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RF: Factor _copy_header, update bias image #4

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Merged
merged 1 commit into from
May 19, 2017
Merged

RF: Factor _copy_header, update bias image #4

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19 changes: 12 additions & 7 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -392,16 +392,21 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
runtime, correct_return_codes)

if self.inputs.copy_header and runtime.returncode in correct_return_codes:
import nibabel as nb
in_img = nb.load(self.inputs.input_image)
out_file = self._gen_filename('output_image')
out_img = nb.load(out_file, mmap=False)
new_img = out_img.__class__(out_img.get_data(), in_img.affine, in_img.header)
new_img.set_data_dtype(out_img.get_data_dtype())
new_img.to_filename(out_file)
self._copy_header(self._gen_filename('output_image'))
if self.inputs.save_bias or isdefined(self.inputs.bias_image):
self._copy_header(self._gen_filename('bias_image'))

return runtime

def _copy_header(self, fname):
"""Copy header from input image to an output image"""
import nibabel as nb
in_img = nb.load(self.inputs.input_image)
out_img = nb.load(fname, mmap=False)
new_img = out_img.__class__(out_img.get_data(), in_img.affine,
in_img.header)
new_img.set_data_dtype(out_img.get_data_dtype())
new_img.to_filename(fname)


class CorticalThicknessInputSpec(ANTSCommandInputSpec):
Expand Down