc826-1ad2-4563-a19a-aceadec0c483",
+ "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
+ "GeneratedBy": "urn:b66435cb-d795-4c33-b2e8-eeda2aab4832"
},
{
- "@id": "urn:ce469927-3e7f-4362-b6fc-0cca4d0aa043",
+ "@id": "urn:4d1dd6f4-b4e4-40c8-b95f-5ec76e8bd89b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:e1c44cbe-f3d0-4f0e-a12c-b3228ede5239"
+ "GeneratedBy": "urn:bf189218-ad14-4b5f-ba55-945ce218f2f7"
},
{
- "@id": "urn:4125e09e-1e8f-485f-a75a-200cf5ed26c0",
+ "@id": "urn:cac6aef4-2dc3-4335-861e-a393fffa2d09",
"Label": "SPM.mat",
- "GeneratedBy": "urn:6bf8a2e7-b254-4869-8156-8a248aa6d888"
+ "GeneratedBy": "urn:77c710e3-0894-4482-b181-3c7abd3a69ce"
},
{
- "@id": "urn:64845e67-36b3-45b7-a4bb-2e3a3460a920",
+ "@id": "urn:0636ee2d-a3a6-4f30-87fa-789e47259146",
"Label": "SPM.mat",
- "GeneratedBy": "urn:b24277ee-2b84-4d0b-b76e-53234bf3a1ca"
+ "GeneratedBy": "urn:b51eb436-940b-4b1b-9e47-f995a797d1cf"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png
index c50e3b980..da107a79a 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfdrp05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
index fdbc6b6d5..e32cc73da 100644
--- a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "@id": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:d1e1cda7-db65-4013-a6e5-eff822140f17",
+ "@id": "urn:423da7a2-7b60-42aa-b8ab-02fed4206f6d",
"Label": "Move file",
"Used": [
- "urn:4e0d8bea-e775-47bd-b9b7-3e7d46641b11"
+ "urn:59a1ea45-0220-470e-939b-f58dd721e19d"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:0e3d9bab-2776-4009-8c33-f64c88a586c0",
+ "@id": "urn:3e1129c4-1668-4d2a-86a6-ec65ba4cdf22",
"Label": "Move file",
"Used": [
- "urn:4e86443f-aeb9-467a-87cd-921d8561e79d"
+ "urn:d6919dba-cce0-4138-93ba-d152dbf4e35e"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:4bbba145-a298-46fc-9d71-59ec7c739744",
+ "@id": "urn:4eb29210-41a9-45a5-96b6-1222aa0ae290",
"Label": "Gunzip",
"Used": [
- "urn:bd40b1fe-f58d-4f57-abba-63275e76d0c1"
+ "urn:07996bd3-d168-4ddb-a41a-250a3564c17e"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:ffbf1f1d-cc38-47b8-a1a2-c0242ca8e8f8",
+ "@id": "urn:52ef7053-9448-4734-8612-22ba6363b93f",
"Label": "Gunzip",
"Used": [
- "urn:c512daa6-81d5-4f4b-b599-ad2406137f3c"
+ "urn:ae9cf233-1cae-4123-a0a2-7d87c41578fa"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:e0406187-21ba-4e5f-bf3f-52b211052757",
+ "@id": "urn:ec5adfc3-1f39-4145-a708-6aaee3ff4ea1",
"Label": "Realign",
"Used": [
- "urn:dd2a855c-e782-42f5-ba65-a3a396a789de"
+ "urn:a7350c2c-f7d3-4b41-ace6-4cbea8187db7"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:9749c11a-671c-4c79-9951-10d84f2c77a6",
+ "@id": "urn:f1fd52b2-0cea-408d-86e1-3d09209e9366",
"Label": "Coregister",
"Used": [
- "urn:3f1fbed3-59f6-40e0-ad6f-8bda59adde98",
- "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286"
+ "urn:4996c5fe-2a70-4450-9878-684597230cfe",
+ "urn:884190c2-d08b-4691-a22d-6a606a505216"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
+ "@id": "urn:c86b2317-ab5f-4ba3-afa9-3fbd93c338eb",
"Label": "Segment",
"Used": [
- "urn:3f1fbed3-59f6-40e0-ad6f-8bda59adde98"
+ "urn:4996c5fe-2a70-4450-9878-684597230cfe"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:deec3fb9-4e28-4d7c-8a47-599403e4edcd",
+ "@id": "urn:74a1b1be-9778-4f7e-84ca-39eceecae1d3",
"Label": "Normalize",
"Used": [
- "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d",
- "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286"
+ "urn:810d1d25-c45f-487c-aece-3d12edc22e68",
+ "urn:884190c2-d08b-4691-a22d-6a606a505216"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:4cef8fb6-2bfe-4c0e-85b8-4020e5ea01e3",
+ "@id": "urn:ce66913e-b094-471b-bcc6-d99a9b2baac6",
"Label": "Normalize",
"Used": [
- "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d"
