feat: Output fsLR meshes on subject surfaces (#3411)

Integration of nipreps/smriprep#460.

Author: effigies

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -14,11 +14,17 @@ sub-01/anat/sub-01_desc-ribbon_mask.json
 sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
 sub-01/anat/sub-01_hemi-L_desc-preproc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_desc-preproc_white.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_desc-preproc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_desc-preproc_white.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_desc-preproc_white.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii

.circleci/ds005_partial_outputs.txt

@@ -25,6 +25,9 @@ sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.h5
 sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-L_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_pial.surf.gii
+sub-01/anat/sub-01_hemi-L_space-fsLR_den-32k_white.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
@@ -34,6 +37,9 @@ sub-01/anat/sub-01_hemi-L_thickness.shape.gii
 sub-01/anat/sub-01_hemi-L_white.surf.gii
 sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
 sub-01/anat/sub-01_hemi-R_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_pial.surf.gii
+sub-01/anat/sub-01_hemi-R_space-fsLR_den-32k_white.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/anat/sub-01_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii

fmriprep/workflows/base.py

@@ -156,13 +156,14 @@ def init_single_subject_wf(subject_id: str):
     from smriprep.workflows.outputs import (
         init_ds_anat_volumes_wf,
         init_ds_grayord_metrics_wf,
+        init_ds_surfaces_wf,
         init_template_iterator_wf,
     )
     from smriprep.workflows.surfaces import (
         init_gifti_morphometrics_wf,
         init_hcp_morphometrics_wf,
         init_morph_grayords_wf,
-        init_resample_midthickness_wf,
+        init_resample_surfaces_wf,
     )
 
     from fmriprep.workflows.bold.base import init_bold_wf
@@ -449,7 +450,8 @@ def init_single_subject_wf(subject_id: str):
                 grayord_density=config.workflow.cifti_output,
                 omp_nthreads=omp_nthreads,
             )
-            resample_midthickness_wf = init_resample_midthickness_wf(
+            resample_surfaces_wf = init_resample_surfaces_wf(
+                surfaces=['white', 'pial', 'midthickness'],
                 grayord_density=config.workflow.cifti_output,
             )
             ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(
@@ -458,6 +460,15 @@ def init_single_subject_wf(subject_id: str):
                 metrics=['curv', 'thickness', 'sulc'],
                 cifti_output=config.workflow.cifti_output,
             )
+            ds_fsLR_surfaces_wf = init_ds_surfaces_wf(
+                output_dir=fmriprep_dir,
+                surfaces=['white', 'pial', 'midthickness'],
+                entities={
+                    'space': 'fsLR',
+                    'density': '32k' if config.workflow.cifti_output == '91k' else '59k',
+                },
+                name='ds_fsLR_surfaces_wf',
+            )
 
             workflow.connect([
                 (anat_fit_wf, curv_wf, [
@@ -473,7 +484,9 @@ def init_single_subject_wf(subject_id: str):
                 (curv_wf, hcp_morphometrics_wf, [
                     ('outputnode.curv', 'inputnode.curv'),
                 ]),
-                (anat_fit_wf, resample_midthickness_wf, [
+                (anat_fit_wf, resample_surfaces_wf, [
+                    ('outputnode.white', 'inputnode.white'),
+                    ('outputnode.pial', 'inputnode.pial'),
                     ('outputnode.midthickness', 'inputnode.midthickness'),
                     (
                         f"outputnode.sphere_reg_{'msm' if msm_sulc else 'fsLR'}",
@@ -493,12 +506,15 @@ def init_single_subject_wf(subject_id: str):
                     ('outputnode.sulc', 'inputnode.sulc'),
                     ('outputnode.roi', 'inputnode.roi'),
                 ]),
-                (resample_midthickness_wf, morph_grayords_wf, [
+                (resample_surfaces_wf, morph_grayords_wf, [
                     ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                 ]),
                 (anat_fit_wf, ds_grayord_metrics_wf, [
                     ('outputnode.t1w_valid_list', 'inputnode.source_files'),
                 ]),
+                (anat_fit_wf, ds_fsLR_surfaces_wf, [
+                    ('outputnode.t1w_valid_list', 'inputnode.source_files'),
+                ]),
                 (morph_grayords_wf, ds_grayord_metrics_wf, [
                     ('outputnode.curv_fsLR', 'inputnode.curv'),
                     ('outputnode.curv_metadata', 'inputnode.curv_metadata'),
@@ -507,6 +523,11 @@ def init_single_subject_wf(subject_id: str):
                     ('outputnode.sulc_fsLR', 'inputnode.sulc'),
                     ('outputnode.sulc_metadata', 'inputnode.sulc_metadata'),
                 ]),
+                (resample_surfaces_wf, ds_fsLR_surfaces_wf, [
+                    ('outputnode.white_fsLR', 'inputnode.white'),
+                    ('outputnode.pial_fsLR', 'inputnode.pial'),
+                    ('outputnode.midthickness_fsLR', 'inputnode.midthickness'),
+                ]),
             ])  # fmt:skip
 
     if config.workflow.anat_only:
@@ -740,7 +761,7 @@ def init_single_subject_wf(subject_id: str):
                     (hcp_morphometrics_wf, bold_wf, [
                         ('outputnode.roi', 'inputnode.cortex_mask'),
                     ]),
-                    (resample_midthickness_wf, bold_wf, [
+                    (resample_surfaces_wf, bold_wf, [
                         ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                     ]),
                 ])  # fmt:skip

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "pybids >= 0.16",
     "requests >= 2.27",
     "sdcflows >= 2.10.0",
-    "smriprep >= 0.16.0",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git",
     "tedana >= 23.0.2",
     "templateflow >= 24.2.2",
     "transforms3d >= 0.4",

scripts/fetch_templates.py

@@ -16,7 +16,9 @@ def fetch_MNI2009():
     Expected templates:
 
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
+    tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T2w.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz
@@ -25,7 +27,7 @@ def fetch_MNI2009():
     """
     template = 'MNI152NLin2009cAsym'
 
-    tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    tf.get(template, resolution=(1, 2), desc=None, suffix=['T1w', 'T2w'])
     tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
     tf.get(template, resolution=1, atlas=None, desc='carpet', suffix='dseg')
     tf.get(template, resolution=2, desc='fMRIPrep', suffix='boldref')