even better naming

PennLINC · Dec 13, 2024 · 93c0e9c · 93c0e9c
1 parent 14849a3
commit 93c0e9c
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Showing 6 changed files with 108 additions and 59 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -145,7 +145,7 @@ jobs:
       - persist_to_workspace:
           root: /src/coverage/
           paths:
-            - /src/coverage/.coverage.ss3t_fod_autotrack
+            - .coverage.ss3t_fod_autotrack
       - store_artifacts:
           path: /src/qsirecon/.circleci/out/ss3t_fod_autotrack/
 

diff --git a/qsirecon/data/pipelines/ss3t_fod_autotrack.yaml b/qsirecon/data/pipelines/ss3t_fod_autotrack.yaml
@@ -7,17 +7,9 @@ nodes:
     name: dsistudio_gqi
     parameters:
         method: gqi
-    qsirecon_suffix: GQIAutoTrack
+    qsirecon_suffix: SS3TAutoTrack
     software: DSI Studio
 
-    # Performs the registration of QA+ISO to template
-    # also passes through the GQI fib/etc
-# -   action: autotrack_registration
-#     software: DSI Studio
-#     name: autotrack_register
-#     input: dsistudio_gqi
-#     qsirecon_suffix: DSIStudio
-
     # Select just one shell + b=0 for autotrack
 -   action: select_gradients
     input: qsirecon
@@ -41,6 +33,24 @@ nodes:
             algorithm: dhollander
     qsirecon_suffix: SS3TAutoTrack
 
+    # Get 3D images of DSI Studio's scalar maps
+-   action: export
+    input: dsistudio_gqi
+    name: gqi_scalars
+    qsirecon_suffix: SS3TAutoTrack
+    software: DSI Studio
+
+# Uncomment to map scalar maps to template space
+# -   action: template_map
+#     input: qsirecon
+#     name: template_map
+#     parameters:
+#         interpolation: NearestNeighbor
+#     scalars_from:
+#     - gqi_scalars
+#     - dipy_dki
+#     software: qsirecon
+
 -   action: fod_fib_merge
     name: create_fod_fib
     # to include the fib file and the map file
@@ -49,18 +59,6 @@ nodes:
     # outputs include the FOD fib file and the map file is passed through
     qsirecon_suffix: SS3TAutoTrack
 
