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[FIX]Deduplicate dcm2niix output

1

fix for #3579

mauriliogenovese

[FIX]Add cropped files to dcm2niix output

1

fix for #3557

mauriliogenovese

Add Workflow Community Initiative (WCI) descriptor

3

Fixes https://github.com/nipy/nipype/issues/3607

u11kumar

See https://workflows.community/systems/contribute for more info, an example on https://github.com/frobnitzem/mpi_list/blob/master/docs/.wci.yml and here is a PR to adjust or to chase with another one to add pointer to such a file: https://github.com/workflowscommunity/workflowscommunity.github.io/pull/74

yarikoptic

Doesn't quote paths in the invocation of dcm2niix - directory with a space makes execution fail

2

### Summary Originally reported by a fella co-developer against heudiconv that it crashed when path contained a space in it. In heudiconv we depend on nipype to just run `dcm2niix`...

yarikoptic

Run tests whenever TMPDIR points to some folder with spaces in the name

2

See https://github.com/nipy/nipype/issues/3604 for the motivation

yarikoptic

### Summary The PETsurfer module in Freesurfer (centered around the functions mri_gtmpvc, gtmseg and mri_glmfit) needs minor updates to make the newest implementations to be in line with nipype. This...

mnoergaard

dcm2niix - Do consider exit 1 to be an error

4

Based on information in https://github.com/rordenlab/dcm2niix/issues/733#issuecomment-1646261249 > Exit code 0 is for success, exit code 1 is the undefined error. Handling of exit 1 as successful was added in 6ecd4a9fce3c9cf1ff23d5b895db319343ae0576 AKA...

yarikoptic

### Summary When using `fsl.FAST()` the outout files are written to a completely different output dir than specified. For other FSL tools like BET or FLIRT everything works without problems,...

Ede1994

Allow use of glob patterns in in_files for fsl.Merge

1

`fslmerge` command in cmdline already supports glob patterns such as /*/ and /**/ so I don't see a point in them not working in nipype. The reason I'm complaining about...

somso2e