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fixed mcflirt mean image output #776

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Merged
chrisgorgo merged 1 commit into from
Jan 31, 2014
Merged

fixed mcflirt mean image output #776

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11 changes: 10 additions & 1 deletion nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -678,8 +678,17 @@ def _list_outputs(self):
'_variance.ext', cwd=cwd)
outputs['std_img'] = self._gen_fname(outputs['out_file'] +
'_sigma.ext', cwd=cwd)

# The mean image created if -stats option is specified ('meanvol')
# is missing the top and bottom slices. Therefore we only expose the
# mean image created by -meanvol option ('mean_reg') which isn't
# corrupted.
# Note that the same problem holds for the std and variance image.

if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
outputs['mean_img'] = self._gen_fname(outputs['out_file'] +
'_meanvol.ext', cwd=cwd)
'_mean_reg.ext', cwd=cwd)

if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
_, filename = os.path.split(outputs['out_file'])
matpathname = os.path.join(cwd, filename + '.mat')
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