Merge pull request #427 from mgxd/enh/smriprep-master

ENH: Output fsLR meshes on subject surfaces

Author: mgxd

.circleci/bcp_anat_t2only_outputs.txt

@@ -12,14 +12,19 @@ sub-01/ses-1mo
 sub-01/ses-1mo/anat
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.json
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_desc-preproc_T2w.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNI152NLin6Asym_to-T2w_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-MNIInfant+1_to-T2w_mode-image_xfm.h5
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNI152NLin6Asym_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNIInfant+1_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-fsnative_mode-image_xfm.txt
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T2w_mode-image_xfm.txt
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_den-32k_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_den-32k_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_space-fsaverage_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sphere.surf.gii
@@ -30,6 +35,9 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_curv.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_inflated.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_midthickness.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_den-32k_midthickness.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_den-32k_pial.surf.gii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_den-32k_white.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_space-fsaverage_desc-reg_sphere.surf.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_sphere.surf.gii
@@ -52,4 +60,10 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_dseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_label-CSF_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_label-GM_probseg.nii.gz
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-T2w_label-WM_probseg.nii.gz
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_curv.dscalar.nii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_curv.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_sulc.dscalar.nii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_sulc.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_thickness.dscalar.nii
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_space-fsLR_den-91k_thickness.json
 sub-01_ses-1mo.html

.circleci/config.yml

@@ -16,7 +16,6 @@ _python_defaults: &python_defaults
       password: $DOCKER_PAT
   working_directory: /tmp/src/nibabies
 
-
 _docker_auth: &docker_auth
   name: Docker authentication
   command: |
@@ -160,7 +159,6 @@ jobs:
         - /tmp/docker
         - /tmp/images
 
-
   get_data:
     !!merge <<: *python_defaults
     working_directory: /home/circleci/data
@@ -279,7 +277,6 @@ jobs:
     - store_artifacts:
         path: /tmp/data/reports
 
-
   test_bcp:
     !!merge <<: *machine_defaults
     environment:
@@ -412,7 +409,7 @@ jobs:
               --nthreads 4 -vv --age-months 2 --sloppy \
               --surface-recon-method infantfs \
               --derivatives precomputed=/tmp/data/${DATASET}-t2only/derivatives/bibsnet \
-              --output-layout bids --anat-only
+              --output-layout bids --anat-only --cifti-output
     - run:
         name: Checking outputs of T2-only nibabies anat
         command: |
@@ -427,7 +424,6 @@ jobs:
     - store_artifacts:
         path: /tmp/bcp/derivatives
 
-
   deploy_docker_patches:
     !!merge <<: *machine_defaults
     working_directory: *src
@@ -464,7 +460,6 @@ jobs:
           docker tag nipreps/nibabies:dev nipreps/nibabies:${CIRCLE_BRANCH#docker/}
           docker push nipreps/nibabies:${CIRCLE_BRANCH#docker/}
 
-
   deploy_docker:
     !!merge <<: *machine_defaults
     steps:
@@ -503,7 +498,6 @@ jobs:
             fi
           fi
 
-
   test_deploy_pypi:
     !!merge <<: *python_defaults
     steps:
@@ -559,7 +553,6 @@ jobs:
     - store_artifacts:
         path: /tmp/src/nibabies/wrapper/dist
 
-
   deploy_pypi:
     !!merge <<: *python_defaults
     steps:
@@ -584,14 +577,12 @@ jobs:
           # upload wrapper
           python -m twine upload wrapper/dist/nibabies*
 
-
   deployable:
     docker:
     - image: busybox:latest
     steps:
     - run: echo Deploying!
 
-
 workflows:
   version: 2
   build_test_deploy:

nibabies/workflows/anatomical/apply.py

@@ -11,13 +11,13 @@
 from smriprep.workflows.surfaces import (
     init_hcp_morphometrics_wf,
     init_morph_grayords_wf,
-    init_resample_midthickness_wf,
+    init_resample_surfaces_wf,
     init_surface_derivatives_wf,
 )
 
 from nibabies import config
 from nibabies.workflows.anatomical.outputs import init_ds_seg_wf
-from nibabies.workflows.anatomical.surfaces import init_resample_midthickness_dhcp_wf
+from nibabies.workflows.anatomical.surfaces import init_resample_surfaces_dhcp_wf
 
 if ty.TYPE_CHECKING:
     from niworkflows.utils.spaces import SpatialReferences
@@ -57,6 +57,8 @@ def init_infant_anat_apply_wf(
                 'sulc',
                 'template',
                 'thickness',
+                'white',
+                'pial',
                 'midthickness',
                 reg_sphere,
                 # template workflow inputs
@@ -185,17 +187,28 @@ def init_infant_anat_apply_wf(
         if cifti_output:
             hcp_morphometrics_wf = init_hcp_morphometrics_wf(omp_nthreads=omp_nthreads)
             if recon_method == 'mcribs':
-                resample_midthickness_wf = init_resample_midthickness_dhcp_wf(
-                    grayord_density=cifti_output
+                resample_surfaces_wf = init_resample_surfaces_dhcp_wf(
+                    surfaces=['white', 'pial', 'midthickness'],
+                    grayord_density=cifti_output,
                 )
             else:
-                resample_midthickness_wf = init_resample_midthickness_wf(
-                    grayord_density=cifti_output
+                resample_surfaces_wf = init_resample_surfaces_wf(
+                    surfaces=['white', 'pial', 'midthickness'], grayord_density=cifti_output
                 )
             morph_grayords_wf = init_morph_grayords_wf(
                 grayord_density=cifti_output, omp_nthreads=omp_nthreads
             )
 
+            ds_fsLR_surfaces_wf = init_ds_surfaces_wf(
+                output_dir=output_dir,
+                surfaces=['white', 'pial', 'midthickness'],
+                entities={
+                    'space': 'dhcpAsym' if recon_method == 'mcribs' else 'fsLR',
+                    'density': '32k' if cifti_output == '91k' else '59k',
+                },
+                name='ds_fsLR_surfaces_wf',
+            )
+
             ds_grayord_metrics_wf = init_ds_grayord_metrics_wf(
                 bids_root=bids_root,
                 output_dir=output_dir,
@@ -213,7 +226,9 @@ def init_infant_anat_apply_wf(
                 (surface_derivatives_wf, hcp_morphometrics_wf, [
                     ('outputnode.curv', 'inputnode.curv'),
                 ]),
-                (inputnode, resample_midthickness_wf, [
+                (inputnode, resample_surfaces_wf, [
+                    ('white', 'inputnode.white'),
+                    ('pial', 'inputnode.pial'),
                     ('midthickness', 'inputnode.midthickness'),
                     (reg_sphere, 'inputnode.sphere_reg_fsLR'),
                 ]),
@@ -230,12 +245,20 @@ def init_infant_anat_apply_wf(
                 (hcp_morphometrics_wf, outputnode, [
                     ('outputnode.roi', 'roi'),
                 ]),
-                (resample_midthickness_wf, morph_grayords_wf, [
+                (resample_surfaces_wf, morph_grayords_wf, [
                     ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                 ]),
-                (resample_midthickness_wf, outputnode, [
+                (inputnode, ds_fsLR_surfaces_wf, [
+                    ('anat_valid_list', 'inputnode.source_files'),
+                ]),
+                (resample_surfaces_wf, outputnode, [
                     ('outputnode.midthickness_fsLR', 'midthickness_fsLR'),
                 ]),
+                (resample_surfaces_wf, ds_fsLR_surfaces_wf, [
+                    ('outputnode.white_fsLR', 'inputnode.white'),
+                    ('outputnode.pial_fsLR', 'inputnode.pial'),
+                    ('outputnode.midthickness_fsLR', 'inputnode.midthickness'),
+                ]),
                 (inputnode, ds_grayord_metrics_wf, [
                     ('anat_valid_list', 'inputnode.source_files'),
                 ]),

nibabies/workflows/anatomical/surfaces.py

@@ -415,9 +415,10 @@ def init_make_midthickness_wf(
     return workflow
 
 
-def init_resample_midthickness_dhcp_wf(
+def init_resample_surfaces_dhcp_wf(
+    surfaces: list[str],
     grayord_density: ty.Literal['91k', '170k'],
-    name: str = 'resample_midthickness_wf',
+    name: str = 'resample_surfaces_dhcp_wf',
 ):
     """
     Resample subject midthickness surface to specified density.
@@ -427,20 +428,20 @@ def init_resample_midthickness_dhcp_wf(
             :graph2use: colored
             :simple_form: yes
 
-            from nibabies.workflows.anatomical.surfaces import init_resample_midthickness_wf
-            wf = init_resample_midthickness_wf(grayord_density="91k")
+            from nibabies.workflows.anatomical.surfaces import init_resample_surfaces_dhcp_wf
+            wf = init_resample_surfaces_dhcp_wf(surfaces=['white', grayord_density='91k')
 
