McFlirt incorrect output filename expected

[stebo85]

Summary

The mcflirt node crashes when .inputs.stats_imgs = True

when using FSL 6.0.5.1:57b01774 because

it expects the output filename to be: BASEFILENAME_variance.nii.gz

but FSL outputs: BASEFILENAME.nii.gz_variance.nii.gz

There is a switch here that seems to fix this:

nipype/nipype/interfaces/fsl/preprocess.py

Line 914 in 450be34

# FSL <6.0 outputs have .nii.gz_variance.nii.gz as extension

There it seems that this is a behavior for older FSL versions below 6.0.0. Is anyone else getting this in newer versions as well? Should this version switch be adapted to include newer versions as well?

Actual behavior

FSL 6.0.5.1:57b01774 outputs: BASEFILENAME.nii.gz_variance.nii.gz
Nipype expects BASEFILENAME_variance.nii.gz

Expected behavior

Nipype should expect: BASEFILENAME.nii.gz_variance.nii.gz

How to replicate the behavior

mcflirt_run1 = fsl.MCFLIRT()
mcflirt_run1.inputs.ref_vol = 0
mcflirt_run1.inputs.save_mats = True
mcflirt_run1.inputs.save_plots = True

#error when stats_img = True -> works with False because image is not expected
mcflirt_run1.inputs.stats_imgs = True

mcflirt_run1.inputs.in_file = 'bold.nii.gz'
mcflirt_run1.inputs.out_file = 'mcflirt_bold.nii.gz'

mcflirt_run1.run()

Script/Workflow details

Please put URL to code or code here (if not too long).

Platform details:

{'commit_hash': '%h',
 'commit_source': 'archive substitution',
 'networkx_version': '2.8.8',
 'nibabel_version': '4.0.2',
 'nipype_version': '1.8.5',
 'numpy_version': '1.23.5',
 'pkg_path': '/opt/conda/lib/python3.10/site-packages/nipype',
 'scipy_version': '1.9.3',
 'sys_executable': '/opt/conda/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.10.4 | packaged by conda-forge | (main, Mar 24 2022, '
                '17:38:57) [GCC 10.3.0]',
 'traits_version': '6.4.1'}

[stebo85]

@kimsin98 - it looks like you added this if condition in 2019 - did you get a different behaviour with versions newer than 6.0.0?

[kimsin98]

I think this was added when FSL 6.0 was pretty new. If more recent versions changed outputs again, they should be fixed!

#2925
https://neurostars.org/t/output-files-issue-with-mcflirt-nipype-1-2-0/4840

[effigies]

@stebo85 Please feel free to submit a PR.