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[FIX] Fix bug in filtering by bval, where b0 calculation used mismatched dwi and gtab #1158

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Aug 29, 2024
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[FIX] Fix bug in filtering by bval, where b0 calculation used mismatched dwi and gtab #1158

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10 changes: 4 additions & 6 deletions AFQ/tasks/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,15 +94,13 @@ def get_data_gtab(dwi_data_file, bval_file, bvec_file, min_bval=None,

@pimms.calc("b0")
@as_file('_desc-b0_dwi.nii.gz')
def b0(dwi_data_file, gtab):
def b0(dwi, gtab):
"""
full path to a nifti file containing the mean b0
"""
data = nib.load(dwi_data_file)
mean_b0 = np.mean(data.get_fdata()[..., gtab.b0s_mask], -1)
mean_b0_img = nib.Nifti1Image(mean_b0, data.affine)
meta = dict(b0_threshold=gtab.b0_threshold,
source=dwi_data_file)
mean_b0 = np.mean(dwi.get_fdata()[..., gtab.b0s_mask], -1)
mean_b0_img = nib.Nifti1Image(mean_b0, dwi.affine)
meta = dict(b0_threshold=gtab.b0_threshold)
return mean_b0_img, meta


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9 changes: 9 additions & 0 deletions AFQ/tests/test_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -604,6 +604,15 @@ def test_AFQ_pydra():
pga.export("dti_fa")


def test_AFQ_filterb():
_, bids_path, _ = get_temp_hardi()
myafq = GroupAFQ(
bids_path=bids_path,
preproc_pipeline='vistasoft',
max_bval=1000)
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Would this actually test this functionality? This data doesn't have b-vals above 1000 does it? I'll merge for now but just wondering whether there's a better test.

myafq.export("b0")


@pytest.mark.nightly_pft
def test_AFQ_pft():
"""
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