--   action: autotrack
-    input: dsistudio_gqi
-    name: autotrack_gqi
-    parameters:
-        tolerance: 22,26,30
-        track_id: Association,Projection,Commissure,Cerebellum,CranialNerve
-        track_voxel_ratio: 2.0
-        yield_rate: 1.0e-06
-    qsirecon_suffix: GQIAutoTrack
-    software: DSI Studio
-
-
 -   action: autotrack
     input: create_fod_fib
     name: autotrack_fod
@@ -70,4 +68,4 @@ nodes:
         track_voxel_ratio: 2.0
         yield_rate: 1.0e-06
     qsirecon_suffix: SS3TAutoTrack
-    software: DSI Studio
+    software: DSI Studio
diff --git a/qsirecon/tests/data/ss3t_fod_autotrack_outputs.txt b/qsirecon/tests/data/ss3t_fod_autotrack_outputs.txt
@@ -1,41 +1,71 @@
-atlases
-atlases/atlas-Gordon333Ext
-atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_dseg.tsv
-atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_space-MNI152NLin2009cAsym_res-01_dseg.json
-atlases/atlas-Gordon333Ext/atlas-Gordon333Ext_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz
-atlases/dataset_description.json
 dataset_description.json
 derivatives
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/dataset_description.json
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.bib
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.html
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.md
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/logs/CITATION.tex
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC.html
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_connectivity.mat
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_exemplarbundles.zip
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-mtnorm_param-inliermask_dwimap.nii.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-mtnorm_param-norm_dwimap.nii.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sdstream_streamlines.tck.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sift2_mu.txt
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-sift2_streamlineweights.csv
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.mif.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.txt
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-GM_dwimap.mif.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-GM_dwimap.txt
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.mif.gz
-derivatives/qsirecon-MRtrix3_fork-SS3T_act-FAST/sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_model-ss3t_param-fod_label-WM_dwimap.txt
+derivatives/qsirecon-SS3TAutoTrack
+derivatives/qsirecon-SS3TAutoTrack/dataset_description.json
+derivatives/qsirecon-SS3TAutoTrack/logs
+derivatives/qsirecon-SS3TAutoTrack/logs/CITATION.bib
+derivatives/qsirecon-SS3TAutoTrack/logs/CITATION.html
+derivatives/qsirecon-SS3TAutoTrack/logs/CITATION.md
+derivatives/qsirecon-SS3TAutoTrack/logs/CITATION.tex
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusL_streamlines.tck.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundle-AssociationArcuateFasciculusR_streamlines.tck.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_bundlestats.csv
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_mapping.map.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_dwimap.fib.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-gfa_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-gfa_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-iso_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-iso_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-qa_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-gqi_param-qa_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mtnorm_param-inliermask_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-mtnorm_param-norm_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd1_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd1_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd2_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-rdi_param-rd2_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_dwimap.fib.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.mif.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-CSF_dwimap.txt
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-GM_dwimap.mif.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-GM_dwimap.txt
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-WM_dwimap.mif.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-ss3t_param-fod_label-WM_dwimap.txt
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ad_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-fa_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ha_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-ha_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-md_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-md_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-rd_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-rd_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txx_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txx_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txy_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txy_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txz_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-txz_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tyy_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tyy_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tyz_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tyz_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tzz_dwimap.json
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/dwi/sub-ABCD_acq-10per000_space-T1w_model-tensor_param-tzz_dwimap.nii.gz
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_acq-10per000_space-T1w_desc-GQIODF_odfs.png
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_acq-10per000_space-T1w_desc-GQIODF_peaks.png
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_acq-10per000_space-T1w_desc-wmFOD_odfs.png
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_acq-10per000_space-T1w_desc-wmFOD_peaks.png
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_desc-about_T1w.html
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/figures/sub-ABCD_desc-summary_T1w.html
+derivatives/qsirecon-SS3TAutoTrack/sub-ABCD/sub-ABCD.html
 logs
 logs/CITATION.bib
 logs/CITATION.html
 logs/CITATION.md
 logs/CITATION.tex
-sub-PNC
-sub-PNC/dwi
-sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.mif.gz
-sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.nii.gz
-sub-PNC/dwi/sub-PNC_acq-realistic_space-T1w_seg-Gordon333Ext_dseg.txt
+sub-ABCD
diff --git a/qsirecon/workflows/recon/converters.py b/qsirecon/workflows/recon/converters.py
@@ -150,7 +150,9 @@ def init_fod_fib_wf(inputs_dict, name="fod_fib", qsirecon_suffix="", params={}):
         ds_fibgz = pe.Node(
             DerivativesDataSink(
                 dismiss_entities=("desc",),
+                suffix="dwimap",
                 extension=".fib.gz",
+                model="ss3t",
                 compress=True,
             ),
             name="ds_fibgz",

diff --git a/qsirecon/workflows/recon/dsi_studio.py b/qsirecon/workflows/recon/dsi_studio.py
@@ -147,6 +147,7 @@ def init_dsi_studio_recon_wf(inputs_dict, name="dsi_studio_recon", qsirecon_suff
                 dismiss_entities=("desc",),
                 suffix="dwimap",
                 extension=".fib.gz",
+                model="gqi",
                 compress=True,
             ),
             name="ds_gqi_fibgz",

diff --git a/qsirecon/workflows/recon/utils.py b/qsirecon/workflows/recon/utils.py
@@ -62,7 +62,16 @@ def init_discard_repeated_samples_wf(
         niu.IdentityInterface(fields=recon_workflow_input_fields), name="inputnode"
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=["dwi_file", "bval_file", "bvec_file", "local_bvec_file"]),
+        niu.IdentityInterface(
+            fields=[
+                "dwi_file",
+                "bval_file",
+                "bvec_file",
+                "local_bvec_file",
+                "b_file",
+                "btable_file",
+            ]
+        ),
         name="outputnode",
     )
     workflow = Workflow(name=name)
@@ -97,7 +106,16 @@ def init_gradient_select_wf(
         niu.IdentityInterface(fields=recon_workflow_input_fields), name="inputnode"
     )
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=["dwi_file", "bval_file", "bvec_file", "local_bvec_file"]),
+        niu.IdentityInterface(
+            fields=[
+                "dwi_file",
+                "bval_file",
+                "bvec_file",
+                "local_bvec_file",
+                "b_file",
+                "btable_file",
+            ]
+        ),
         name="outputnode",
     )
     workflow = Workflow(name=name)