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Enh/eddy assign outputs #1793

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Merged
merged 3 commits into from
Feb 8, 2017
Merged

Enh/eddy assign outputs #1793

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1f12f11
assign auto-generated EDDY outputs
ariekahn Jan 29, 2017
6c50369
assign auto-generated EDDY outputs
ariekahn Jan 29, 2017
53364d4
Merge branch 'enh/eddy_assign_outputs' of github.com:ariekahn/nipype …
ariekahn Feb 1, 2017
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38 changes: 38 additions & 0 deletions nipype/interfaces/fsl/epi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -454,6 +454,20 @@ class EddyOutputSpec(TraitedSpec):
out_parameter = File(exists=True,
desc=('text file with parameters definining the '
'field and movement for each scan'))
out_rotated_bvecs = File(exists=True,
desc=('File containing rotated b-values for all volumes'))
out_movement_rms = File(exists=True,
desc=('Summary of the "total movement" in each volume'))
out_restricted_movement_rms = File(exists=True,
desc=('Summary of the "total movement" in each volume '
'disregarding translation in the PE direction'))
out_shell_alignment_parameters = File(exists=True,
desc=('File containing rigid body movement parameters '
'between the different shells as estimated by a '
'post-hoc mutual information based registration'))
out_outlier_report = File(exists=True,
desc=('Text-file with a plain language report '
'on what outlier slices eddy has found'))


class Eddy(FSLCommand):
Expand Down Expand Up @@ -526,6 +540,30 @@ def _list_outputs(self):
'%s.nii.gz' % self.inputs.out_base)
outputs['out_parameter'] = os.path.abspath(
'%s.eddy_parameters' % self.inputs.out_base)

# File generation might depend on the version of EDDY
out_rotated_bvecs = os.path.abspath(
'%s.eddy_rotated_bvecs' % self.inputs.out_base)
out_movement_rms = os.path.abspath(
'%s.eddy_movement_rms' % self.inputs.out_base)
out_restricted_movement_rms = os.path.abspath(
'%s.eddy_restricted_movement_rms' % self.inputs.out_base)
out_shell_alignment_parameters = os.path.abspath(
'%s.eddy_post_eddy_shell_alignment_parameters' % self.inputs.out_base)
out_outlier_report = os.path.abspath(
'%s.eddy_outlier_report' % self.inputs.out_base)

if os.path.exists(out_rotated_bvecs):
outputs['out_rotated_bvecs'] = out_rotated_bvecs
if os.path.exists(out_movement_rms):
outputs['out_movement_rms'] = out_movement_rms
if os.path.exists(out_restricted_movement_rms):
outputs['out_restricted_movement_rms'] = out_restricted_movement_rms
if os.path.exists(out_shell_alignment_parameters):
outputs['out_shell_alignment_parameters'] = out_shell_alignment_parameters
if os.path.exists(out_outlier_report):
outputs['out_outlier_report'] = out_outlier_report

return outputs


Expand Down