FIX: Disable boldref-space outputs unless requested (#3159)

If `--level full`, boldref-space outputs are generated. This is due to a
misplaced logical OR instead of AND. The intended effect of the line was
to disable boldref-space outputs unless `level == 'full'`.

Author: effigies

.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

.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

.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

.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

.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

.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

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: