ENH dwi2mask (dev): SynthStrip

[Lestropie]

https://www.sciencedirect.com/science/article/pii/S1053811922005900 https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/

Simply one to add to the list. On initial inspection it appears to be single-volume input only, ie. can't use multiple shells.

[bjeurissen]

Tried it and seems to work as advertised

[Lestropie]

• [x] Initial familiarization

  • [x] Install latest FreeSurfer version
  • [x] Execute mri_synthstrip on exemplar data
  • [x] Examine command-line interface and options available

• [x] Generate template dwi2mask algorithm

  • [x] Ensure that the dev branch of MRtrix3 is installed and working
  • [x] Create copy of an existing dwi2mask algorithm with a new name
  • [x] Ensure that "new" algorithm is accessible from the command-line through the dwi2mask interface
  • [x] Ensure that behaviour of new algorithm is identical to that copied

• [x] Generate implementation of SynthStrip-based dwi2mask algorithm

  • [x] Generate mean b=0 image from DWI input (Note: dwi2mask wrapper provides this)
  • [x] Convert to NIfTI format as required for compatibility with FreeSurfer
  • [x] Capture output of SynthStrip and convert back into MRtrix3 .mif format
    • [x] Check if the SynthStrip output file has the same orientation as the image that was input to dwi2mask; if it does not, modify strides of .mif file to match that of the user's input DWI series Edit: dwi2mask wrapper already does this
    • [x] Make output file of bitwise data type
  • [x] Implement command-line options that echo SynthStrip options, and feed any user-specified options to the SynthStrip command
  • [x] Integrate SynthStrip algorithm into the dwi2mask consensus algorithm
  • [x] (Optional) When generating NIfTI for input to SynthStrip, modify strides such that image conforms to the orientations used in network training; this will obviate the need for SynthStrip to perform this step internally Edit: Not pursuing, not worth the complexity given the dwi2mask wrapper provides this image

• [x] Generate Pull Request (New plan is to generate this pull request before dealing with the container dependencies)

• [ ] Add external dependencies for new dwi2mask algorithm to containers

  • [ ] Repeat instructions in #2529 in this context