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ENH: antsIntroduction handles RA and RI transformations #1009

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Merged
merged 5 commits into from
Jan 20, 2015
Merged

ENH: antsIntroduction handles RA and RI transformations #1009

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ecb3713
antsIntroduction handles RA and RI transformations
lsqshr Dec 8, 2014
0612a37
add isdefined(transmode)
lsqshr Dec 19, 2014
a8dbcc7
Update CHANGES
lsqshr Jan 10, 2015
3209c42
consider default -t = GR
lsqshr Jan 12, 2015
b92de07
Merge branch 'master' of https://github.com/nipy/nipype into antsIntr…
lsqshr Jan 12, 2015
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2 changes: 1 addition & 1 deletion CHANGES
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Next release
============

* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
argument formatting consistent. Cleaned ants.segmentation according to PEP8.
(https://github.com/nipy/nipype/pull/990/files)
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17 changes: 11 additions & 6 deletions nipype/interfaces/ants/legacy.py
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Expand Up @@ -94,16 +94,21 @@ class antsIntroduction(ANTSCommand):

def _list_outputs(self):
outputs = self._outputs().get()
transmodel = self.inputs.transformation_model

# When transform is set as 'RI'/'RA', wrap fields should not be expected
# The default transformation is GR, which outputs the wrap fields
if not isdefined(transmodel) or (isdefined(transmodel) and transmodel not in ['RI', 'RA']):
outputs['warp_field'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'Warp.nii.gz')
outputs['inverse_warp_field'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'InverseWarp.nii.gz')

outputs['affine_transformation'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'Affine.txt')
outputs['warp_field'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'Warp.nii.gz')
outputs['inverse_warp_field'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'InverseWarp.nii.gz')
outputs['input_file'] = os.path.join(os.getcwd(),
self.inputs.out_prefix +
'repaired.nii.gz')
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