From 8eb8215e9a4e246883a4d525bc68b68510671e57 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Wed, 27 Mar 2024 16:48:54 -0400 Subject: [PATCH] Track Sources for standard-space outputs (#3262) References #3261. ## Changes proposed in this pull request - Track `Sources` for standard-space outputs --------- Co-authored-by: Chris Markiewicz --- .circleci/ds005_partial_fasttrack_outputs.txt | 6 ++++++ .circleci/ds005_partial_outputs.txt | 6 ++++++ .circleci/ds054_fasttrack_outputs.txt | 4 ++++ .circleci/ds054_outputs.txt | 4 ++++ .circleci/ds210_fasttrack_outputs.txt | 2 ++ .circleci/ds210_outputs.txt | 2 ++ fmriprep/workflows/bold/outputs.py | 4 ++++ 7 files changed, 28 insertions(+) diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_partial_fasttrack_outputs.txt index 39533d137..6ba7a14a6 100644 --- a/.circleci/ds005_partial_fasttrack_outputs.txt +++ b/.circleci/ds005_partial_fasttrack_outputs.txt @@ -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 diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt index 80e9078ca..e7db76d14 100644 --- a/.circleci/ds005_partial_outputs.txt +++ b/.circleci/ds005_partial_outputs.txt @@ -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 diff --git a/.circleci/ds054_fasttrack_outputs.txt b/.circleci/ds054_fasttrack_outputs.txt index 694d1e932..0f6b9da3e 100644 --- a/.circleci/ds054_fasttrack_outputs.txt +++ b/.circleci/ds054_fasttrack_outputs.txt @@ -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 @@ -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 diff --git a/.circleci/ds054_outputs.txt b/.circleci/ds054_outputs.txt index b8748a02f..54c980b96 100644 --- a/.circleci/ds054_outputs.txt +++ b/.circleci/ds054_outputs.txt @@ -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 @@ -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 diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt index 5030a97cd..442283e85 100644 --- a/.circleci/ds210_fasttrack_outputs.txt +++ b/.circleci/ds210_fasttrack_outputs.txt @@ -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 diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt index 32f864cbf..4ee3a1e94 100644 --- a/.circleci/ds210_outputs.txt +++ b/.circleci/ds210_outputs.txt @@ -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 diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py index 89931ef0b..e41f356ba 100644 --- a/fmriprep/workflows/bold/outputs.py +++ b/fmriprep/workflows/bold/outputs.py @@ -790,6 +790,7 @@ def init_ds_volumes_wf( ('cohort', 'cohort'), ('resolution', 'resolution'), ]), + (sources, ds_bold, [('out', 'Sources')]), ]) # fmt:skip resample_ref = pe.Node( @@ -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)