+ "urn:810d1d25-c45f-487c-aece-3d12edc22e68"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:331280a9-cad6-443e-8ec0-0bd032dec1f7",
+ "@id": "urn:ffda532d-a9a3-4afe-ae56-0c197afed2e5",
"Label": "Smooth",
"Used": [
- "urn:bd25383b-d975-4195-831d-bb521d441d8b"
+ "urn:ad54aeea-950d-4781-96b7-9042c66660de"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:48031bc4-634d-494c-aeb4-970f39ebb304",
+ "@id": "urn:6f6cc0d2-9b58-407b-8c51-732f0dbaaeda",
"Label": "Stat Design",
"Used": [
- "urn:62cef0cc-1cb3-4d9b-b110-a01298294d4b",
- "urn:fd23797b-703e-44e6-9ce0-93a6c6659007"
+ "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631",
+ "urn:c9d09354-17e6-47d9-9ed7-be2474d8a292"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_FWE_p005'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:cf72bf6d-c398-4e69-9a8d-dbd8c530a31e",
+ "@id": "urn:d8cc0c56-0ddc-4d6b-aa2b-6b5f38ecee47",
"Label": "Estimate stat.",
"Used": [
- "urn:8b99d805-d291-4e91-b46b-a85013a83cfb"
+ "urn:f62083f2-8dde-4cc3-a24c-d446e46978ad"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:0f2a2124-3de2-4554-af3f-3833d2222dae",
+ "@id": "urn:5470a0ab-86dc-40d7-b2c2-cf0cf4dbb0a8",
"Label": "Estimate contrast",
"Used": [
- "urn:8adb28e5-349d-4f53-8b18-4ed3975fae39"
+ "urn:e9aece2a-e134-463e-82bb-80691c416208"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:9686bceb-c078-427b-bb3f-d03889dc3a4d",
+ "@id": "urn:227413e0-9f8c-4ec6-8469-9de994444e70",
"Label": "Threshold",
"Used": [
- "urn:14a31446-8871-49fa-b1e0-e00260791d2c"
+ "urn:f2155199-6a8c-432a-ba46-a02d59102b8b"
],
- "AssociatedWith": "urn:75ff7e84-a2f8-4fcd-9c17-97f92cfcec40",
+ "AssociatedWith": "urn:99bcea95-afc5-45e7-88a1-4cbbc4a5fe50",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'FWE';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 0.05;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:4e0d8bea-e775-47bd-b9b7-3e7d46641b11",
+ "@id": "urn:59a1ea45-0220-470e-939b-f58dd721e19d",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:4e86443f-aeb9-467a-87cd-921d8561e79d",
+ "@id": "urn:d6919dba-cce0-4138-93ba-d152dbf4e35e",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:bd40b1fe-f58d-4f57-abba-63275e76d0c1",
+ "@id": "urn:07996bd3-d168-4ddb-a41a-250a3564c17e",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:d1e1cda7-db65-4013-a6e5-eff822140f17"
+ "GeneratedBy": "urn:423da7a2-7b60-42aa-b8ab-02fed4206f6d"
},
{
- "@id": "urn:c512daa6-81d5-4f4b-b599-ad2406137f3c",
+ "@id": "urn:ae9cf233-1cae-4123-a0a2-7d87c41578fa",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:0e3d9bab-2776-4009-8c33-f64c88a586c0"
+ "GeneratedBy": "urn:3e1129c4-1668-4d2a-86a6-ec65ba4cdf22"
},
{
- "@id": "urn:dd2a855c-e782-42f5-ba65-a3a396a789de",
+ "@id": "urn:a7350c2c-f7d3-4b41-ace6-4cbea8187db7",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:4bbba145-a298-46fc-9d71-59ec7c739744"
+ "GeneratedBy": "urn:4eb29210-41a9-45a5-96b6-1222aa0ae290"
},
{
- "@id": "urn:cff0d752-9ae5-4404-92c9-6fff79dcd286",
+ "@id": "urn:884190c2-d08b-4691-a22d-6a606a505216",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:e0406187-21ba-4e5f-bf3f-52b211052757"
+ "GeneratedBy": "urn:ec5adfc3-1f39-4145-a708-6aaee3ff4ea1"
},
{
- "@id": "urn:3f1fbed3-59f6-40e0-ad6f-8bda59adde98",
+ "@id": "urn:4996c5fe-2a70-4450-9878-684597230cfe",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:ffbf1f1d-cc38-47b8-a1a2-c0242ca8e8f8"
+ "GeneratedBy": "urn:52ef7053-9448-4734-8612-22ba6363b93f"
},
{
- "@id": "urn:859bef03-d16d-49d0-95d7-526e5a3b3e9d",
+ "@id": "urn:810d1d25-c45f-487c-aece-3d12edc22e68",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
+ "GeneratedBy": "urn:c86b2317-ab5f-4ba3-afa9-3fbd93c338eb",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:1c42556b-6ea5-40c5-ba7f-d049ffbfac3c",
+ "@id": "urn:dbca62fd-97b2-444f-b31a-4ed6d5c82310",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:a28a1432-8e3d-4d39-9cf9-e6acda7ca2fc",
