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ENH: --out_itk option for LTAConvert #2176

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Merged
merged 7 commits into from
Sep 7, 2017
Merged

ENH: --out_itk option for LTAConvert #2176

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1e0831c
ConvertLTA can export to ITK-format
Gilles86 Sep 4, 2017
5327a65
Added test for lta_convert with out_itk
Gilles86 Sep 4, 2017
6f5a7a1
Added myself to .zenodo (although maybe bit much for 3 lines of code …
Gilles86 Sep 4, 2017
73237af
Added out_itk to tes_LTAConvert_outputs()
Gilles86 Sep 7, 2017
2403a98
Added option for --in_itk to LTAConvert
Gilles86 Sep 7, 2017
c7e2a33
Fixed test_auto_LTAConvert.py using 'make specs'
Gilles86 Sep 7, 2017
8495a87
DOC: Add comma to zenodo.json
effigies Sep 7, 2017
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5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -524,6 +524,11 @@
"name": "Lukas Snoek",
"orcid": "0000-0001-8972-204X"
}
{
"affiliation": "Vrije Universiteit, Amsterdam",
"name": "Gilles de Hollander",
"orcid": "0000-0003-1988-5091"
}
],
"keywords": [
"neuroimaging",
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2 changes: 2 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_LTAConvert.py
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Expand Up @@ -45,6 +45,8 @@ def test_LTAConvert_inputs():
),
out_reg=dict(argstr='--outreg %s',
),
out_itk=dict(argstr='--outitk %s',
),
source_file=dict(argstr='--src %s',
),
target_conform=dict(argstr='--trgconform',
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6 changes: 5 additions & 1 deletion nipype/interfaces/freesurfer/utils.py
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Expand Up @@ -3110,6 +3110,8 @@ class LTAConvertInputSpec(CommandLineInputSpec):
desc='output transform in MNI/XFM format')
out_reg = traits.Either(traits.Bool, File, argstr='--outreg %s',
desc='output transform in reg dat format')
out_itk = traits.Either(traits.Bool, File, argstr='--outitk %s',
desc='output transform in ITK format')
# Optional flags
invert = traits.Bool(argstr='--invert')
ltavox2vox = traits.Bool(argstr='--ltavox2vox', requires=['out_lta'])
Expand All @@ -3124,6 +3126,7 @@ class LTAConvertOutputSpec(TraitedSpec):
out_fsl = File(exists=True, desc='output transform in FSL format')
out_mni = File(exists=True, desc='output transform in MNI/XFM format')
out_reg = File(exists=True, desc='output transform in reg dat format')
out_itk = File(exists=True, desc='output transform in ITK format')


class LTAConvert(CommandLine):
Expand All @@ -3146,7 +3149,8 @@ def _format_arg(self, name, spec, value):
def _list_outputs(self):
outputs = self.output_spec().get()
for name, default in (('out_lta', 'out.lta'), ('out_fsl', 'out.mat'),
('out_mni', 'out.xfm'), ('out_reg', 'out.dat')):
('out_mni', 'out.xfm'), ('out_reg', 'out.dat'),
('out_itk', 'out.txt')):
attr = getattr(self.inputs, name)
if attr:
fname = default if attr is True else attr
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