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[ENH] Enable cnr_maps and residuals outputs for FSL eddy #2750

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Merged
merged 4 commits into from
Dec 10, 2018
Merged

[ENH] Enable cnr_maps and residuals outputs for FSL eddy #2750

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a5b5aab
Add new parameters 'cnr_maps' and 'residuals' to FSL eddy interface
niklasfoe Oct 24, 2018
a8b157d
Merge branch 'master' into eddy
niklasfoe Nov 28, 2018
91ba894
Add min_ver flag to the new eddy input-traits
niklasfoe Dec 10, 2018
66ea26f
Merge branch 'master' into eddy
niklasfoe Dec 10, 2018
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16 changes: 16 additions & 0 deletions nipype/interfaces/fsl/epi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -659,6 +659,8 @@ class EddyInputSpec(FSLCommandInputSpec):
"the field specified by --field and first volume "
"in file --imain")
use_cuda = traits.Bool(False, desc="Run eddy using cuda gpu")
cnr_maps = traits.Bool(False, desc='Output CNR-Maps', argstr='--cnr_maps')
residuals = traits.Bool(False, desc='Output Residuals', argstr='--residuals')
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Do we know if these were introduced in a particular version? If so, we should set the min_ver flag.

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I added 5.0.10 as the minimum version since this is the one i am using and that is working (despite the parameters not showing in the usage page). I messaged eddy's developers and they said that these parameters are actually planned to be released with eddy 6.0.1, they did not yet answer why the parameters are already usable in lower versions.



class EddyOutputSpec(TraitedSpec):
Expand All @@ -685,6 +687,10 @@ class EddyOutputSpec(TraitedSpec):
exists=True,
desc=('Text-file with a plain language report on what '
'outlier slices eddy has found'))
out_cnr_maps = File(
exists=True, desc='path/name of file with the cnr_maps')
out_residuals = File(
exists=True, desc='path/name of file with the residuals')


class Eddy(FSLCommand):
Expand Down Expand Up @@ -787,6 +793,16 @@ def _list_outputs(self):
self.inputs.out_base)
out_outlier_report = os.path.abspath(
'%s.eddy_outlier_report' % self.inputs.out_base)
if isdefined(self.inputs.cnr_maps) and self.inputs.cnr_maps:
out_cnr_maps = os.path.abspath(
'%s.eddy_cnr_maps.nii.gz' % self.inputs.out_base)
if os.path.exists(out_cnr_maps):
outputs['out_cnr_maps'] = out_cnr_maps
if isdefined(self.inputs.residuals) and self.inputs.residuals:
out_residuals = os.path.abspath(
'%s.eddy_residuals.nii.gz' % self.inputs.out_base)
if os.path.exists(out_residuals):
outputs['out_residuals'] = out_residuals

if os.path.exists(out_rotated_bvecs):
outputs['out_rotated_bvecs'] = out_rotated_bvecs
Expand Down
4 changes: 4 additions & 0 deletions nipype/interfaces/fsl/tests/test_auto_Eddy.py
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Expand Up @@ -74,6 +74,8 @@ def test_Eddy_inputs():
session=dict(argstr='--session=%s', ),
slm=dict(argstr='--slm=%s', ),
use_cuda=dict(),
cnr_maps=dict(argstr='--cnr_maps', ),
residuals=dict(argstr='--residuals', ),
)
inputs = Eddy.input_spec()

Expand All @@ -89,6 +91,8 @@ def test_Eddy_outputs():
out_restricted_movement_rms=dict(),
out_rotated_bvecs=dict(),
out_shell_alignment_parameters=dict(),
out_cnr_maps=dict(),
out_residuals=dict(),
)
outputs = Eddy.output_spec()

Expand Down