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fix: Calculate premask from BOLD when sbref is provided #3574

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fix: Calculate premask from BOLD when sbref is provided #3574

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a631a58
tmp: Pin nipreps/niworkflows#1001
effigies Nov 26, 2025
15f65d9
[DATALAD RUNCMD] bash -c '! pixi lock --check || git chec...
effigies Nov 26, 2025
1c8b499
fix: Calculate premask from BOLD when sbref is provided
effigies Nov 26, 2025
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46 changes: 31 additions & 15 deletions fmriprep/workflows/bold/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,11 @@
import nibabel as nb
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf, init_skullstrip_bold_wf
from niworkflows.func.util import (
init_bold_premask_wf,
init_enhance_and_skullstrip_bold_wf,
init_skullstrip_bold_wf,
)
from niworkflows.interfaces.header import ValidateImage
from niworkflows.interfaces.nitransforms import ConcatenateXFMs
from niworkflows.interfaces.utility import KeySelect
Expand Down Expand Up @@ -549,16 +553,28 @@ def init_bold_fit_wf(
if not coreg_boldref:
config.loggers.workflow.info('Stage 4: Adding coregistration boldref workflow')

# If sbref files are available, add them to the list of sources
if sbref_files and nb.load(sbref_files[0]).ndim > 3:
raw_sbref_wf = init_raw_boldref_wf(
name='raw_sbref_wf',
bold_file=sbref_files[0],
multiecho=len(sbref_files) > 1,
)
workflow.connect(raw_sbref_wf, 'outputnode.boldref', fmapref_buffer, 'sbref_files')
enhance_and_skullstrip_bold_wf = init_enhance_and_skullstrip_bold_wf(
omp_nthreads=omp_nthreads,
pre_mask=bool(sbref_files),
)

if sbref_files:
if nb.load(sbref_files[0]).ndim > 3: # multivolume
raw_sbref_wf = init_raw_boldref_wf(
name='raw_sbref_wf',
bold_file=sbref_files[0],
multiecho=len(sbref_files) > 1,
)
workflow.connect(raw_sbref_wf, 'outputnode.boldref', fmapref_buffer, 'sbref_files')

bold_premask_wf = init_bold_premask_wf(omp_nthreads=omp_nthreads)
workflow.connect([
(hmcref_buffer, bold_premask_wf, [('boldref', 'inputnode.in_file')]),
(bold_premask_wf, enhance_and_skullstrip_bold_wf, [
('outputnode.mask_file', 'inputnode.pre_mask'),
]),
]) # fmt:skip

enhance_boldref_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)
coreg_ref_source_files = pe.Node(
niu.Merge(3), name='coreg_ref_source_files', run_without_submitting=True
)
Expand All @@ -578,7 +594,7 @@ def init_bold_fit_wf(
)

workflow.connect([
(fmapref_buffer, enhance_boldref_wf, [('out', 'inputnode.in_file')]),
(fmapref_buffer, enhance_and_skullstrip_bold_wf, [('out', 'inputnode.in_file')]),
(fmapref_buffer, coreg_ref_source_files, [('out', 'in1')]),
(coreg_ref_source_files, ds_coreg_boldref_wf, [('out', 'inputnode.source_files')]),
(ds_coreg_boldref_wf, regref_buffer, [('outputnode.boldref', 'boldref')]),
Expand Down Expand Up @@ -608,7 +624,7 @@ def init_bold_fit_wf(

workflow.connect([
(fmapref_buffer, unwarp_boldref, [('out', 'ref_file')]),
(enhance_boldref_wf, unwarp_boldref, [
(enhance_and_skullstrip_bold_wf, unwarp_boldref, [
('outputnode.bias_corrected_file', 'in_file'),
]),
(boldref_fmap, unwarp_boldref, [('out_file', 'fieldmap')]),
Expand All @@ -631,17 +647,17 @@ def init_bold_fit_wf(

if not boldref2fmap_xform:
workflow.connect([
(enhance_boldref_wf, fmapreg_wf, [
(enhance_and_skullstrip_bold_wf, fmapreg_wf, [
('outputnode.bias_corrected_file', 'inputnode.target_ref'),
('outputnode.mask_file', 'inputnode.target_mask'),
]),
]) # fmt:skip
else:
workflow.connect([
(enhance_boldref_wf, ds_coreg_boldref_wf, [
(enhance_and_skullstrip_bold_wf, ds_coreg_boldref_wf, [
('outputnode.bias_corrected_file', 'inputnode.boldref'),
]),
(enhance_boldref_wf, ds_boldmask_wf, [
(enhance_and_skullstrip_bold_wf, ds_boldmask_wf, [
('outputnode.mask_file', 'inputnode.boldmask'),
]),
]) # fmt:skip
Expand Down
71 changes: 35 additions & 36 deletions pixi.lock
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ dependencies = [
"nireports >= 24.1.0",
"nitime >= 0.9",
"nitransforms >= 25.0.1",
"niworkflows >= 1.14.2",
"niworkflows @ git+https://github.com/nipreps/niworkflows.git@refs/pull/1001/head",
"numpy >= 2.0",
"packaging >= 24",
"pandas >= 2.2",
Expand Down