ENH: Add cortex mask

.circleci/bcp_anat_outputs.txt

@@ -21,6 +21,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.t
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-T1w_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T1w_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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-cortex_mask.label.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
@@ -31,6 +33,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-cortex_mask.label.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

.circleci/bcp_anat_t2only_outputs.txt

@@ -19,6 +19,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-MNIInfant+1_mode-image_xf
 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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-cortex_mask.label.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
@@ -32,6 +34,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-cortex_mask.label.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

.circleci/bcp_full_outputs.txt

@@ -21,6 +21,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T1w_to-fsnative_mode-image_xfm.t
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-T2w_to-T1w_mode-image_xfm.h5
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_from-fsnative_to-T1w_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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_desc-cortex_mask.label.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
@@ -31,6 +33,8 @@ sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_sulc.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_thickness.shape.gii
 sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-L_white.surf.gii
 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_desc-cortex_mask.json
+sub-01/ses-1mo/anat/sub-01_ses-1mo_run-001_hemi-R_desc-cortex_mask.label.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

nibabies/data/io_spec_anat.json

@@ -232,6 +232,14 @@
           "desc": "msmsulc",
           "suffix": "sphere",
           "extension": ".surf.gii"
+        },
+        "cortex_mask": {
+          "datatype": "anat",
+          "hemi": ["L", "R"],
+          "space": null,
+          "desc": "cortex",
+          "suffix": "mask",
+          "extension": ".label.gii"
         }
       },
       "masks": {

nibabies/workflows/anatomical/apply.py

@@ -62,6 +62,7 @@ def init_infant_anat_apply_wf(
                 'white',
                 'pial',
                 'midthickness',
+                'cortex_mask',
                 reg_sphere,
                 # template workflow inputs
                 'std_t1w',
@@ -75,7 +76,7 @@ def init_infant_anat_apply_wf(
     )
 
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=['anat_aseg', 'anat_aparc', 'midthickness_fsLR', 'roi']),
+        niu.IdentityInterface(fields=['anat_aseg', 'anat_aparc', 'midthickness_fsLR']),
         name='outputnode',
     )
 
@@ -235,17 +236,14 @@ def init_infant_anat_apply_wf(
                     (reg_sphere, 'inputnode.sphere_reg_fsLR'),
                 ]),
                 (inputnode, morph_grayords_wf, [
+                    ('cortex_mask', 'inputnode.roi'),
                     ('midthickness', 'inputnode.midthickness'),
                     (reg_sphere, 'inputnode.sphere_reg_fsLR'),
                 ]),
                 (hcp_morphometrics_wf, morph_grayords_wf, [
                     ('outputnode.curv', 'inputnode.curv'),
                     ('outputnode.sulc', 'inputnode.sulc'),
                     ('outputnode.thickness', 'inputnode.thickness'),
-                    ('outputnode.roi', 'inputnode.roi'),
-                ]),
-                (hcp_morphometrics_wf, outputnode, [
-                    ('outputnode.roi', 'roi'),
                 ]),
                 (resample_surfaces_wf, morph_grayords_wf, [
                     ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),