+ "GeneratedBy": "urn:c86b2317-ab5f-4ba3-afa9-3fbd93c338eb",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:bd25383b-d975-4195-831d-bb521d441d8b",
+ "@id": "urn:ad54aeea-950d-4781-96b7-9042c66660de",
"Label": "wsegment1",
- "GeneratedBy": "urn:deec3fb9-4e28-4d7c-8a47-599403e4edcd"
+ "GeneratedBy": "urn:74a1b1be-9778-4f7e-84ca-39eceecae1d3"
},
{
- "@id": "urn:fd23797b-703e-44e6-9ce0-93a6c6659007",
+ "@id": "urn:c9d09354-17e6-47d9-9ed7-be2474d8a292",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:62cef0cc-1cb3-4d9b-b110-a01298294d4b",
+ "@id": "urn:6dac2074-75b1-4e6b-9f4a-37a6d6310631",
"Label": "swsegment1",
- "GeneratedBy": "urn:331280a9-cad6-443e-8ec0-0bd032dec1f7"
+ "GeneratedBy": "urn:ffda532d-a9a3-4afe-ae56-0c197afed2e5"
},
{
- "@id": "urn:8b99d805-d291-4e91-b46b-a85013a83cfb",
+ "@id": "urn:f62083f2-8dde-4cc3-a24c-d446e46978ad",
"Label": "SPM.mat",
- "GeneratedBy": "urn:48031bc4-634d-494c-aeb4-970f39ebb304"
+ "GeneratedBy": "urn:6f6cc0d2-9b58-407b-8c51-732f0dbaaeda"
},
{
- "@id": "urn:8adb28e5-349d-4f53-8b18-4ed3975fae39",
+ "@id": "urn:e9aece2a-e134-463e-82bb-80691c416208",
"Label": "SPM.mat",
- "GeneratedBy": "urn:cf72bf6d-c398-4e69-9a8d-dbd8c530a31e"
+ "GeneratedBy": "urn:d8cc0c56-0ddc-4d6b-aa2b-6b5f38ecee47"
},
{
- "@id": "urn:14a31446-8871-49fa-b1e0-e00260791d2c",
+ "@id": "urn:f2155199-6a8c-432a-ba46-a02d59102b8b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:0f2a2124-3de2-4554-af3f-3833d2222dae"
+ "GeneratedBy": "urn:5470a0ab-86dc-40d7-b2c2-cf0cf4dbb0a8"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png
index 9e85640bf..cb40d9bce 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png and b/examples/from_parsers/spm/spm_thr_voxelfwep05_batch.png differ
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
index 02e3a325b..a3246119b 100644
--- a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
+++ b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.jsonld
@@ -4,7 +4,7 @@
"Records": {
"Software": [
{
- "@id": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "@id": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"RRID": "RRID:SCR_007037",
"@type": "prov:SoftwareAgent",
"Label": "SPM",
@@ -13,54 +13,54 @@
],
"Activities": [
{
- "@id": "urn:da3b9dcd-0842-4839-80f4-0af1be995a20",
+ "@id": "urn:e085e4ed-61ad-41bb-8450-cffef55b7cc8",
"Label": "Move file",
"Used": [
- "urn:41002437-cbf0-4db7-9a60-637d98c15b27"
+ "urn:7a60ceed-9253-40d3-ab98-9dbcceac5361"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz'};\nmatlabbatch{1}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/FUNCTIONAL'}"
}
},
{
- "@id": "urn:b463f3ce-4f90-4f0c-8df8-992655455333",
+ "@id": "urn:95ca1050-f815-482f-a5d5-50df9eb5fcc6",
"Label": "Move file",
"Used": [
- "urn:9beabfc2-fadd-47a3-bbca-4307262fbcae"
+ "urn:b000ce49-ee34-4b4a-a104-841943e9bc11"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.files = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz'};\nmatlabbatch{2}.cfg_basicio.file_dir.file_ops.file_move.action.copyto = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'};",
"Parameters": {
"action.copyto": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ANATOMICAL'}"
}
},
{
- "@id": "urn:2e4207ad-de38-44b4-85b0-5c1ac384e6c8",
+ "@id": "urn:c49d5a06-0a28-4dff-8d3f-b322c4f36291",
"Label": "Gunzip",
"Used": [
- "urn:04b2b95f-4706-4a8e-be80-12e76066f1b1"
+ "urn:e4e35b1a-0ffb-4b69-91ed-079440711b3b"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{3}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:fcef7c15-eb1a-43d0-a496-81c1c8943ae1",
+ "@id": "urn:fac26c4d-38f9-49b0-9faf-062fe892a8ff",
"Label": "Gunzip",
"Used": [
- "urn:338b602f-d83f-4655-8404-32c1d8fb3a51"
