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FIX: Validate and summarize multi-volume sbrefs #3320

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merged 2 commits into from
Jul 10, 2024
Merged

FIX: Validate and summarize multi-volume sbrefs #3320

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FIX: Validate and summarize multi-volume sbrefs
effigies Jul 9, 2024
2516724
TEST: Ensure the first sbref files are loadable
effigies Jul 10, 2024
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8 changes: 8 additions & 0 deletions fmriprep/workflows/bold/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -465,6 +465,14 @@ def init_bold_fit_wf(

# Select initial boldref, enhance contrast, and generate mask
fmapref_buffer.inputs.sbref_files = sbref_files
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_boldref_wf = init_enhance_and_skullstrip_bold_wf(omp_nthreads=omp_nthreads)

ds_coreg_boldref_wf = init_ds_boldref_wf(
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3 changes: 3 additions & 0 deletions fmriprep/workflows/bold/tests/test_base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,15 +56,18 @@ def test_bold_wf(
bold_series = [
str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_bold.nii.gz'),
]
sbref = str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_sbref.nii.gz')
elif task == 'nback':
bold_series = [
str(bids_root / 'sub-01' / 'func' / f'sub-01_task-nback_echo-{i}_bold.nii.gz')
for i in range(1, 4)
]
sbref = str(bids_root / 'sub-01' / 'func' / 'sub-01_task-nback_echo-1_sbref.nii.gz')

# The workflow will attempt to read file headers
for path in bold_series:
img.to_filename(path)
img.to_filename(sbref)

with mock_config(bids_dir=bids_root):
config.workflow.bold2anat_init = bold2anat_init
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4 changes: 4 additions & 0 deletions fmriprep/workflows/bold/tests/test_fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,15 +89,19 @@ def test_bold_fit_precomputes(
bold_series = [
str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_bold.nii.gz'),
]
sbref = str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_sbref.nii.gz')
elif task == 'nback':
bold_series = [
str(bids_root / 'sub-01' / 'func' / f'sub-01_task-nback_echo-{i}_bold.nii.gz')
for i in range(1, 4)
]
sbref = str(bids_root / 'sub-01' / 'func' / 'sub-01_task-nback_echo-1_sbref.nii.gz')

# The workflow will attempt to read file headers
for path in bold_series:
img.to_filename(path)
# Single volume sbref; multi-volume tested in test_base
img.slicer[:, :, :, 0].to_filename(sbref)

dummy_nifti = str(tmp_path / 'dummy.nii')
dummy_affine = str(tmp_path / 'dummy.txt')
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