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FIX: Write out Freesurfer-derived outputs #3512

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Merged
merged 5 commits into from
Aug 29, 2025
Merged

FIX: Write out Freesurfer-derived outputs #3512

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6584125
Write out surface outputs.
tsalo Aug 27, 2025
af8c1bd
Remove duplicate import.
tsalo Aug 27, 2025
1f10e16
Update expected outputs.
tsalo Aug 27, 2025
7fef4ea
I missed some.
tsalo Aug 27, 2025
8cdb4ec
Apply suggestions from code review
tsalo Aug 27, 2025
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6 changes: 6 additions & 0 deletions .circleci/ds005_fasttrack_outputs.txt
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -10,17 +10,23 @@ logs/CITATION.md
logs/CITATION.tex
sub-01
sub-01/anat
sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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_curv.shape.gii
sub-01/anat/sub-01_hemi-L_desc-preproc_inflated.surf.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_curv.shape.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_inflated.surf.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
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6 changes: 6 additions & 0 deletions .circleci/ds005_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ logs/CITATION.md
logs/CITATION.tex
sub-01
sub-01/anat
sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
sub-01/anat/sub-01_desc-brain_mask.json
sub-01/anat/sub-01_desc-brain_mask.nii.gz
sub-01/anat/sub-01_desc-preproc_T1w.json
Expand All @@ -21,8 +23,10 @@ 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_curv.shape.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-L_inflated.surf.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
Expand All @@ -32,8 +36,10 @@ 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_curv.shape.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_inflated.surf.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
Expand Down
6 changes: 6 additions & 0 deletions .circleci/ds005_partial_fasttrack_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,14 @@ logs/CITATION.md
logs/CITATION.tex
sub-01
sub-01/anat
sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
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_curv.shape.gii
sub-01/anat/sub-01_hemi-L_desc-preproc_inflated.surf.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 @@ -24,6 +28,8 @@ 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_curv.shape.gii
sub-01/anat/sub-01_hemi-R_desc-preproc_inflated.surf.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
Expand Down
10 changes: 8 additions & 2 deletions .circleci/ds005_partial_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,8 @@ logs/CITATION.md
logs/CITATION.tex
sub-01
sub-01/anat
sub-01/anat/sub-01_desc-aparcaseg_dseg.nii.gz
sub-01/anat/sub-01_desc-aseg_dseg.nii.gz
sub-01/anat/sub-01_desc-brain_mask.json
sub-01/anat/sub-01_desc-brain_mask.nii.gz
sub-01/anat/sub-01_desc-preproc_T1w.json
Expand All @@ -23,8 +25,10 @@ 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_curv.shape.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-L_inflated.surf.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 @@ -37,8 +41,10 @@ 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_curv.shape.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_inflated.surf.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
Expand Down
43 changes: 42 additions & 1 deletion fmriprep/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,7 @@ def init_single_subject_wf(subject_id: str):
if 't2w' in config.workflow.ignore:
subject_data['t2w'] = []

freesurfer = config.workflow.run_reconall
anat_only = config.workflow.anat_only
# Make sure we always go through these two checks
if not anat_only and not subject_data['bold']:
Expand Down Expand Up @@ -319,7 +320,7 @@ def init_single_subject_wf(subject_id: str):
anat_fit_wf = init_anat_fit_wf(
bids_root=bids_root,
output_dir=fmriprep_dir,
freesurfer=config.workflow.run_reconall,
freesurfer=freesurfer,
hires=config.workflow.hires,
fs_no_resume=config.workflow.fs_no_resume,
longitudinal=config.workflow.longitudinal,
Expand Down Expand Up @@ -419,6 +420,46 @@ def init_single_subject_wf(subject_id: str):
]),
]) # fmt:skip

if freesurfer:
from smriprep.workflows.outputs import init_ds_fs_segs_wf, init_ds_surface_metrics_wf
from smriprep.workflows.surfaces import init_surface_derivatives_wf

ds_fs_segs_wf = init_ds_fs_segs_wf(bids_root=bids_root, output_dir=fmriprep_dir)
surface_derivatives_wf = init_surface_derivatives_wf()
ds_surfaces_wf = init_ds_surfaces_wf(output_dir=fmriprep_dir, surfaces=['inflated'])
ds_curv_wf = init_ds_surface_metrics_wf(
bids_root=bids_root,
output_dir=fmriprep_dir,
metrics=['curv'],
name='ds_curv_wf',
)

workflow.connect([
(anat_fit_wf, surface_derivatives_wf, [
('outputnode.t1w_preproc', 'inputnode.reference'),
('outputnode.subjects_dir', 'inputnode.subjects_dir'),
('outputnode.subject_id', 'inputnode.subject_id'),
('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2anat_xfm'),
]),
(anat_fit_wf, ds_surfaces_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(surface_derivatives_wf, ds_surfaces_wf, [
('outputnode.inflated', 'inputnode.inflated'),
]),
(anat_fit_wf, ds_curv_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(surface_derivatives_wf, ds_curv_wf, [('outputnode.curv', 'inputnode.curv')]),
(anat_fit_wf, ds_fs_segs_wf, [
('outputnode.t1w_valid_list', 'inputnode.source_files'),
]),
(surface_derivatives_wf, ds_fs_segs_wf, [
('outputnode.out_aseg', 'inputnode.anat_fs_aseg'),
('outputnode.out_aparc', 'inputnode.anat_fs_aparc'),
]),
]) # fmt:skip

# Thread MNI152NLin6Asym standard outputs to CIFTI subworkflow, skipping
# the iterator, which targets only output spaces.
# This can lead to duplication in the working directory if people actually
Expand Down
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