Skip to content

Track Sources for standard-space outputs #3262

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Mar 27, 2024
Merged

Track Sources for standard-space outputs #3262

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
49e7037
Track Sources for standard-space outputs.
tsalo Mar 25, 2024
3e5c031
CI: Expect boldref/brainmask sidecars in template space
effigies Mar 27, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions .circleci/ds005_partial_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,15 +73,21 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
Expand Down
6 changes: 6 additions & 0 deletions .circleci/ds005_partial_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,15 +95,21 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.func.
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-R_space-fsnative_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
Expand Down
4 changes: 4 additions & 0 deletions .circleci/ds054_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,9 @@ sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.nii.gz
Expand All @@ -72,7 +74,9 @@ sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.nii.gz
Expand Down
4 changes: 4 additions & 0 deletions .circleci/ds054_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,9 @@ sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_space-T1w_desc-preproc_bold.nii.gz
Expand All @@ -82,7 +84,9 @@ sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-brain_mask.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_space-T1w_desc-preproc_bold.nii.gz
Expand Down
2 changes: 2 additions & 0 deletions .circleci/ds210_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,9 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Expand Down
2 changes: 2 additions & 0 deletions .circleci/ds210_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,9 @@ sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Expand Down
4 changes: 4 additions & 0 deletions fmriprep/workflows/bold/outputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -790,6 +790,7 @@ def init_ds_volumes_wf(
('cohort', 'cohort'),
('resolution', 'resolution'),
]),
(sources, ds_bold, [('out', 'Sources')]),
]) # fmt:skip

resample_ref = pe.Node(
Expand Down Expand Up @@ -881,6 +882,9 @@ def init_ds_volumes_wf(
('resolution', 'resolution'),
])
for datasink in datasinks
] + [
(sources, datasink, [('out', 'Sources')])
for datasink in datasinks
] + [
(resampler, datasink, [('output_image', 'in_file')])
for resampler, datasink in zip(resamplers, datasinks, strict=False)
Expand Down