Output fsLR meshes on subject surfaces

Implementation of nipreps/fmriprep#3411.

Author: tsalo

aslprep/workflows/base.py

@@ -128,13 +128,14 @@ 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 aslprep.interfaces.bids import BIDSDataGrabber
@@ -422,7 +423,8 @@ 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(
@@ -431,6 +433,15 @@ 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=aslprep_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, [
@@ -446,7 +457,9 @@ 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'}",
@@ -466,12 +479,15 @@ 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'),
@@ -480,6 +496,11 @@ 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:
@@ -713,7 +734,7 @@ def init_single_subject_wf(subject_id: str):
                     (select_MNI6_xfm, asl_wf, [('anat2std_xfm', 'inputnode.anat2mni6_xfm')]),
                     (select_MNI6_tpl, asl_wf, [('brain_mask', 'inputnode.mni6_mask')]),
                     (hcp_morphometrics_wf, asl_wf, [('outputnode.roi', 'inputnode.cortex_mask')]),
-                    (resample_midthickness_wf, asl_wf, [
+                    (resample_surfaces_wf, asl_wf, [
                         ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                     ]),
                 ])  # fmt:skip

pyproject.toml

@@ -36,7 +36,7 @@ dependencies = [
     "requests",
     "sdcflows <= 2.11.0",
     "sentry-sdk <= 2.19.2",
-    "smriprep <= 0.16.1",
+    "smriprep <= 0.17.0",
     "templateflow <= 24.2.2",
     "toml",
 ]