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Merged
merged 11 commits into from
Sep 26, 2025
Merged

enh: add boldref / sbref to source metadata #3532

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fbe4601
enh: add coreg bold to sources when resampling bold series
mgxd Sep 24, 2025
e343f00
enh: add sbref (if used) to sources prior to final boldref
mgxd Sep 24, 2025
f6660d0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 24, 2025
207a25a
rf: pass in bold first
mgxd Sep 25, 2025
a47758e
fix: append as string
mgxd Sep 25, 2025
9b7ded1
rf: Use merge buffers to collect source files
effigies Sep 26, 2025
440d3e2
rf: Use HMC boldref saved to output for further processing
effigies Sep 26, 2025
acd563a
rf: Pass BOLD source_file to datasink workflows as kwarg
effigies Sep 26, 2025
0a46429
chore: Pin to sdcflows@main
effigies Sep 26, 2025
61d073b
chore: pixi lock
effigies Sep 26, 2025
10c20b9
chore(ci): Update expected file lists
effigies Sep 26, 2025
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5 changes: 3 additions & 2 deletions .circleci/ds005_partial_fasttrack_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_desc-preproc_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_desc-preproc_probseg.nii.gz
sub-01/fmap
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-brain_mask.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
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
Expand All @@ -76,8 +77,8 @@ 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_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
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-auto00000_mode-image_desc-fmap_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt
sub-01/func/sub-01_task-mixedgamblestask_run-02_hemi-L_space-fsaverage5_bold.func.gii
Expand Down
5 changes: 3 additions & 2 deletions .circleci/ds005_partial_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,7 @@ sub-01/anat/sub-01_space-MNI152NLin6Asym_label-CSF_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-GM_probseg.nii.gz
sub-01/anat/sub-01_space-MNI152NLin6Asym_label-WM_probseg.nii.gz
sub-01/fmap
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-brain_mask.nii.gz
sub-01/fmap/sub-01_run-02_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
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
Expand All @@ -96,8 +97,8 @@ 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_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-auto00000_mode-image_desc-fmap_xfm.json
sub-01/func/sub-01_task-mixedgamblestask_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
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
Expand Down
9 changes: 5 additions & 4 deletions .circleci/ds054_fasttrack_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_desc-prepro
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_desc-preproc_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_desc-preproc_probseg.nii.gz
sub-100185/fmap
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-brain_mask.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-preproc_fieldmap.json
Expand All @@ -33,8 +34,8 @@ sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand All @@ -61,8 +62,8 @@ sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand Down
9 changes: 5 additions & 4 deletions .circleci/ds054_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-CSF_probseg.nii
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-GM_probseg.nii.gz
sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_res-2_label-WM_probseg.nii.gz
sub-100185/fmap
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-brain_mask.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-100185/fmap/sub-100185_fmapid-auto00000_desc-preproc_fieldmap.json
Expand All @@ -43,8 +44,8 @@ sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-01_desc-hmc_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-01_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-01_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand All @@ -71,8 +72,8 @@ sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.json
sub-100185/func/sub-100185_task-machinegame_run-02_desc-hmc_boldref.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.json
sub-100185/func/sub-100185_task-machinegame_run-02_desc-preproc_bold.nii.gz
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
sub-100185/func/sub-100185_task-machinegame_run-02_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt
sub-100185/func/sub-100185_task-machinegame_run-02_from-orig_to-boldref_mode-image_desc-hmc_xfm.json
Expand Down
5 changes: 3 additions & 2 deletions .circleci/ds210_fasttrack_outputs.txt
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_desc-preproc_probseg.nii.
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_desc-preproc_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_desc-preproc_probseg.nii.gz
sub-02/fmap
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-brain_mask.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
Expand All @@ -36,8 +37,8 @@ sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
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
Expand Down
5 changes: 3 additions & 2 deletions .circleci/ds210_outputs.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz
sub-02/anat/sub-02_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz
sub-02/fmap
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-brain_mask.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-coeff_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-magnitude_fieldmap.nii.gz
sub-02/fmap/sub-02_run-01_fmapid-auto00000_desc-preproc_fieldmap.json
Expand All @@ -46,8 +47,8 @@ sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-2_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.json
sub-02/func/sub-02_task-cuedSGT_run-01_echo-3_desc-preproc_bold.nii.gz
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.json
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-auto00000_mode-image_desc-fmap_xfm.txt
sub-02/func/sub-02_task-cuedSGT_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.json
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
Expand Down
15 changes: 12 additions & 3 deletions fmriprep/workflows/bold/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -314,6 +314,7 @@ def init_bold_wf(

