Skip to content
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

NF: Output BOLD HMC transforms and reference volume #2860

Merged
merged 1 commit into from
Oct 12, 2022
Merged

NF: Output BOLD HMC transforms and reference volume #2860

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
4 changes: 4 additions & 0 deletions .circleci/ds005_bids_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,16 +10,20 @@ bids/logs/CITATION.md
bids/logs/CITATION.tex
bids/sub-01
bids/sub-01/func
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
4 changes: 4 additions & 0 deletions .circleci/ds005_bids_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,16 +33,20 @@ bids/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
bids/sub-01/anat/sub-01_label-GM_probseg.nii.gz
bids/sub-01/anat/sub-01_label-WM_probseg.nii.gz
bids/sub-01/func
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.func.gii
bids/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
bids/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
4 changes: 4 additions & 0 deletions .circleci/ds005_legacy_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,10 @@ fmriprep/logs/CITATION.md
fmriprep/logs/CITATION.tex
fmriprep/sub-01
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
Expand All @@ -22,8 +24,10 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
4 changes: 4 additions & 0 deletions .circleci/ds005_legacy_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,10 @@ fmriprep/sub-01/anat/sub-01_label-CSF_probseg.nii.gz
fmriprep/sub-01/anat/sub-01_label-GM_probseg.nii.gz
fmriprep/sub-01/anat/sub-01_label-WM_probseg.nii.gz
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-L_space-fsaverage5_bold.func.gii
Expand All @@ -45,8 +47,10 @@ fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsaverage5_bold.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.func.gii
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-01_hemi-R_space-fsnative_bold.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
2 changes: 2 additions & 0 deletions .circleci/ds005_legacy_partial_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,9 +17,11 @@ fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
2 changes: 2 additions & 0 deletions .circleci/ds005_legacy_partial_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,9 +58,11 @@ fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.json
fmriprep/sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-preproc_fieldmap.nii.gz
fmriprep/sub-01/func
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_AROMAnoiseICs.csv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_boldref.nii.gz
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.json
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_desc-MELODIC_mixing.tsv
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
2 changes: 2 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 @@ -25,6 +25,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_times
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_timeseries.tsv
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
Expand All @@ -48,6 +49,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_times
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
Expand Down
2 changes: 2 additions & 0 deletions .circleci/ds054_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_times
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-confounds_timeseries.tsv
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
Expand All @@ -67,6 +68,7 @@ fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_times
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-confounds_timeseries.tsv
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-100185/func/sub-100185_task-machinegame_run-02_space-MNI152NLin2009cAsym_res-2_boldref.nii.gz
Expand Down
1 change: 1 addition & 0 deletions .circleci/ds210_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,7 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
Expand Down
1 change: 1 addition & 0 deletions .circleci/ds210_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-boldref_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-scanner_to-T1w_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_from-T1w_to-scanner_mode-image_xfm.txt
fmriprep/sub-02/func/sub-02_task-cuedSGT_run-01_space-boldref_T2starmap.json
Expand Down
7 changes: 7 additions & 0 deletions fmriprep/workflows/bold/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,8 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
Affine transform from BOLD reference space to T1w space
anat2bold_xfm
Affine transform from T1w space to BOLD reference space
hmc_xforms
Affine transforms for each BOLD volume to the BOLD reference
bold_mask_t1
BOLD series mask in T1w space
bold_aseg_t1
Expand Down Expand Up @@ -369,6 +371,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
"bold_t1_ref",
"bold2anat_xfm",
"anat2bold_xfm",
"hmc_xforms",
"bold_mask_t1",
"bold_aseg_t1",
"bold_aparc_t1",
Expand Down Expand Up @@ -453,6 +456,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
("bold_t1_ref", "inputnode.bold_t1_ref"),
("bold2anat_xfm", "inputnode.bold2anat_xfm"),
("anat2bold_xfm", "inputnode.anat2bold_xfm"),
("hmc_xforms", "inputnode.hmc_xforms"),
("bold_aseg_t1", "inputnode.bold_aseg_t1"),
("bold_aparc_t1", "inputnode.bold_aparc_t1"),
("bold_mask_t1", "inputnode.bold_mask_t1"),
Expand Down Expand Up @@ -622,6 +626,9 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
("outputnode.raw_ref_image", "inputnode.raw_ref_image"),
("outputnode.bold_file", "inputnode.bold_file"),
]),
(bold_hmc_wf, outputnode, [
("outputnode.xforms", "hmc_xforms"),
]),
# EPI-T1w registration workflow
(inputnode, bold_reg_wf, [
("t1w_dseg", "inputnode.t1w_dseg"),
Expand Down
48 changes: 35 additions & 13 deletions fmriprep/workflows/bold/outputs.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -220,6 +220,7 @@ def init_func_derivatives_wf(
't2star_std',
'bold2anat_xfm',
'anat2bold_xfm',
'hmc_xforms',
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

And this one to the docstring inputs

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

This function doesn't have docstrings for input/output nodes.

'acompcor_masks',
'tcompcor_mask',
]
Expand Down Expand Up @@ -280,6 +281,40 @@ def init_func_derivatives_wf(
])
# fmt:on

# Output HMC and reference volume
ds_bold_hmc_xfm = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
to='boldref',
mode='image',
suffix='xfm',
extension='.txt',
dismiss_entities=('echo',),
**{'from': 'scanner'},
),
name='ds_bold_hmc_xfm',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB,
)

ds_bold_native_ref = pe.Node(
DerivativesDataSink(
base_directory=output_dir, suffix='boldref', compress=True, dismiss_entities=("echo",)
),
name='ds_bold_native_ref',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB,
)

# fmt:off
workflow.connect([
(inputnode, ds_bold_hmc_xfm, [('source_file', 'source_file'),
('hmc_xforms', 'in_file')]),
(inputnode, ds_bold_native_ref, [('source_file', 'source_file'),
('bold_native_ref', 'in_file')])
])
# fmt:on

bold_output = nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref'))
if bold_output:
ds_bold_native = pe.Node(
Expand All @@ -304,17 +339,6 @@ def init_func_derivatives_wf(

# Save masks and boldref if we're going to save either orig BOLD series or echos
if bold_output or multiecho and config.execution.me_output_echos:
ds_bold_native_ref = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
suffix='boldref',
compress=True,
dismiss_entities=("echo",),
),
name='ds_bold_native_ref',
run_without_submitting=True,
mem_gb=DEFAULT_MEMORY_MIN_GB,
)
ds_bold_mask_native = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
Expand All @@ -329,8 +353,6 @@ def init_func_derivatives_wf(
)
# fmt:off
workflow.connect([
(inputnode, ds_bold_native_ref, [('source_file', 'source_file'),
('bold_native_ref', 'in_file')]),
(inputnode, ds_bold_mask_native, [('source_file', 'source_file'),
('bold_mask_native', 'in_file')]),
(raw_sources, ds_bold_mask_native, [('out', 'RawSources')]),
Expand Down