     Parameters
     ----------
     grayord_density : :obj:`str`
         Either `91k` or `170k`, representing the total of vertices or *grayordinates*.
     name : :obj:`str`
-        Unique name for the subworkflow (default: ``"resample_midthickness_wf"``)
+        Unique name for the subworkflow (default: ``"resample_surfaces_dhcp_wf``)
 
     Inputs
     ------
-    midthickness
-        GIFTI surface mesh corresponding to the midthickness surface
+    ``<surface>``
+        Left and right GIFTIs for each surface name passed to ``surfaces``
     sphere_reg_fsLR
         GIFTI surface mesh corresponding to the subject's fsLR registration sphere
 
@@ -454,11 +455,19 @@ def init_resample_midthickness_dhcp_wf(
     fslr_density = '32k' if grayord_density == '91k' else '59k'
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=['midthickness', 'sphere_reg_fsLR']),
+        niu.IdentityInterface(fields=[*surfaces, 'sphere_reg_fsLR']),
         name='inputnode',
     )
 
-    outputnode = pe.Node(niu.IdentityInterface(fields=['midthickness_fsLR']), name='outputnode')
+    outputnode = pe.Node(
+        niu.IdentityInterface(fields=[f'{surf}_fsLR' for surf in surfaces]), name='outputnode'
+    )
+
+    surface_list = pe.Node(
+        niu.Merge(len(surfaces), ravel_inputs=True),
+        name='surface_list',
+        run_without_submitting=True,
+    )
 
     resampler = pe.MapNode(
         SurfaceResample(method='BARYCENTRIC'),
@@ -477,20 +486,45 @@ def init_resample_midthickness_dhcp_wf(
                 extension='.surf.gii',
             )
         )
+        # Order matters. Iterate over surfaces, then hemis to get L R L R L R
+        for _surf in surfaces
         for hemi in ['L', 'R']
     ]
 
+    surface_groups = pe.Node(
+        niu.Split(splits=[2] * len(surfaces)),
+        name='surface_groups',
+        run_without_submitting=True,
+    )
+
     workflow.connect([
+        (inputnode, surface_list, [
+            ((surf, _sorted_by_basename), f'in{i}')
+            for i, surf in enumerate(surfaces, start=1)
+        ]),
         (inputnode, resampler, [
-            ('midthickness', 'surface_in'),
-            ('sphere_reg_fsLR', 'current_sphere'),
+            (('sphere_reg_fsLR', _repeat, len(surfaces)), 'current_sphere'),
+        ]),
+        (surface_list, resampler, [('out', 'surface_in')]),
+        (resampler, surface_groups, [('surface_out', 'inlist')]),
+        (surface_groups, outputnode, [
+            (f'out{i}', f'{surf}_fsLR') for i, surf in enumerate(surfaces, start=1)
         ]),
-        (resampler, outputnode, [('surface_out', 'midthickness_fsLR')]),
     ])  # fmt:skip
 
     return workflow
 
 
+def _sorted_by_basename(inlist):
+    from os.path import basename
+
+    return sorted(inlist, key=lambda x: str(basename(x)))
+
+
+def _repeat(seq: list, count: int) -> list:
+    return seq * count
+
+
 def _parent(p):
     from pathlib import Path
 

nibabies/workflows/base.py

@@ -513,6 +513,8 @@ def init_single_subject_wf(
                 ('outputnode.anat_dseg', 'inputnode.anat_dseg'),
                 ('outputnode.anat_tpms', 'inputnode.anat_tpms'),
                 ('outputnode.fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
+                ('outputnode.white', 'inputnode.white'),
+                ('outputnode.pial', 'inputnode.pial'),
                 ('outputnode.midthickness', 'inputnode.midthickness'),
                 (f'outputnode.{reg_sphere}', f'inputnode.{reg_sphere}'),
                 ('outputnode.sulc', 'inputnode.sulc'),

pyproject.toml

@@ -34,8 +34,7 @@ dependencies = [
     "pybids >= 0.15.0",
     "requests",
     "sdcflows >= 2.10.0",
-#    "smriprep >= 0.16.1",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@dev-nibabies",
+    "smriprep >= 0.17.0",
     "tedana >= 23.0.2",
     "templateflow >= 24.2.0",
     "toml",