Use out_prefix instead of "w" in spm.Normalize12

[servoz]

Please consider this PR that will be fast to review:

I think there are two solutions.
1- Remove the out_prefix parameter and the prefix remains always at "w"
or
2- use the out_prefix parameter instead of the hard-coded "w" value.

I think the second solution is the right one.
I propose a slight modification to this effect.

[effigies]

This seems reasonable, but does it work? I don't see where the updated file names would be passed to SPM to tell it to write to those files.

[servoz]

Yes it is working.
Using this little change in nipype.interfaces.spm.Normalize12:

$ python Python 3.11.4 (main, Jun 7 2023, 00:00:00) [GCC 12.3.1 20230508 (Red Hat 12.3.1-1)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import nipype.interfaces.spm as spm >>> import os >>> matlab_cmd = '/data/softs/SPM12standalone/spm12_r7771_Linux_R2019b/spm12/run_spm12.sh /data/softs/MATLAB_Runtime/v97 script' >>> spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True) >>> norm12 = spm.Normalize12() >>> norm12.inputs.jobtype = 'estwrite' >>> norm12.inputs.image_to_align = '/home/Desktop/testNipypeNormalize12/anat.nii' >>> norm12.inputs.out_prefix = 'test' >>> os.listdir('/home/Desktop/testNipypeNormalize12') ['anat.nii', 'ref'] >>> norm12.run() <nipype.interfaces.base.support.InterfaceResult object at 0x7f537d58fc10> >>> os.listdir('/home/Desktop/testNipypeNormalize12') ['y_anat.nii', 'anat.nii', 'ref', 'testanat.nii'] 

I don't see where the updated file names would be passed to SPM to tell it to write to those files.

I confess I didn't look into the nipype machinery to see exactly where the updated filenames would be passed to SPM to tell it to write to those files. ... However, concretely, with the small modification I propose, it works directly with nipype or in our environment (populse).

[effigies]

Sounds good. Could you go ahead and run black on this file? My guess is we have a line length issue.

[codecov]

Codecov Report

Patch coverage: 50.00% and no project coverage change.

Comparison is base (83d52f9) 63.18% compared to head (b9cac5e) 63.18%.
Report is 2 commits behind head on master.

Additional details and impacted files

@@ Coverage Diff @@ ## master #3600 +/- ## ======================================= Coverage 63.18% 63.18% ======================================= Files 308 308 Lines 40809 40809 Branches 5652 5652 ======================================= Hits 25784 25784 Misses 14013 14013 Partials 1012 1012 

Files Changed	Coverage Δ
nipype/interfaces/spm/preprocess.py	49.52% <50.00%> (ø)

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[servoz]

Could you go ahead and run black on this file?

Done!

[effigies]

Thanks!