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[RTM] ENH: Clear header extensions when making ref image #188

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Jul 29, 2017
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[RTM] ENH: Clear header extensions when making ref image #188

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8 changes: 6 additions & 2 deletions niworkflows/interfaces/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -292,15 +292,19 @@ def _run_interface(self, runtime):
global_signal = data_slice.mean(axis=0).mean(
axis=0).mean(axis=0)

# Slicing may induce inconsistencies with shape-dependent values in extensions.
# For now, remove all. If this turns out to be a mistake, we can select extensions
# that don't break pipeline stages.
in_nii.header.extensions.clear()

n_volumes_to_discard = is_outlier(global_signal)

out_ref_fname = os.path.abspath("ref_image.nii.gz")

if n_volumes_to_discard == 0:
if in_nii.shape[-1] > 40:
slice = data_slice[:, :, :, 20:40]
slice_fname = os.path.abspath("slice.nii.gz")
nb.Nifti1Image(slice, in_nii.affine,
nb.Nifti1Image(data_slice[:, :, :, 20:40], in_nii.affine,
in_nii.header).to_filename(slice_fname)
else:
slice_fname = self.inputs.in_file
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