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[ENH] Add ExtractedBrainN4 output to ANTs CorticalThickness interface #2784

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Merged
merged 5 commits into from
Nov 26, 2018
Merged

[ENH] Add ExtractedBrainN4 output to ANTs CorticalThickness interface #2784

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15cba85
enh: add extracted brain to antsCorticalThickness
satra Nov 18, 2018
f70f32d
fix: input name for spm RealignUnwarp
satra Nov 18, 2018
aed7f16
fix: missing auto specs
satra Nov 18, 2018
e72334a
fix: resolved conflicts
satra Nov 18, 2018
bca9dfe
Merge remote-tracking branch 'upstream/master' into enh/antsCT
satra Nov 25, 2018
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4 changes: 4 additions & 0 deletions nipype/interfaces/ants/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -560,6 +560,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec):

class CorticalThicknessOutputSpec(TraitedSpec):
BrainExtractionMask = File(exists=True, desc='brain extraction mask')
ExtractedBrainN4 = File(exists=True, desc='extracted brain from N4 image')
BrainSegmentation = File(exists=True, desc='brain segmentaion image')
BrainSegmentationN4 = File(exists=True, desc='N4 corrected image')
BrainSegmentationPosteriors = OutputMultiPath(
Expand Down Expand Up @@ -645,6 +646,9 @@ def _list_outputs(self):
outputs['BrainExtractionMask'] = os.path.join(
os.getcwd(), self.inputs.out_prefix + 'BrainExtractionMask.' +
self.inputs.image_suffix)
outputs['ExtractedBrainN4'] = os.path.join(
os.getcwd(), self.inputs.out_prefix + 'ExtractedBrain0N4.' +
self.inputs.image_suffix)
outputs['BrainSegmentation'] = os.path.join(
os.getcwd(), self.inputs.out_prefix + 'BrainSegmentation.' +
self.inputs.image_suffix)
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1 change: 1 addition & 0 deletions nipype/interfaces/ants/tests/test_auto_CorticalThickness.py
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Expand Up @@ -75,6 +75,7 @@ def test_CorticalThickness_outputs():
BrainVolumes=dict(),
CorticalThickness=dict(),
CorticalThicknessNormedToTemplate=dict(),
ExtractedBrainN4=dict(),
SubjectToTemplate0GenericAffine=dict(),
SubjectToTemplate1Warp=dict(),
SubjectToTemplateLogJacobian=dict(),
Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/spm/preprocess.py
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Expand Up @@ -524,12 +524,12 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec):
est_re_est_mov_par = traits.Bool(
field='uweoptions.rem',
desc='Re-estimate movement parameters at each unwarping iteration.')
est_num_of_interations = traits.ListInt(
est_num_of_iterations = traits.ListInt(
[5],
field='uweoptions.noi',
minlen=1,
maxlen=1,
usedfault=True,
usedefault=True,
desc='Number of iterations.')
est_taylor_expansion_point = traits.String(
'Average',
Expand Down
4 changes: 2 additions & 2 deletions nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py
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Expand Up @@ -8,11 +8,11 @@ def test_RealignUnwarp_inputs():
est_basis_func=dict(field='uweoptions.basfcn', ),
est_first_order_effects=dict(field='uweoptions.fot', ),
est_jacobian_deformations=dict(field='uweoptions.jm', ),
est_num_of_interations=dict(
est_num_of_iterations=dict(
field='uweoptions.noi',
maxlen=1,
minlen=1,
usedfault=True,
usedefault=True,
),
est_re_est_mov_par=dict(field='uweoptions.rem', ),
est_reg_factor=dict(
Expand Down