+ "urn:308e722d-3011-4493-b217-f569373f2c39"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{4}.cfg_basicio.file_dir.file_ops.cfg_gunzip_files.files(1) = cfg_dep('Move/Delete Files: Moved/Copied Files', substruct('.','val', '{}',{2}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));"
},
{
- "@id": "urn:1c715c78-02eb-4649-93ce-b416be729b3b",
+ "@id": "urn:65a49861-ebb5-4b47-b2f8-400979e419dc",
"Label": "Realign",
"Used": [
- "urn:85f2163f-cfc5-4ede-9da5-a69c4e234514"
+ "urn:fe99ab29-ca34-4fb3-a31c-865b7fde6579"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{5}.spm.spatial.realign.estwrite.data{1}(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{3}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.quality = 0.9;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.sep = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.fwhm = 5;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.rtm = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.interp = 2;\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.eoptions.weight = '';\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.which = [0 1];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.interp = 4;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.mask = 1;\nmatlabbatch{5}.spm.spatial.realign.estwrite.roptions.prefix = 'r';",
"Parameters": {
"eoptions.quality": "0.9",
@@ -78,13 +78,13 @@
}
},
{
- "@id": "urn:12361698-19e6-44f0-b3c4-b740dfe8a626",
+ "@id": "urn:9e7316c6-b46b-4b93-b667-1785f7503f51",
"Label": "Coregister",
"Used": [
- "urn:3717a4e1-99f6-4b60-9f13-13f30a9f180d",
- "urn:ba95b31e-c044-4e0b-ae51-ca7bdbacd87e"
+ "urn:65c14f0f-4471-4ee4-b76b-0837fffadfee",
+ "urn:c153fb7f-09ea-4050-a6df-7fb63bcfa826"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{6}.spm.spatial.coreg.estimate.ref(1) = cfg_dep('Realign: Estimate & Reslice: Mean Image', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','rmean'));\nmatlabbatch{6}.spm.spatial.coreg.estimate.source(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{6}.spm.spatial.coreg.estimate.other = {''};\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.cost_fun = 'nmi';\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.sep = [4 2];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.tol = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];\nmatlabbatch{6}.spm.spatial.coreg.estimate.eoptions.fwhm = [7 7];",
"Parameters": {
"other": "{''}",
@@ -95,12 +95,12 @@
}
},
{
- "@id": "urn:b66b5e86-c268-4d21-9bda-3d10f0361c09",
+ "@id": "urn:9293b57e-bed7-40ac-b1e7-d6552e21881c",
"Label": "Segment",
"Used": [
- "urn:ba95b31e-c044-4e0b-ae51-ca7bdbacd87e"
+ "urn:65c14f0f-4471-4ee4-b76b-0837fffadfee"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{7}.spm.spatial.preproc.channel.vols(1) = cfg_dep('GunZip Files: GunZipped Files', substruct('.','val', '{}',{4}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{':'}));\nmatlabbatch{7}.spm.spatial.preproc.channel.biasreg = 0.001;\nmatlabbatch{7}.spm.spatial.preproc.channel.biasfwhm = 60;\nmatlabbatch{7}.spm.spatial.preproc.channel.write = [0 1];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,1'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(1).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,2'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).ngaus = 1;\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(2).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,3'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(3).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,4'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).ngaus = 3;\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(4).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,5'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).ngaus = 4;\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).native = [1 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(5).