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MCFLIRT naming error with FSL 6.0.7.13 #3684

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b1060t opened this issue Sep 28, 2024 · 1 comment
Open

MCFLIRT naming error with FSL 6.0.7.13 #3684

b1060t opened this issue Sep 28, 2024 · 1 comment
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@b1060t
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b1060t commented Sep 28, 2024

Summary

I'm walking through miykael's tutorial and found the output of mcflirt could not be correctly recognized:

FileNotFoundError: No such file or directory '/xxx/working_dir/preprocWF/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_mcf_mean_reg.nii.gz' for output 'mean_img' of a MCFLIRT interface

and the real output name of mcflirt was sub-01_ses-test_task-fingerfootlips_bold_mcf.nii.gz_mean_reg.nii.gz.
I think this issue should have been resolved after referring to a previous commit.

By simply replacing this line with the hardcoded path of the output file, the workflow finished without any error.

I don't know if this pattern of filename (.nii.gz_mean_reg.nii.gz) shouldn't appear in FLS 6, or there's something wrong on nipype side?

Platform details:

{'commit_hash': '62fc392',
 'commit_source': 'repository',
 'networkx_version': '3.3',
 'nibabel_version': '5.2.1',
 'nipype_version': '1.8.6',
 'numpy_version': '1.26.3',
 'pkg_path': '/xxx/.pyenv/versions/3.11.10/lib/python3.11/site-packages/nipype',
 'scipy_version': '1.14.1',
 'sys_executable': '/xxx/.pyenv/versions/3.11.10/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.11.10 (main, Sep 23 2024, 14:48:25) [GCC 7.5.0]',
 'traits_version': '6.3.2'}

Execution environment

FSL: 6.0.7.13

@effigies
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I'm not sure. If you're able to describe an environment and minimal reproducible example, we could definitely debug this.

@effigies effigies added the bug label Nov 18, 2024
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