nibabies/workflows/anatomical/fit.py

@@ -13,21 +13,23 @@
 from niworkflows.utils.connections import pop_file
 from smriprep.workflows.anatomical import (
     _is_skull_stripped,
-    init_anat_ribbon_wf,
     init_anat_template_wf,
 )
 from smriprep.workflows.fit.registration import init_register_template_wf
 from smriprep.workflows.outputs import (
     init_ds_dseg_wf,
     init_ds_fs_registration_wf,
     init_ds_mask_wf,
+    init_ds_surface_masks_wf,
     init_ds_surface_metrics_wf,
     init_ds_surfaces_wf,
     init_ds_template_registration_wf,
     init_ds_template_wf,
     init_ds_tpms_wf,
 )
 from smriprep.workflows.surfaces import (
+    init_anat_ribbon_wf,
+    init_cortex_masks_wf,
     init_fsLR_reg_wf,
     init_gifti_morphometrics_wf,
     init_gifti_surfaces_wf,
@@ -147,6 +149,7 @@ def init_infant_anat_fit_wf(
                 'sphere_reg',
                 'sphere_reg_fsLR',
                 'sphere_reg_msm',
+                'cortex_mask',
                 'anat_ribbon',
                 # Reverse transform; not computable from forward transform
                 'std2anat_xfm',
@@ -1273,13 +1276,13 @@ def init_infant_anat_fit_wf(
             (fsnative_buffer, gifti_surfaces_wf, [
                 ('fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
-            (gifti_surfaces_wf, surfaces_buffer, [
-                (f'outputnode.{surf}', surf) for surf in surfs
-            ]),
             (sourcefile_buffer, ds_surfaces_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_surfaces_wf, ds_surfaces_wf, [
                 (f'outputnode.{surf}', f'inputnode.{surf}') for surf in surfs
             ]),
+            (ds_surfaces_wf, surfaces_buffer, [
+                (f'outputnode.{surf}', surf) for surf in surfs
+            ]),
         ])  # fmt:skip
     if spheres:
         gifti_spheres_wf = init_gifti_surfaces_wf(
@@ -1297,13 +1300,13 @@ def init_infant_anat_fit_wf(
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 # No transform for spheres, following HCP pipelines' lead
             ]),
-            (gifti_spheres_wf, surfaces_buffer, [
-                (f'outputnode.{sphere}', sphere) for sphere in spheres
-            ]),
             (sourcefile_buffer, ds_spheres_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_spheres_wf, ds_spheres_wf, [
                 (f'outputnode.{sphere}', f'inputnode.{sphere}') for sphere in spheres
             ]),
+            (ds_spheres_wf, surfaces_buffer, [
+                (f'outputnode.{sphere}', sphere) for sphere in spheres
+            ]),
         ])  # fmt:skip
     metrics = [metric for metric in needed_metrics if metric not in found_surfs]
     if metrics:
@@ -1321,13 +1324,13 @@ def init_infant_anat_fit_wf(
                 ('outputnode.subject_id', 'inputnode.subject_id'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
             ]),
-            (gifti_morph_wf, surfaces_buffer, [
-                (f'outputnode.{metric}', metric) for metric in metrics
-            ]),
             (sourcefile_buffer, ds_morph_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_morph_wf, ds_morph_wf, [
                 (f'outputnode.{metric}', f'inputnode.{metric}') for metric in metrics
             ]),
+            (ds_morph_wf, surfaces_buffer, [
+                (f'outputnode.{metric}', metric) for metric in metrics
+            ]),
         ])  # fmt:skip
 
     if 'anat_ribbon' not in precomputed:
@@ -1413,6 +1416,32 @@ def init_infant_anat_fit_wf(
         else:
             LOGGER.info('ANAT Stage 9: Found pre-computed fsLR registration sphere')
             fsLR_buffer.inputs.sphere_reg_fsLR = sorted(precomputed['sphere_reg_fsLR'])
+
+    # Stage 10: Cortical surface mask
+    if len(precomputed.get('cortex_mask', [])) < 2:
+        LOGGER.info('ANAT Stage 11: Creating cortical surface mask')
+
+        cortex_masks_wf = init_cortex_masks_wf()
+        ds_cortex_masks_wf = init_ds_surface_masks_wf(
+            output_dir=output_dir,
+            mask_type='cortex',
+            name='ds_cortex_masks_wf',
+        )
+
+        workflow.connect([
+            (surfaces_buffer, cortex_masks_wf, [
+                ('midthickness', 'inputnode.midthickness'),
+                ('thickness', 'inputnode.thickness'),
+            ]),
+            (cortex_masks_wf, ds_cortex_masks_wf, [
+                ('outputnode.cortex_masks', 'inputnode.mask_files'),
+                ('outputnode.source_files', 'inputnode.source_files'),
+            ]),
+            (ds_cortex_masks_wf, outputnode, [('outputnode.mask_files', 'cortex_mask')]),
+        ])  # fmt:skip
+    else:
+        LOGGER.info('ANAT Stage 11: Found pre-computed cortical surface mask')
+        outputnode.inputs.cortex_mask = sorted(precomputed['cortex_mask'])
     return workflow
 
 
@@ -1476,6 +1505,7 @@ def init_infant_single_anat_fit_wf(
                 'sphere_reg',
                 'sphere_reg_fsLR',
                 'sphere_reg_msm',
+                'cortex_mask',
                 'anat_ribbon',
                 # Reverse transform; not computable from forward transform
                 'std2anat_xfm',
@@ -2202,13 +2232,13 @@ def init_infant_single_anat_fit_wf(
             (fsnative_buffer, gifti_surfaces_wf, [
                 ('fsnative2anat_xfm', 'inputnode.fsnative2anat_xfm'),
             ]),
-            (gifti_surfaces_wf, surfaces_buffer, [
-                (f'outputnode.{surf}', surf) for surf in surfs
-            ]),
             (sourcefile_buffer, ds_surfaces_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_surfaces_wf, ds_surfaces_wf, [
                 (f'outputnode.{surf}', f'inputnode.{surf}') for surf in surfs
             ]),
+            (ds_surfaces_wf, surfaces_buffer, [
+                (f'outputnode.{surf}', surf) for surf in surfs
+            ]),
         ])  # fmt:skip
     if spheres:
         gifti_spheres_wf = init_gifti_surfaces_wf(
@@ -2226,13 +2256,13 @@ def init_infant_single_anat_fit_wf(
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
                 # No transform for spheres, following HCP pipelines' lead
             ]),
-            (gifti_spheres_wf, surfaces_buffer, [
-                (f'outputnode.{sphere}', sphere) for sphere in spheres
-            ]),
             (sourcefile_buffer, ds_spheres_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_spheres_wf, ds_spheres_wf, [
                 (f'outputnode.{sphere}', f'inputnode.{sphere}') for sphere in spheres
             ]),
+            (ds_spheres_wf, surfaces_buffer, [
+                (f'outputnode.{sphere}', sphere) for sphere in spheres
+            ]),
         ])  # fmt:skip
     metrics = [metric for metric in needed_metrics if metric not in found_surfs]
     if metrics:
@@ -2250,13 +2280,13 @@ def init_infant_single_anat_fit_wf(
                 ('outputnode.subject_id', 'inputnode.subject_id'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
             ]),
-            (gifti_morph_wf, surfaces_buffer, [
-                (f'outputnode.{metric}', metric) for metric in metrics
-            ]),
             (sourcefile_buffer, ds_morph_wf, [('anat_source_files', 'inputnode.source_files')]),
             (gifti_morph_wf, ds_morph_wf, [
                 (f'outputnode.{metric}', f'inputnode.{metric}') for metric in metrics
             ]),
+            (ds_morph_wf, surfaces_buffer, [
+                (f'outputnode.{metric}', metric) for metric in metrics
+            ]),
         ])  # fmt:skip
 