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).tpm = {'/storage/essicd/data/NIDM-Ex/spm12_update/tpm/TPM.nii,6'};\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).ngaus = 2;\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).native = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.tissue(6).warped = [0 0];\nmatlabbatch{7}.spm.spatial.preproc.warp.mrf = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.cleanup = 1;\nmatlabbatch{7}.spm.spatial.preproc.warp.reg = [0 0.001 0.5 0.05 0.2];\nmatlabbatch{7}.spm.spatial.preproc.warp.affreg = 'mni';\nmatlabbatch{7}.spm.spatial.preproc.warp.fwhm = 0;\nmatlabbatch{7}.spm.spatial.preproc.warp.samp = 3;\nmatlabbatch{7}.spm.spatial.preproc.warp.write = [0 1];",
"Parameters": {
"channel.biasreg": "0.001",
@@ -140,13 +140,13 @@
}
},
{
- "@id": "urn:d6f63e96-ea88-4593-82e8-42fed8a33dfd",
+ "@id": "urn:3dbc753d-ec5f-4933-816b-b57d17bdb32d",
"Label": "Normalize",
"Used": [
- "urn:3717a4e1-99f6-4b60-9f13-13f30a9f180d",
- "urn:d66f2975-367e-471e-b934-9427c9784ed2"
+ "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522",
+ "urn:c153fb7f-09ea-4050-a6df-7fb63bcfa826"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{8}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{8}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Realign: Estimate & Reslice: Realigned Images (Sess 1)', substruct('.','val', '{}',{5}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','sess', '()',{1}, '.','cfiles'));\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{8}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -156,12 +156,12 @@
}
},
{
- "@id": "urn:d839cce9-09a1-4f7f-98a1-1111d118824c",
+ "@id": "urn:9f51d912-394a-4bb7-8858-1674aed5be7c",
"Label": "Normalize",
"Used": [
- "urn:d66f2975-367e-471e-b934-9427c9784ed2"
+ "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{9}.spm.spatial.normalise.write.subj.def(1) = cfg_dep('Segment: Forward Deformations', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','fordef', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.subj.resample(1) = cfg_dep('Segment: Bias Corrected (1)', substruct('.','val', '{}',{7}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','channel', '()',{1}, '.','biascorr', '()',{':'}));\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.bb = [-78 -112 -70 78 76 85];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.vox = [2 2 2];\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.interp = 4;\nmatlabbatch{9}.spm.spatial.normalise.write.woptions.prefix = 'w';",
"Parameters": {
"woptions.bb": "[-78, -112, -70, 78, 76, 85]",
@@ -171,12 +171,12 @@
}
},
{
- "@id": "urn:fa3c3aa3-0929-4ee2-a5b3-08a8f94c74ff",
+ "@id": "urn:0df558d3-86a4-4596-82b9-2026fa148678",
"Label": "Smooth",
"Used": [
- "urn:8b5fda69-66b3-4b80-b1b8-4e9f3526efb9"
+ "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{10}.spm.spatial.smooth.data(1) = cfg_dep('Normalise: Write: Normalised Images (Subj 1)', substruct('.','val', '{}',{8}, '.','val', '{}',{1}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('()',{1}, '.','files'));\nmatlabbatch{10}.spm.spatial.smooth.fwhm = [6 6 6];\nmatlabbatch{10}.spm.spatial.smooth.dtype = 0;\nmatlabbatch{10}.spm.spatial.smooth.im = 0;\nmatlabbatch{10}.spm.spatial.smooth.prefix = 's';",
"Parameters": {
"fwhm": "[6, 6, 6]",
@@ -186,13 +186,13 @@
}
},
{
- "@id": "urn:18090ee8-2b42-44ac-a89c-2bbc77ce84d2",
+ "@id": "urn:5c3a9cf4-7f25-47ac-a792-27f8c421ff6d",
"Label": "Stat Design",
"Used": [
- "urn:b7e3dec0-55c8-47e7-841e-342eaf436e58",
- "urn:7c5d805c-8cc9-4593-99f1-fc70e69f54c5"
+ "urn:7a75f677-aee4-4241-bc66-2169ae57d63d",
