Skip to content

Commit ab58dc9

Browse files
authored
ENH: Write out goodvoxels mask (#3513)
Closes #3510. I'm happy to move the DerivativesDataSink into `init_goodvoxels_bold_mask_wf` if the current approach clutters up the workflow too much. ## Changes proposed in this pull request - Add a DerivativesDataSink to `init_bold_wf` to write out the goodvoxels mask. - Update the expected outputs for relevant tests.
2 parents 566592a + eaaab2b commit ab58dc9

File tree

3 files changed

+21
-0
lines changed

3 files changed

+21
-0
lines changed

.circleci/ds005_partial_fasttrack_outputs.txt

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -106,6 +106,7 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.json
106106
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
107107
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
108108
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
109+
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-goodvoxels_mask.nii.gz
109110
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
110111
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
111112
sub-01.html

.circleci/ds005_partial_outputs.txt

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -128,6 +128,7 @@ sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.json
128128
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_boldref.nii.gz
129129
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.json
130130
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-brain_mask.nii.gz
131+
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-goodvoxels_mask.nii.gz
131132
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.json
132133
sub-01/func/sub-01_task-mixedgamblestask_run-02_space-T1w_desc-preproc_bold.nii.gz
133134
sub-01.html

fmriprep/workflows/bold/base.py

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -572,6 +572,25 @@ def init_bold_wf(
572572
(bold_anat_wf, goodvoxels_bold_mask_wf, [
573573
('outputnode.bold_file', 'inputnode.bold_file'),
574574
]),
575+
]) # fmt:skip
576+
577+
ds_goodvoxels_mask = pe.Node(
578+
DerivativesDataSink(
579+
base_directory=fmriprep_dir,
580+
dismiss_entities=dismiss_echo(),
581+
compress=True,
582+
space='T1w',
583+
desc='goodvoxels',
584+
suffix='mask',
585+
),
586+
name='ds_goodvoxels_mask',
587+
run_without_submitting=True,
588+
)
589+
ds_goodvoxels_mask.inputs.source_file = bold_file
590+
workflow.connect([
591+
(goodvoxels_bold_mask_wf, ds_goodvoxels_mask, [
592+
('outputnode.goodvoxels_mask', 'in_file'),
593+
]),
575594
(goodvoxels_bold_mask_wf, bold_fsLR_resampling_wf, [
576595
('outputnode.goodvoxels_mask', 'inputnode.volume_roi'),
577596
]),

0 commit comments

Comments
 (0)