     if 'anat_ribbon' not in precomputed:
@@ -2342,4 +2372,30 @@ def init_infant_single_anat_fit_wf(
         else:
             LOGGER.info('ANAT Stage 9: Found pre-computed fsLR registration sphere')
             fsLR_buffer.inputs.sphere_reg_fsLR = sorted(precomputed['sphere_reg_fsLR'])
+
+    # Stage 10: Cortical surface mask
+    if len(precomputed.get('cortex_mask', [])) < 2:
+        LOGGER.info('ANAT Stage 11: Creating cortical surface mask')
+
+        cortex_masks_wf = init_cortex_masks_wf()
+        ds_cortex_masks_wf = init_ds_surface_masks_wf(
+            output_dir=output_dir,
+            mask_type='cortex',
+            name='ds_cortex_masks_wf',
+        )
+
+        workflow.connect([
+            (surfaces_buffer, cortex_masks_wf, [
+                ('midthickness', 'inputnode.midthickness'),
+                ('thickness', 'inputnode.thickness'),
+            ]),
+            (cortex_masks_wf, ds_cortex_masks_wf, [
+                ('outputnode.cortex_masks', 'inputnode.mask_files'),
+                ('outputnode.source_files', 'inputnode.source_files'),
+            ]),
+            (ds_cortex_masks_wf, outputnode, [('outputnode.mask_files', 'cortex_mask')]),
+        ])  # fmt:skip
+    else:
+        LOGGER.info('ANAT Stage 11: Found pre-computed cortical surface mask')
+        outputnode.inputs.cortex_mask = sorted(precomputed['cortex_mask'])
     return workflow

nibabies/workflows/base.py

@@ -534,6 +534,7 @@ def init_single_subject_wf(
                 ('outputnode.white', 'inputnode.white'),
                 ('outputnode.pial', 'inputnode.pial'),
                 ('outputnode.midthickness', 'inputnode.midthickness'),
+                ('outputnode.cortex_mask', 'inputnode.cortex_mask'),
                 (f'outputnode.{reg_sphere}', f'inputnode.{reg_sphere}'),
                 ('outputnode.sulc', 'inputnode.sulc'),
                 ('outputnode.subjects_dir', 'inputnode.subjects_dir'),
@@ -809,8 +810,10 @@ def init_single_subject_wf(
 
             if config.workflow.cifti_output:
                 workflow.connect([
+                    (anat_fit_wf, bold_wf, [
+                        ('outputnode.cortex_mask', 'inputnode.cortex_mask'),
+                    ]),
                     (anat_apply_wf, bold_wf, [
-                        ('outputnode.roi', 'inputnode.cortex_mask'),
                         ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                         ('outputnode.anat_aseg', 'inputnode.anat_aseg'),
                     ]),

pyproject.toml

@@ -25,8 +25,7 @@ dependencies = [
     "nireports >= 23.2.0",
     "nitime",
     "nitransforms >= 24.1.1",
-    #"niworkflows >= 1.13.1",
-    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
+    "niworkflows >= 1.14.1",
     "numpy >= 1.21.0",
     "packaging",
     "pandas < 3",
@@ -35,7 +34,7 @@ dependencies = [
     "pybids >= 0.15.0",
     "requests",
     "sdcflows >= 2.13.0",
-    "smriprep >= 0.17.0",
+    "smriprep >= 0.19.1",
     "tedana >= 23.0.2",
     "templateflow >= 24.2.0",
     "toml",