+ "urn:041f3508-d4c5-4ef0-947d-4fc6d5de0a0f"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{11}.spm.stats.fmri_spec.dir = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'};\nmatlabbatch{11}.spm.stats.fmri_spec.timing.units = 'secs';\nmatlabbatch{11}.spm.stats.fmri_spec.timing.RT = 2;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t = 16;\nmatlabbatch{11}.spm.stats.fmri_spec.timing.fmri_t0 = 8;\nmatlabbatch{11}.spm.stats.fmri_spec.sess.scans(1) = cfg_dep('Smooth: Smoothed Images', substruct('.','val', '{}',{10}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','files'));\nmatlabbatch{11}.spm.stats.fmri_spec.sess.cond = struct('name', {}, 'onset', {}, 'duration', {}, 'tmod', {}, 'pmod', {}, 'orth', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi = {'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat'};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.regress = struct('name', {}, 'val', {});\nmatlabbatch{11}.spm.stats.fmri_spec.sess.multi_reg = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.sess.hpf = 128;\nmatlabbatch{11}.spm.stats.fmri_spec.fact = struct('name', {}, 'levels', {});\nmatlabbatch{11}.spm.stats.fmri_spec.bases.hrf.derivs = [0 0];\nmatlabbatch{11}.spm.stats.fmri_spec.volt = 1;\nmatlabbatch{11}.spm.stats.fmri_spec.global = 'None';\nmatlabbatch{11}.spm.stats.fmri_spec.mthresh = 0.8;\nmatlabbatch{11}.spm.stats.fmri_spec.mask = {''};\nmatlabbatch{11}.spm.stats.fmri_spec.cvi = 'AR(1)';",
"Parameters": {
"dir": "{'/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/TEST/nidmresults-examples/spm_voxelwise_t4'}",
@@ -214,12 +214,12 @@
}
},
{
- "@id": "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c",
+ "@id": "urn:695318d9-1169-4e52-a4e7-75d46de608a2",
"Label": "Estimate stat.",
"Used": [
- "urn:ec7ca64d-b4b1-4d1a-b564-051260583801"
+ "urn:a7de91f4-6659-4288-9fa1-daeb0fd5f01b"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{12}.spm.stats.fmri_est.spmmat(1) = cfg_dep('fMRI model specification: SPM.mat File', substruct('.','val', '{}',{11}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{12}.spm.stats.fmri_est.write_residuals = 0;\nmatlabbatch{12}.spm.stats.fmri_est.method.Classical = 1;",
"Parameters": {
"write_residuals": "0",
@@ -227,12 +227,12 @@
}
},
{
- "@id": "urn:e1eb98a2-f3af-47ec-812f-653e62f5e544",
+ "@id": "urn:48c32de6-d8cc-4932-9033-005392de7601",
"Label": "Estimate contrast",
"Used": [
- "urn:9f9a7b54-8e6c-416f-9fde-1ef0401fb67a"
+ "urn:6591f358-d675-4355-a6fa-74c22467f6bf"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{13}.spm.stats.con.spmmat(1) = cfg_dep('Model estimation: SPM.mat File', substruct('.','val', '{}',{12}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.name = 'tone counting vs baseline';\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.weights = [1 0];\nmatlabbatch{13}.spm.stats.con.consess{1}.tcon.sessrep = 'none';\nmatlabbatch{13}.spm.stats.con.delete = 0;",
"Parameters": {
"consess{1}.tcon.name": "'tone counting vs baseline'",
@@ -242,12 +242,12 @@
}
},
{
- "@id": "urn:cfc74850-74d6-422e-b165-d1170d07bbfc",
+ "@id": "urn:172bd5a5-991c-451d-826c-b88c1cc58855",
"Label": "Threshold",
"Used": [
- "urn:ceab5453-bdfe-47df-b649-f9d6fda5dbce"
+ "urn:83b8a0a0-af45-4d8f-9a2e-35c24bcb3c0c"
],
- "AssociatedWith": "urn:29e0b780-0d6b-4417-9475-2753d3da59a3",
+ "AssociatedWith": "urn:df8b62e7-fee0-43de-bb45-e25ae1a262f2",
"Command": "matlabbatch{14}.spm.stats.results.spmmat(1) = cfg_dep('Contrast Manager: SPM.mat File', substruct('.','val', '{}',{13}, '.','val', '{}',{1}, '.','val', '{}',{1}), substruct('.','spmmat'));\nmatlabbatch{14}.spm.stats.results.conspec.titlestr = '';\nmatlabbatch{14}.spm.stats.results.conspec.contrasts = Inf;\nmatlabbatch{14}.spm.stats.results.conspec.threshdesc = 'none';\nmatlabbatch{14}.spm.stats.results.conspec.thresh = 4;\nmatlabbatch{14}.spm.stats.results.conspec.extent = 0;\nmatlabbatch{14}.spm.stats.results.conspec.conjunction = 1;\nmatlabbatch{14}.spm.stats.results.conspec.mask.none = 1;\nmatlabbatch{14}.spm.stats.results.units = 1;\nmatlabbatch{14}.spm.stats.results.print = 'pdf';\nmatlabbatch{14}.spm.stats.results.write.tspm.basename = 'thresh';",
