ENH: Write out cortex mask GIFTIs (#3491)

Closes #3433.

## Changes proposed in this pull request

- Collect cortex mask GIFTIs from `anat_fit_wf` instead of
`hcp_morphometrics_wf`.

Author: effigies

.circleci/ds005_fasttrack_outputs.txt

@@ -12,11 +12,15 @@ sub-01
 sub-01/anat
 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-cortex_mask.json
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.label.gii
 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_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-cortex_mask.json
+sub-01/anat/sub-01_hemi-R_desc-cortex_mask.label.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_desc-msmsulc_sphere.surf.gii

.circleci/ds005_outputs.txt

@@ -21,6 +21,8 @@ sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
 sub-01/anat/sub-01_from-MNI152NLin2009cAsym_to-T1w_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 sub-01/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.json
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.label.gii
 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_desc-msmsulc_sphere.surf.gii
@@ -30,6 +32,8 @@ sub-01/anat/sub-01_hemi-L_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 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_desc-cortex_mask.json
+sub-01/anat/sub-01_hemi-R_desc-cortex_mask.label.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_desc-msmsulc_sphere.surf.gii

.circleci/ds005_partial_fasttrack_outputs.txt

@@ -12,6 +12,8 @@ sub-01
 sub-01/anat
 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-cortex_mask.json
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.label.gii
 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
@@ -20,6 +22,8 @@ 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-cortex_mask.json
+sub-01/anat/sub-01_hemi-R_desc-cortex_mask.label.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

.circleci/ds005_partial_outputs.txt

@@ -23,6 +23,8 @@ sub-01/anat/sub-01_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.h5
 sub-01/anat/sub-01_from-T1w_to-fsnative_mode-image_xfm.txt
 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_desc-cortex_mask.json
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.label.gii
 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
@@ -35,6 +37,8 @@ sub-01/anat/sub-01_hemi-L_sphere.surf.gii
 sub-01/anat/sub-01_hemi-L_sulc.shape.gii
 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-L_desc-cortex_mask.json
+sub-01/anat/sub-01_hemi-L_desc-cortex_mask.label.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

docs/outputs.rst

@@ -137,6 +137,7 @@ If FreeSurfer reconstructions are used, the following surface files are generate
       sub-<subject_label>_hemi-[LR]_desc-reg_sphere.surf.gii
       sub-<subject_label>_hemi-[LR]_space-fsLR_desc-reg_sphere.surf.gii
       sub-<subject_label>_hemi-[LR]_space-fsLR_desc-msmsulc_sphere.surf.gii
+      sub-<subject_label>_hemi-[LR]_desc-cortex_mask.label.gii
 
 The registration spheres target ``fsaverage`` and ``fsLR`` spaces. If MSM
 is enabled (i.e., the ``--no-msm`` flag is not passed), then the ``msmsulc``

fmriprep/workflows/base.py

@@ -503,12 +503,12 @@ def init_single_subject_wf(subject_id: str):
                         f'outputnode.sphere_reg_{"msm" if msm_sulc else "fsLR"}',
                         'inputnode.sphere_reg_fsLR',
                     ),
+                    ('outputnode.cortex_mask', 'inputnode.roi'),
                 ]),
                 (hcp_morphometrics_wf, morph_grayords_wf, [
                     ('outputnode.curv', 'inputnode.curv'),
                     ('outputnode.thickness', 'inputnode.thickness'),
                     ('outputnode.sulc', 'inputnode.sulc'),
-                    ('outputnode.roi', 'inputnode.roi'),
                 ]),
                 (resample_surfaces_wf, morph_grayords_wf, [
                     ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
@@ -842,9 +842,7 @@ def init_single_subject_wf(subject_id: str):
                 workflow.connect([
                     (select_MNI6_xfm, bold_wf, [('anat2std_xfm', 'inputnode.anat2mni6_xfm')]),
                     (select_MNI6_tpl, bold_wf, [('brain_mask', 'inputnode.mni6_mask')]),
-                    (hcp_morphometrics_wf, bold_wf, [
-                        ('outputnode.roi', 'inputnode.cortex_mask'),
-                    ]),
+                    (anat_fit_wf, bold_wf, [('outputnode.cortex_mask', 'inputnode.cortex_mask')]),
                     (resample_surfaces_wf, bold_wf, [
                         ('outputnode.midthickness_fsLR', 'inputnode.midthickness_fsLR'),
                     ]),

pyproject.toml

@@ -27,15 +27,15 @@ dependencies = [
     "nireports >= 24.1.0",
     "nitime >= 0.9",
     "nitransforms >= 24.1.1",
-    "niworkflows >= 1.12.2",
+    "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
     "numpy >= 1.24",
     "packaging >= 24",
     "pandas >= 1.2",
     "psutil >= 5.4",
     "pybids >= 0.16",
     "requests >= 2.27",
     "sdcflows >= 2.13.1",
-    "smriprep >= 0.18.0",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
     "tedana >= 25.0.0",
     "templateflow >= 24.2.2",
     "transforms3d >= 0.4",