Skip to content

Mrtrix3's dwibiascorrect interface crashes due to "-" #3247

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
GalKepler opened this issue Sep 10, 2020 · 0 comments · Fixed by #3248
Closed

Mrtrix3's dwibiascorrect interface crashes due to "-" #3247

GalKepler opened this issue Sep 10, 2020 · 0 comments · Fixed by #3248

Comments

@GalKepler
Copy link
Contributor

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: 1

The 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
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant