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Interface crashes because of "-" before algorithm specification.
RuntimeError: Command:dwibiascorrect -mask <mask_file> -ants <in_file> <out_file>
Standard output:
Standard error:
Error: argument algorithm: invalid choice: <in_file> (choose from 'ants', 'fsl')
Usage: dwibiascorrect algorithm [ options ] ...
(Run dwibiascorrect -help for more information)
Return code: 1The expected behavior would be to execute the following command:
dwibiascorrect ants [options] <in_file> <out_file>To replicate the behavior, simply execute:
import nipype.interface.mrtrix3 as mrt
bc = mrt.DWIBiasCorrect()
bc.inputs.in_file = <in_file>
bc.inputs.out_file = <out_file>
bc.inputs.use_ants = True
bc.run()Running on a 64 bit Linux machine (Ubuntu)
{'commit_hash': '72945ef34',
'commit_source': 'installation',
'networkx_version': '2.4',
'nibabel_version': '3.0.0',
'nipype_version': '1.5.0',
'numpy_version': '1.19.0',
'pkg_path': '/home/groot/Projects/labbing/venv/lib/python3.7/site-packages/nipype',
'scipy_version': '1.5.0',
'sys_executable': '/home/groot/Projects/labbing/venv/bin/python',
'sys_platform': 'linux',
'sys_version': '3.7.8 (default, Jun 29 2020, 04:26:04) \n[GCC 9.3.0]',
'traits_version': '6.1.1'}
- My python environment outside container
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