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FIX: Construct MCFLIRT output paths relative to out_file #2703

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merged 1 commit into from
Sep 18, 2018
Merged

FIX: Construct MCFLIRT output paths relative to out_file #2703

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10 changes: 5 additions & 5 deletions nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -820,16 +820,16 @@ def _format_arg(self, name, spec, value):
return super(MCFLIRT, self)._format_arg(name, spec, value)

def _list_outputs(self):
cwd = os.getcwd()
outputs = self._outputs().get()

outputs['out_file'] = self._gen_outfilename()
output_dir = os.path.dirname(outputs['out_file'])

if isdefined(self.inputs.stats_imgs) and self.inputs.stats_imgs:
outputs['variance_img'] = self._gen_fname(
outputs['out_file'] + '_variance.ext', cwd=cwd)
outputs['out_file'] + '_variance.ext', cwd=output_dir)
outputs['std_img'] = self._gen_fname(
outputs['out_file'] + '_sigma.ext', cwd=cwd)
outputs['out_file'] + '_sigma.ext', cwd=output_dir)

# The mean image created if -stats option is specified ('meanvol')
# is missing the top and bottom slices. Therefore we only expose the
Expand All @@ -839,11 +839,11 @@ def _list_outputs(self):

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

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')
matpathname = os.path.join(output_dir, filename + '.mat')
_, _, _, timepoints = load(self.inputs.in_file).shape
outputs['mat_file'] = []
for t in range(timepoints):
Expand Down