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Description
I am trying on ANTs' LaplacianThickness interface to not specify output_image
(if I do - another issue, will report separately):
from nipype.interfaces.ants import LaplacianThickness
cort_thick = LaplacianThickness()
d = 'antsCorticalThicknessExample/ResultsT1Only/'
cort_thick.inputs.input_wm = d + 'exampleBrainSegmentationPosteriors3.nii.gz'
cort_thick.inputs.input_gm = d + 'exampleBrainSegmentationPosteriors2.nii.gz'
# cort_thick.inputs.output_image = 'output_thickness.nii.gz'
print(cort_thick.cmdline)
print("Running")
print(cort_thick.run())
$> python nipype-undefined-output.py
LaplacianThickness antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors3.nii.gz antsCorticalThicknessExample/ResultsT1Only/exampleBrainSegmentationPosteriors2.nii.gz exampleBrainSegmentationPosteriors3_thickness.nii.gz
Running
181012-13:50:48,584 nipype.interface INFO:
stdout 2018-10-12T13:50:48.584522: using tolerance 0.001
...
181012-13:50:48,833 nipype.interface INFO:
stdout 2018-10-12T13:50:48.833009: writing exampleBrainSegmentationPosteriors3_thickness.nii.gz
Traceback (most recent call last):
File "nipype-undefined-output.py", line 9, in <module>
print(cort_thick.run())
File "/home/yoh/deb/gits/pkg-exppsy/nipype/nipype/interfaces/base/core.py", line 524, in run
outputs = self.aggregate_outputs(runtime)
File "/home/yoh/deb/gits/pkg-exppsy/nipype/nipype/interfaces/base/core.py", line 602, in aggregate_outputs
predicted_outputs = self._list_outputs()
File "/home/yoh/deb/gits/pkg-exppsy/nipype/nipype/interfaces/ants/segmentation.py", line 254, in _list_outputs
(name, self.inputs.output_image, ext)))
TypeError: sequence item 1: expected string or Unicode, _Undefined found
System
$> python -c "import nipype; from pprint import pprint; pprint(nipype.get_info())"
{'commit_hash': '3ec80655f',
'commit_source': 'repository',
'networkx_version': '2.1',
'nibabel_version': '2.3.1',
'nipype_version': '1.1.4-dev+g3ec80655f',
'numpy_version': '1.14.5',
'pkg_path': '/home/yoh/deb/gits/pkg-exppsy/nipype/nipype',
'scipy_version': '0.19.1',
'sys_executable': '/home/yoh/proj/flywheel/gearificator/venvs/dev/bin/python',
'sys_platform': 'linux2',
'sys_version': '2.7.14 (default, Sep 17 2017, 18:50:44) \n[GCC 7.2.0]',
'traits_version': '4.6.0'}
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