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Merged
merged 11 commits into from
Aug 8, 2025
Merged

ENH: Write out cortex mask GIFTIs #3491

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fc77f48
Write out cortex mask giftis.
tsalo Jul 31, 2025
d1e8056
Wrong entity name.
tsalo Jul 31, 2025
1528839
Update fmriprep/workflows/base.py
tsalo Jul 31, 2025
9fddc77
Fix expected outputs.
tsalo Jul 31, 2025
1a9a235
Merge remote-tracking branch 'upstream/master' into cortex-mask
tsalo Aug 4, 2025
2cb878c
Prepare for sMRIPrep PR.
tsalo Aug 4, 2025
ae78fde
Add JSONs to expected outputs.
tsalo Aug 6, 2025
8c1bf9c
Pin niworkflows and smriprep.
tsalo Aug 6, 2025
2bd0d9b
Merge branch 'master' into cortex-mask
effigies Aug 7, 2025
ca5b76e
Add cortex mask to list of outputs.
tsalo Aug 7, 2025
0d9c10e
Update expected outputs.
tsalo Aug 8, 2025
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2 changes: 2 additions & 0 deletions .circleci/ds005_partial_fasttrack_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ 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.shape.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
Expand All @@ -20,6 +21,7 @@ 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.shape.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
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2 changes: 2 additions & 0 deletions .circleci/ds005_partial_outputs.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ 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.shape.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
Expand All @@ -35,6 +36,7 @@ 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.shape.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
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13 changes: 13 additions & 0 deletions fmriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -473,6 +473,18 @@ def init_single_subject_wf(subject_id: str):
},
name='ds_fsLR_surfaces_wf',
)
ds_cortex_mask = pe.MapNode(
DerivativesDataSink(
base_directory=config.execution.fmriprep_dir,
datatype='anat',
desc='cortex',
suffix='mask',
dismiss_entities=dismiss_echo(),
),
iterfield=['in_file', 'hemi'],
name='ds_cortex_mask',
)
ds_cortex_mask.inputs.hemi = ['L', 'R']

workflow.connect([
(anat_fit_wf, curv_wf, [
Expand Down Expand Up @@ -504,6 +516,7 @@ def init_single_subject_wf(subject_id: str):
'inputnode.sphere_reg_fsLR',
),
]),
(hcp_morphometrics_wf, ds_cortex_mask, [('outputnode.roi', 'in_file')]),
(hcp_morphometrics_wf, morph_grayords_wf, [
('outputnode.curv', 'inputnode.curv'),
('outputnode.thickness', 'inputnode.thickness'),
Expand Down
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