From 9a3400556a9488a2fabaccde5428c818661ec37f Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Mon, 27 Nov 2023 10:49:44 -0500 Subject: [PATCH 1/2] FIX: Disable boldref-space outputs unless requested --- fmriprep/workflows/bold/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py index 950c0b029..11c84be13 100644 --- a/fmriprep/workflows/bold/base.py +++ b/fmriprep/workflows/bold/base.py @@ -335,7 +335,7 @@ def init_bold_wf( ]) # fmt:skip boldref_out = bool(nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref'))) - boldref_out |= config.workflow.level == 'full' + boldref_out &= config.workflow.level == 'full' echos_out = multiecho and config.execution.me_output_echos if boldref_out or echos_out: From 904038c161b76fb21cb5929725f517490cab512b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Mon, 27 Nov 2023 11:38:22 -0500 Subject: [PATCH 2/2] CI: Remove extra outputs from expected outputs --- .circleci/ds005_fasttrack_outputs.txt | 8 -------- .circleci/ds005_outputs.txt | 8 -------- .circleci/ds005_partial_fasttrack_outputs.txt | 4 ---- .circleci/ds005_partial_outputs.txt | 4 ---- .circleci/ds210_fasttrack_outputs.txt | 4 ---- .circleci/ds210_outputs.txt | 4 ---- 6 files changed, 32 deletions(-) diff --git a/.circleci/ds005_fasttrack_outputs.txt b/.circleci/ds005_fasttrack_outputs.txt index 4785687aa..1b2052d68 100644 --- a/.circleci/ds005_fasttrack_outputs.txt +++ b/.circleci/ds005_fasttrack_outputs.txt @@ -23,16 +23,12 @@ sub-01/anat/sub-01_hemi-R_desc-reg_sphere.surf.gii sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii sub-01/func -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json @@ -45,16 +41,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json diff --git a/.circleci/ds005_outputs.txt b/.circleci/ds005_outputs.txt index 167d82ee9..1634090d5 100644 --- a/.circleci/ds005_outputs.txt +++ b/.circleci/ds005_outputs.txt @@ -43,16 +43,12 @@ sub-01/anat/sub-01_label-CSF_probseg.nii.gz sub-01/anat/sub-01_label-GM_probseg.nii.gz sub-01/anat/sub-01_label-WM_probseg.nii.gz sub-01/func -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json @@ -65,16 +61,12 @@ sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.fun sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json diff --git a/.circleci/ds005_partial_fasttrack_outputs.txt b/.circleci/ds005_partial_fasttrack_outputs.txt index 9a712a4a2..39533d137 100644 --- a/.circleci/ds005_partial_fasttrack_outputs.txt +++ b/.circleci/ds005_partial_fasttrack_outputs.txt @@ -51,16 +51,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz sub-01/func -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json diff --git a/.circleci/ds005_partial_outputs.txt b/.circleci/ds005_partial_outputs.txt index 40b563d52..80e9078ca 100644 --- a/.circleci/ds005_partial_outputs.txt +++ b/.circleci/ds005_partial_outputs.txt @@ -73,16 +73,12 @@ sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz sub-01/func -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-brain_mask.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-coreg_boldref.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.json sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-hmc_boldref.nii.gz -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.json -sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-preproc_bold.nii.gz sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.json sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_xfm.txt sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json diff --git a/.circleci/ds210_fasttrack_outputs.txt b/.circleci/ds210_fasttrack_outputs.txt index 700c31970..5030a97cd 100644 --- a/.circleci/ds210_fasttrack_outputs.txt +++ b/.circleci/ds210_fasttrack_outputs.txt @@ -31,8 +31,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz -sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json -sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json @@ -45,8 +43,6 @@ 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-boldref_T2starmap.json -sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz 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.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json diff --git a/.circleci/ds210_outputs.txt b/.circleci/ds210_outputs.txt index 3a880afc4..32f864cbf 100644 --- a/.circleci/ds210_outputs.txt +++ b/.circleci/ds210_outputs.txt @@ -41,8 +41,6 @@ sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.json sub-02/func/sub-02_task-cuedSGT_run-01_desc-coreg_boldref.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.json sub-02/func/sub-02_task-cuedSGT_run-01_desc-hmc_boldref.nii.gz -sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.json -sub-02/func/sub-02_task-cuedSGT_run-01_desc-preproc_bold.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.json sub-02/func/sub-02_task-cuedSGT_run-01_echo-1_desc-preproc_bold.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json @@ -55,8 +53,6 @@ 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-boldref_T2starmap.json -sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.nii.gz 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.nii.gz sub-02/func/sub-02_task-cuedSGT_run-01_space-MNI152NLin2009cAsym_desc-preproc_bold.json