[Tracking issue] NHP DWI pipeline descriptors

[nx10]

niwrap should provide all interfaces needed to (in theory) support @kaitj s non-human primate DWI pipeline.

Anatomical:

• [x] NiftyReg: reg_aladin (http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg)
• [x] Freesurfer: python3 /freesurfer/mri_synthstrip
• [x] https://github.com/childmindresearch/niwrap/issues/60
• [x] https://github.com/childmindresearch/niwrap/issues/32
• [x] https://github.com/childmindresearch/niwrap/issues/30
• [x] https://github.com/childmindresearch/niwrap/issues/26
• [x] https://github.com/childmindresearch/niwrap/pull/96
• [x] https://github.com/childmindresearch/niwrap/issues/31
• [x] https://github.com/childmindresearch/niwrap/issues/27

Diffusion:

• [x] MRTrix ?
  • [x] dwidenoise
  • [x] mrdegibbs
  • [x] dwiextract
  • [x] dwibiascorrect (this is just calling ANTS N4BiasCorrection)
• [x] FSL
  • [x] https://github.com/childmindresearch/niwrap/pull/113
  • [x] topup
  • [x] applytopup
• [x] ANTS
  • [x] antsRegistrationSyN.sh
  • [x] c3d
  • [x] antsApplyTransforms
• [x] ~This rotate_bvec script~ → Port to Python, this calls FSL avscale which should be wrapped instead

[kaitj]

Thanks - added a few more (editting your post directly). Some of these might be redundant with whats already been added in another issue or already created - I just haven't had a chance to check across them.

Also not a complete list, just what I can recall off the top of my head. I'll go through and add more when I get a chance to go through the workflow again.

[nx10]

Ok added descriptors for everything here - many of them probably broken, but now we should be able to start implementing and fix as things break