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MATLAB/SPM error with 1.7 update

Open Brainarea opened this issue 2 years ago • 0 comments

Summary

After updating Nipype to 1.7 from 1.6.1, SPM/Matlab setup gives en error

Script/Workflow details

Running this code with 1.7

matlab_cmd = '/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2019b/v97/ script'
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)

Gives the following error:

tty: 'standard input': Inappropriate ioctl for device

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
File /opt/miniconda-latest/envs/neuro/lib/python3.9/site-packages/nipype/utils/spm_docs.py:49, in _strip_header(doc)
     48 try:
---> 49     index = doc.index(hdr)
     50 except ValueError as e:

ValueError: substring not found

The above exception was the direct cause of the following exception:

OSError                                   Traceback (most recent call last)
Input In [2], in <cell line: 2>()
      1 matlab_cmd = '/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2019b/v97/ script'
----> 2 spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)

File /opt/miniconda-latest/envs/neuro/lib/python3.9/site-packages/nipype/interfaces/spm/base.py:323, in SPMCommand.set_mlab_paths(cls, matlab_cmd, paths, use_mcr)

It's working perfectly well with 1.6.1

Platform details:

{'commit_hash': 'b385720',
 'commit_source': 'installation',
 'networkx_version': '2.7.1',
 'nibabel_version': '3.2.2',
 'nipype_version': '1.7.0',
 'numpy_version': '1.22.3',
 'pkg_path': '/opt/miniconda-latest/envs/neuro/lib/python3.9/site-packages/nipype',
 'scipy_version': '1.8.0',
 'sys_executable': '/opt/miniconda-latest/envs/neuro/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.9.10 | packaged by conda-forge | (main, Feb  1 2022, '
                '21:24:11) \n'
                '[GCC 9.4.0]',
 'traits_version': '6.3.2'}

Brainarea avatar Mar 23 '22 16:03 Brainarea