Merge branch 'dev-v2.0.0' into BBtemplate

.dryrun_test_all.sh

@@ -9,9 +9,8 @@ hippunfold test_data/bids_T1w test_out participant -np --modality T1w
 hippunfold test_data/bids_hippb500 test_out participant -np --modality hippb500 
 hippunfold test_data/bids_T1w_longitudinal test_out participant -np --modality T1w 
 hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w 
-hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w 
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz 
-hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L 
+hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
+hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --t1_reg_template 
 hippunfold test_data/bids_singleT2w test_out participant -np --modality T2w --output_space T1w 
 hippunfold test_data/bids_T1w test_out participant -np --modality T1w --use-template-seg 

.github/workflows/python-testing.yml

@@ -94,17 +94,13 @@ jobs:
         run: |
           poetry run hippunfold test_data/bids_singleT2w_longitudinal test_out participant -np --modality T2w
 
-      - name: Test manual seg T2w bids
+      - name: Test manualseg bids, with path override
         run: |
-          poetry run hippunfold test_data/bids_segT2w test_out participant -np --modality segT2w
+          poetry run hippunfold test_data/bids_manualseg test_out participant -np --modality manualseg --path_manualseg test_data/bids_manualseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
 
-      - name: Test cropseg bids, with path override
+      - name: Test manualseg bids, one hemisphere hemi
         run: |
-          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg/sub-{subject}_hemi-{hemi}_dseg.nii.gz
-
-      - name: Test cropseg bids, with path override, left hemi
-        run: |
-          poetry run hippunfold . test_out participant -np --modality cropseg --path_cropseg test_data/data_cropseg_1hemi/sub-{subject}_hemi-{hemi}_dseg.nii.gz --hemi L
+          poetry run hippunfold test_data/bids_manualseg_1hemi test_out participant -np --modality manualseg --hemi L
 
       - name: Test T2w with T1w template registration
         run: |

hippunfold/config/snakebids.yml

@@ -67,19 +67,7 @@ pybids_inputs:
       - acquisition
       - run
 
-  seg:
-    filters:
-      suffix: 'dseg'
-      extension: '.nii.gz'
-      datatype: 'anat'
-      invalid_filters: 'allow'
-    wildcards:
-      - subject
-      - session
-      - acquisition
-      - run
-
-  cropseg:
+  manualseg:
     filters:
       suffix: 'dseg'
       extension: '.nii.gz'
@@ -100,15 +88,13 @@ pybids_inputs:
 parse_args:
 
   --modality:
-    help: 'Type of image to run hippunfold on. Modality prefixed with seg will import an existing (manual) hippocampal tissue segmentation from that space, instead of running neural network (default: %(default)s)'
+    help: 'Type of image to run hippunfold on. For manualseg and be sure to match the label scheme applied in the look up table (lut) online. For best performance, please also make sure the input is approximately aligned to the template space, with separate hemi-L|R in the name(s). (default: %(default)s)'
     required: True
     choices:
       - T1w
       - T2w
       - hippb500
-      - segT1w
-      - segT2w
-      - cropseg
+      - manualseg
 
 
   --template:

hippunfold/resources/label_lut/manual_dseg.tsv

@@ -0,0 +1,9 @@
+index	name	abbreviation
+1	hippocampal grey matter	GM
+2	SRLM or 'dark band'	SRLM
+3	neocortex (entorhinal or parahippocampal)	MTLC
+4	pial surface	Pial
+5	hippocampal-amygdalar transition area	HATA
+6	indusium griseum	IndGris
+7	cysts	Cyst
+8   dentate gyrus	DG

hippunfold/resources/label_lut/subfields_dseg .tsv

@@ -0,0 +1,9 @@
+#No.	Label	R	G	B	A
+1	subiculum	41	43	252	0
+2	CA1	102	209	216	0
+3	CA2	0	179	60	0
+4	CA3	255	182	0	0
+5	CA4	255	43	23	0
+6	dentate_gyrus	245	236	0	0
+7	SRLM	119	54	155	0
+8	cysts	255	255	255	0

hippunfold/workflow/Snakefile

@@ -18,24 +18,19 @@ template_modality = False
 
 
 # set the lists used for output spaces
-if (
-    config["modality"] == "T1w"
-    or config["modality"] == "segT1w"
-    or "T1w" in config["output_spaces"]
-):
+if config["modality"] == "T1w" or "T1w" in config["output_spaces"]:
     ref_spaces.append("T1w")
     crop_ref_spaces.append("cropT1w")
     limit_to_list.add("T1w")
 if (
-    (config["modality"] == "T2w" or config["modality"] == "segT2w")
-    and "native" in config["output_spaces"]
+    config["modality"] == "T2w" and "native" in config["output_spaces"]
 ) or "T2w" in config["output_spaces"]:
     ref_spaces.append("T2w")
     crop_ref_spaces.append("cropT2w")
     limit_to_list.add("T2w")
 if (
     config["modality"] == "hippb500"
-    or config["modality"] == "cropseg"
+    or config["modality"] == "manualseg"
     or "corobl" in config["output_spaces"]
 ):
     ref_spaces.append("corobl")
@@ -64,13 +59,7 @@ elif "T1w" in config["modality"]:
 if config["skip_inject_template_labels"]:  # TODO do we need this?
     config["autotop_labels"] = ["hipp"]
 
-
-# add seg (if chosen) and the modality to the inputs
-if config["modality"][:3] == "seg":  # if modality is segT2w, then add seg
-    limit_to_list.add("seg")
-    limit_to_list.add(config["modality"][3:])
-else:
-    limit_to_list.add(config["modality"])
+limit_to_list.add(config["modality"])
 
 # if atlas doesn't contain alignment features
 if not config["atlas"] == ["multihist7"]:
@@ -118,13 +107,9 @@ if "T1w" in limit_to_list:
 
 
 # include rules only as they are needed..
-if config["modality"] == "segT1w" or config["modality"] == "segT2w":
-
-    include: "rules/preproc_seg.smk"
-
-elif config["modality"] == "cropseg":
+if config["modality"] == "manualseg":
 
-    include: "rules/preproc_cropseg.smk"
+    include: "rules/preproc_manualseg.smk"
 
 else:
 

hippunfold/workflow/rules/common.smk

@@ -32,17 +32,8 @@ def get_avg_or_cp_scans_cmd(wildcards, input, output):
     return cmd
 
 
-def get_modality_key(modality):
-    if modality[:3] == "seg":
-        return "seg"
-    else:
-        return modality
-
-
 def get_modality_suffix(modality):
-    if modality[:3] == "seg":
-        return modality[3:]
-    elif modality[:4] == "hipp":
+    if modality[:4] == "hipp":
         return modality[4:]
     else:
         return modality
@@ -51,7 +42,7 @@ def get_modality_suffix(modality):
 def get_final_spec():
     specs = []
     specs.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
@@ -71,7 +62,7 @@ def get_final_spec():
         )
     )
     specs.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
@@ -94,7 +85,7 @@ def get_final_spec():
 
 
 def get_final_subfields():
-    return inputs[get_modality_key(config["modality"])].expand(
+    return inputs[config["modality"]].expand(
         bids(
             root=root,
             datatype="anat",
@@ -121,7 +112,7 @@ def get_final_coords():
     coords = []
     # compute all laplace coords by default (incl IO)
     coords.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="coords",
@@ -142,7 +133,7 @@ def get_final_coords():
         )
     )
     coords.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="coords",
@@ -168,7 +159,7 @@ def get_final_transforms():
     xfms = []
 
     xfms.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="warps",
@@ -188,7 +179,7 @@ def get_final_transforms():
     )
 
     xfms.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="warps",
@@ -208,7 +199,7 @@ def get_final_transforms():
     )
 