"Parameters": {
"conspec.titlestr": "''",
@@ -265,7 +265,7 @@
],
"Entities": [
{
- "@id": "urn:41002437-cbf0-4db7-9a60-637d98c15b27",
+ "@id": "urn:7a60ceed-9253-40d3-ab98-9dbcceac5361",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/func/sub-01_task-tonecounting_bold.nii.gz",
"digest": {
@@ -273,7 +273,7 @@
}
},
{
- "@id": "urn:9beabfc2-fadd-47a3-bbca-4307262fbcae",
+ "@id": "urn:b000ce49-ee34-4b4a-a104-841943e9bc11",
"Label": "anat_sub-01_T1w.nii.gz",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/DATA/BIDS/ds011/sub-01/anat/sub-01_T1w.nii.gz",
"digest": {
@@ -281,57 +281,57 @@
}
},
{
- "@id": "urn:04b2b95f-4706-4a8e-be80-12e76066f1b1",
+ "@id": "urn:e4e35b1a-0ffb-4b69-91ed-079440711b3b",
"Label": "func_sub-01_task-tonecounting_bold.nii.gz",
- "GeneratedBy": "urn:da3b9dcd-0842-4839-80f4-0af1be995a20"
+ "GeneratedBy": "urn:e085e4ed-61ad-41bb-8450-cffef55b7cc8"
},
{
- "@id": "urn:338b602f-d83f-4655-8404-32c1d8fb3a51",
+ "@id": "urn:308e722d-3011-4493-b217-f569373f2c39",
"Label": "anat_sub-01_T1w.nii.gz",
- "GeneratedBy": "urn:b463f3ce-4f90-4f0c-8df8-992655455333"
+ "GeneratedBy": "urn:95ca1050-f815-482f-a5d5-50df9eb5fcc6"
},
{
- "@id": "urn:85f2163f-cfc5-4ede-9da5-a69c4e234514",
+ "@id": "urn:fe99ab29-ca34-4fb3-a31c-865b7fde6579",
"Label": "func_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:2e4207ad-de38-44b4-85b0-5c1ac384e6c8"
+ "GeneratedBy": "urn:c49d5a06-0a28-4dff-8d3f-b322c4f36291"
},
{
- "@id": "urn:3717a4e1-99f6-4b60-9f13-13f30a9f180d",
+ "@id": "urn:c153fb7f-09ea-4050-a6df-7fb63bcfa826",
"Label": "meanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:1c715c78-02eb-4649-93ce-b416be729b3b"
+ "GeneratedBy": "urn:65a49861-ebb5-4b47-b2f8-400979e419dc"
},
{
- "@id": "urn:ba95b31e-c044-4e0b-ae51-ca7bdbacd87e",
+ "@id": "urn:65c14f0f-4471-4ee4-b76b-0837fffadfee",
"Label": "anat_sub-01_T1w.nii",
- "GeneratedBy": "urn:fcef7c15-eb1a-43d0-a496-81c1c8943ae1"
+ "GeneratedBy": "urn:fac26c4d-38f9-49b0-9faf-062fe892a8ff"
},
{
- "@id": "urn:d66f2975-367e-471e-b934-9427c9784ed2",
+ "@id": "urn:69ce85f3-e1c3-45a4-9eea-f36fac8b7522",
"Label": "segment1",
"Atlocation": "c1xxx.nii.gz",
- "GeneratedBy": "urn:b66b5e86-c268-4d21-9bda-3d10f0361c09",
+ "GeneratedBy": "urn:9293b57e-bed7-40ac-b1e7-d6552e21881c",
"AtLocation": "c1anat_sub-01_T1w.nii",
"digest": {
"sha256": "61ca923955d0a5c9088df9e258f41644067ec964e1c9a83284ba03b0515079b0"
}
},
{
- "@id": "urn:f5deb909-5717-4cc7-abdc-3b6ef5b1e1d0",
+ "@id": "urn:5b6e2538-fc1c-4ad4-903a-6a1930fbc394",
"Label": "segment2",
"Atlocation": "c2xxx.nii.gz",
- "GeneratedBy": "urn:b66b5e86-c268-4d21-9bda-3d10f0361c09",
+ "GeneratedBy": "urn:9293b57e-bed7-40ac-b1e7-d6552e21881c",
"AtLocation": "c2anat_sub-01_T1w.nii",
"digest": {
"sha256": "10ad88ebeebebd0bd03ccbdd4df92d500d28d14715fa5375fd35589caddf49a6"
}
},
{
- "@id": "urn:8b5fda69-66b3-4b80-b1b8-4e9f3526efb9",
- "Label": "wmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:d6f63e96-ea88-4593-82e8-42fed8a33dfd"
+ "@id": "urn:0255aa2c-31b4-488c-97f8-7e4e7a35295e",
+ "Label": "wsegment1",
+ "GeneratedBy": "urn:3dbc753d-ec5f-4933-816b-b57d17bdb32d"
},
{
- "@id": "urn:7c5d805c-8cc9-4593-99f1-fc70e69f54c5",
+ "@id": "urn:041f3508-d4c5-4ef0-947d-4fc6d5de0a0f",
"Label": "ONSETS_sub-01-MultiCond.mat",
"AtLocation": "/storage/essicd/data/NIDM-Ex/BIDS_Data/RESULTS/EXAMPLES/ds011/SPM/PREPROCESSING/ONSETS/sub-01-MultiCond.mat",
"digest": {
@@ -339,24 +339,24 @@
}
},
{
- "@id": "urn:b7e3dec0-55c8-47e7-841e-342eaf436e58",
- "Label": "swmeanfunc_sub-01_task-tonecounting_bold.nii",
- "GeneratedBy": "urn:fa3c3aa3-0929-4ee2-a5b3-08a8f94c74ff"
+ "@id": "urn:7a75f677-aee4-4241-bc66-2169ae57d63d",
+ "Label": "swsegment1",
+ "GeneratedBy": "urn:0df558d3-86a4-4596-82b9-2026fa148678"
