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fsl randomise f_only flag contains typo, can't work #3322

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henrymj opened this issue Apr 2, 2021 · 2 comments · Fixed by #3325
Closed

fsl randomise f_only flag contains typo, can't work #3322

henrymj opened this issue Apr 2, 2021 · 2 comments · Fixed by #3325

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@henrymj
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henrymj commented Apr 2, 2021

Summary

when calling randomise with f_only=True, nipypes interfaces appends --f_only instead of --fonly. This is incorrect and prevents the call from working.

The offending line is here, where the last bit should be argstr="--fonly"

Actual behavior

appending --fonly to the randomise call.

Expected behavior

--f_only is appended, breaking the call.

Script/Workflow details

    fsl_randomise = mem.cache(fsl.Randomise)
    randomise_results = fsl_randomise(
        in_file=`fourdimage.nii`,
        mask=`mask.nii`,
        num_perm=10000,
        f_only=True,
        **kwargs
        )

Platform details:

{'commit_hash': 'c5ce0e2c9',
 'commit_source': 'installation',
 'networkx_version': '2.5',
 'nibabel_version': '3.2.1',
 'nipype_version': '1.4.2',
 'numpy_version': '1.20.1',
 'pkg_path': '/usr/local/miniconda/lib/python3.7/site-packages/nipype',
 'scipy_version': '1.6.1',
 'sys_executable': '/usr/local/miniconda/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.7.4 (default, Aug 13 2019, 20:35:49) \n[GCC 7.3.0]',
 'traits_version': '6.2.0'}
@effigies
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effigies commented Apr 4, 2021

What version of FSL? Are we sure that or didn't change from one to the other?

Would you be up for submitting a PR?

@henrymj
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henrymj commented Apr 5, 2021

FSL Version 6.0. I just scrolled through the FSL history here and didn't see any references to changing the command-line interface, but I may not be digging deep enough.

I can submit a PR later in the week if no objections arise in the meantime!

henrymj added a commit to henrymj/nipype that referenced this issue Apr 9, 2021
effigies added a commit that referenced this issue Apr 9, 2021
[FIX] change fsl interface randomise --f_only to --fonly for #3322
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2 participants