if boldref_out or echos_out:
ds_bold_native_wf = init_ds_bold_native_wf(
source_file=bold_series,
bids_root=str(config.execution.bids_dir),
output_dir=fmriprep_dir,
bold_output=boldref_out,
Expand Down Expand Up @@ -372,9 +373,14 @@ def init_bold_wf(
for node in workflow.list_node_names():
if node.split('.')[-1].startswith('ds_report'):
workflow.get_node(node).inputs.base_directory = fmriprep_dir
workflow.get_node(node).inputs.source_file = bold_file
return workflow

# Pass along BOLD reference as a source file for provenance
merge_bold_sources = pe.Node(
niu.Merge(2), name='merge_bold_sources', run_without_submitting=True
)
merge_bold_sources.inputs.in1 = bold_series

# Resample to anatomical space
bold_anat_wf = init_bold_volumetric_resample_wf(
metadata=all_metadata[0],
Expand Down Expand Up @@ -404,18 +410,19 @@ def init_bold_wf(
('outputnode.bold_minimal', 'inputnode.bold_file'),
('outputnode.motion_xfm', 'inputnode.motion_xfm'),
]),
(bold_fit_wf, merge_bold_sources, [('outputnode.coreg_boldref', 'in2')]),
]) # fmt:skip

# Full derivatives, including resampled BOLD series
if nonstd_spaces.intersection(('anat', 'T1w')):
ds_bold_t1_wf = init_ds_volumes_wf(
source_file=bold_file,
bids_root=str(config.execution.bids_dir),
output_dir=fmriprep_dir,
multiecho=multiecho,
metadata=all_metadata[0],
name='ds_bold_t1_wf',
)
ds_bold_t1_wf.inputs.inputnode.source_files = bold_series
ds_bold_t1_wf.inputs.inputnode.space = 'T1w'

workflow.connect([
Expand All @@ -431,6 +438,7 @@ def init_bold_wf(
('outputnode.bold_file', 'inputnode.bold'),
('outputnode.resampling_reference', 'inputnode.ref_file'),
]),
(merge_bold_sources, ds_bold_t1_wf, [('out', 'inputnode.source_files')]),
]) # fmt:skip

if spaces.cached.get_spaces(nonstandard=False, dim=(3,)):
Expand All @@ -446,13 +454,13 @@ def init_bold_wf(
name='bold_std_wf',
)
ds_bold_std_wf = init_ds_volumes_wf(
source_file=bold_file,
bids_root=str(config.execution.bids_dir),
output_dir=fmriprep_dir,
multiecho=multiecho,
metadata=all_metadata[0],
name='ds_bold_std_wf',
)
ds_bold_std_wf.inputs.inputnode.source_files = bold_series

workflow.connect([
(inputnode, bold_std_wf, [
Expand Down Expand Up @@ -492,6 +500,7 @@ def init_bold_wf(
('outputnode.bold_file', 'inputnode.bold'),
('outputnode.resampling_reference', 'inputnode.ref_file'),
]),
(merge_bold_sources, ds_bold_std_wf, [('out', 'inputnode.source_files')]),
]) # fmt:skip

if config.workflow.run_reconall and freesurfer_spaces:
Expand Down
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