},
{
- "@id": "urn:ec7ca64d-b4b1-4d1a-b564-051260583801",
+ "@id": "urn:a7de91f4-6659-4288-9fa1-daeb0fd5f01b",
"Label": "SPM.mat",
- "GeneratedBy": "urn:18090ee8-2b42-44ac-a89c-2bbc77ce84d2"
+ "GeneratedBy": "urn:5c3a9cf4-7f25-47ac-a792-27f8c421ff6d"
},
{
- "@id": "urn:9f9a7b54-8e6c-416f-9fde-1ef0401fb67a",
+ "@id": "urn:6591f358-d675-4355-a6fa-74c22467f6bf",
"Label": "SPM.mat",
- "GeneratedBy": "urn:813625a1-5cd9-48f5-b1fd-a31afcc8ab5c"
+ "GeneratedBy": "urn:695318d9-1169-4e52-a4e7-75d46de608a2"
},
{
- "@id": "urn:ceab5453-bdfe-47df-b649-f9d6fda5dbce",
+ "@id": "urn:83b8a0a0-af45-4d8f-9a2e-35c24bcb3c0c",
"Label": "SPM.mat",
- "GeneratedBy": "urn:e1eb98a2-f3af-47ec-812f-653e62f5e544"
+ "GeneratedBy": "urn:48c32de6-d8cc-4932-9033-005392de7601"
}
]
}
diff --git a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png
index 04acbe55f..215ffbae2 100644
Binary files a/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png and b/examples/from_parsers/spm/spm_thr_voxelunct4_batch.png differ
diff --git a/launch_parser_on_nidm.py b/launch_parser_on_nidm.py
index 99540d500..60dfb02c8 100644
--- a/launch_parser_on_nidm.py
+++ b/launch_parser_on_nidm.py
@@ -11,13 +11,13 @@
from bids_prov.visualize import main as visualize
-def process_file(context_write, root, file, filename_ss_ext, output_dir, parser_function, verbose, with_blocs=False):
+def process_file(context_write, root, file, filename_ss_ext, output_dir, parser_function, verbose, with_blocks=False):
"""Process a file using the given parser function and save the output to the output directory."""
context_write.write(f" file= {root}/{str(file)}\n")
filename = root + "/" + str(file)
- if with_blocs is False:
+ if with_blocks is False:
shutil.copyfile(filename, output_dir + "/" + str(file))
- output_base = output_dir + "/" + filename_ss_ext if with_blocs is False else output_dir + "/" + filename_ss_ext + "_bloc"
+ output_base = output_dir + "/" + filename_ss_ext if with_blocks is False else output_dir + "/" + filename_ss_ext + "_block"
output_jsonld = output_base + ".jsonld"
output_png = output_base + ".png"
@@ -26,7 +26,7 @@ def process_file(context_write, root, file, filename_ss_ext, output_dir, parser_
output_file=output_jsonld, verbose=verbose)
else:
jsonld_same_as_existing = parser_function(root + "/" + str(file), CONTEXT_URL,
- output_file=output_jsonld, verbose=verbose, with_blocs=with_blocs)
+ output_file=output_jsonld, verbose=verbose, with_blocks=with_blocks)
if not jsonld_same_as_existing: # do not generate the png if the jsonld has not evolved
visualize(output_jsonld, output_file=output_png)
@@ -96,8 +96,8 @@ def main():
else:
filename_ss_ext = file.split(".tcsh")[0]
process_file(context_write, root, file, filename_ss_ext, output_dir_afni, afni_to_bids_prov, opt.verbose)
- # afni bloc
- process_file(context_write, root, file, filename_ss_ext, output_dir_afni, afni_to_bids_prov, opt.verbose, with_blocs=True)
+ # afni block
+ process_file(context_write, root, file, filename_ss_ext, output_dir_afni, afni_to_bids_prov, opt.verbose, with_blocks=True)
else:
print(" -> Extension of file ", file, " not supported")
diff --git a/new_features.md b/new_features.md
index e11306b83..c2017f848 100644
--- a/new_features.md
+++ b/new_features.md
@@ -1,6 +1,6 @@
### New features
-List of all features you can find in `examples/*.json` files, but are not mentionned in [the spec](https://docs.google.com/document/d/1vw3VNDof5cecv2PkFp7Lw_pNUTUo8-m8V4SIdtGJVKs/edit?usp=sharing)
+List of all features you can find in `examples/*.json` files, but are not mentioned in [the spec](https://docs.google.com/document/d/1vw3VNDof5cecv2PkFp7Lw_pNUTUo8-m8V4SIdtGJVKs/edit?usp=sharing)
- [type indexing](https://w3c.github.io/json-ld-syntax/#node-type-indexing)
- Activity definitions, instead of just Agent and Entities