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ENH: Update MCFLIRT outputs for FSL 6+ #3029

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merged 1 commit into from
Sep 16, 2019
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ENH: Update MCFLIRT outputs for FSL 6+ #3029

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25 changes: 19 additions & 6 deletions nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
import numpy as np
from nibabel import load

from ... import LooseVersion
from ...utils.filemanip import split_filename
from ..base import (TraitedSpec, File, InputMultiPath, OutputMultiPath,
Undefined, traits, isdefined)
Expand Down Expand Up @@ -826,10 +827,17 @@ def _list_outputs(self):
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=output_dir)
outputs['std_img'] = self._gen_fname(
outputs['out_file'] + '_sigma.ext', cwd=output_dir)
if LooseVersion(Info.version()) < LooseVersion('6.0.0'):
# FSL <6.0 outputs have .nii.gz_variance.nii.gz as extension
outputs['variance_img'] = self._gen_fname(
outputs['out_file'] + '_variance.ext', cwd=output_dir)
outputs['std_img'] = self._gen_fname(
outputs['out_file'] + '_sigma.ext', cwd=output_dir)
else:
outputs['variance_img'] = self._gen_fname(
outputs['out_file'], suffix='_variance', cwd=output_dir)
outputs['std_img'] = self._gen_fname(
outputs['out_file'], suffix='_sigma', 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 @@ -838,8 +846,13 @@ def _list_outputs(self):
# 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'] + '_mean_reg.ext', cwd=output_dir)
if LooseVersion(Info.version()) < LooseVersion('6.0.0'):
# FSL <6.0 outputs have .nii.gz_mean_img.nii.gz as extension
outputs['mean_img'] = self._gen_fname(
outputs['out_file'] + '_mean_reg.ext', cwd=output_dir)
else:
outputs['mean_img'] = self._gen_fname(
outputs['out_file'], suffix='_mean_reg', cwd=output_dir)

if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
_, filename = os.path.split(outputs['out_file'])
Expand Down