     xfms.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="warps",
@@ -227,10 +218,9 @@ def get_final_transforms():
 
 def get_final_anat():
     anat = []
-
     if "T1w" in ref_spaces or "T2w" in ref_spaces:
         anat.extend(
-            inputs[get_modality_key(config["modality"])].expand(
+            inputs[config["modality"]].expand(
                 bids(
                     root=root,
                     datatype="anat",
@@ -255,7 +245,7 @@ def get_final_qc():
 
     if not template_modality == False:
         qc.extend(
-            inputs[get_modality_key(config["modality"])].expand(
+            inputs[config["modality"]].expand(
                 bids(
                     root=root,
                     datatype="qc",
@@ -269,7 +259,7 @@ def get_final_qc():
             )
         )
     qc.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="qc",
@@ -287,7 +277,7 @@ def get_final_qc():
         )
     )
     qc.extend(
-        inputs[get_modality_key(config["modality"])].expand(
+        inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="qc",
@@ -308,7 +298,7 @@ def get_final_qc():
     )
     if len(config["hemi"]) == 2:
         qc.extend(
-            inputs[get_modality_key(config["modality"])].expand(
+            inputs[config["modality"]].expand(
                 bids(
                     root=root,
                     datatype="qc",
@@ -326,7 +316,7 @@ def get_final_qc():
     if (config["modality"] == "T1w") or (config["modality"] == "T2w"):
         if not config["use_template_seg"]:
             qc.extend(
-                inputs[get_modality_key(config["modality"])].expand(
+                inputs[config["modality"]].expand(
                     bids(
                         root=root,
                         datatype="qc",
@@ -362,27 +352,21 @@ def get_final_output():
     final_output = []
 
     modality_suffix = get_modality_suffix(config["modality"])
-    modality_key = get_modality_key(config["modality"])
+    modality_key = config["modality"]
 
     # use a zip list for subject/session:
     zip_list = inputs[modality_key].zip_lists
     if "session" in zip_list:
         zip_list = snakebids.filter_list(
             zip_list,
-            {
-                "session": inputs[get_modality_key(config["modality"])].zip_lists[
-                    "session"
-                ]
-            },
+            {"session": inputs[config["modality"]].zip_lists["session"]},
         )
-
     final_output.extend(
         expand(
             expand(subj_output, zip, allow_missing=True, **zip_list),
             modality_suffix=modality_suffix,
         )
     )
-
     return final_output
 
 
@@ -425,7 +409,7 @@ def get_final_work_tar():
 
 
 def get_work_dir(wildcards):
-    folder_with_file = inputs[get_modality_key(config["modality"])].expand(
+    folder_with_file = inputs[config["modality"]].expand(
         bids(root=work, **inputs.subj_wildcards), **wildcards
     )
     folder_without_file = os.path.dirname(folder_with_file[0])

hippunfold/workflow/rules/gifti.smk

@@ -1341,9 +1341,7 @@ rule create_spec_file_hipp:
             metric=get_gifti_metric_types(wildcards.label),
             allow_missing=True,
         ),
-        subfields=lambda wildcards: inputs[
-            get_modality_key(config["modality"])
-        ].expand(
+        subfields=lambda wildcards: inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
@@ -1373,9 +1371,7 @@ rule create_spec_file_hipp:
             space=["{space}", "unfold"],
             allow_missing=True,
         ),
-        cifti_metrics=lambda wildcards: inputs[
-            get_modality_key(config["modality"])
-        ].expand(
+        cifti_metrics=lambda wildcards: inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",
@@ -1388,9 +1384,7 @@ rule create_spec_file_hipp:
             cifti=get_cifti_metric_types(wildcards.label),
             allow_missing=True,
         ),
-        cifti_labels=lambda wildcards: inputs[
-            get_modality_key(config["modality"])
-        ].expand(
+        cifti_labels=lambda wildcards: inputs[config["modality"]].expand(
             bids(
                 root=root,
                 datatype="surf",