[Module] Freesurfer registration

[anroy1]

Describe your changes

Initial module PR for registration tool using Freesurfer synthmorph converting transform to ants orientation.

Say which test data are used by your module

Checklist before requesting a review

• Create the tool:
  • Edit ./modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./modules/nf-scil/<category>/<tool>/meta.yml
• Generate the tests:
  • Edit ./tests/modules/nf-scil/<category>/<tool>/main.nf
  • Edit ./tests/modules/nf-scil/<category>/<tool>/nextflow.config
  • Add test data locally for tests with the fork repository
  • Generate the test infrastructure and md5sum for all outputs
• Ensure the syntax is correct :
  • Check indentation abides with the rest of the library (don't hesitate to correct others !)
  • Lint everything. Ensure your variables have good names.

[AlexVCaron]

@nf-scil-bot fix linting

[AlexVCaron]

@nf-scil-bot fix linting

[AlexVCaron]

Great job, almost there ! 💪🏻 To be consistent with the remainder of the library, I would rather this module outputs standard file formats. You're there with Nifti, but lta should be converted to mat/txt, the easiest (mat prefered since binary).

[anroy1]

Regarding your comment on .lta format, it would be possible by adding the lta_convert function, as synthmorph affine output only .lta in RAS orientation. Making this module able to combine would require then to change the docker container: freesurfer/synthmorph --> freesurfer/freesurfer, which then require the licence management. This is mainly why I decided to split to create a separate module registration/convert. This is something we can discuss and think through.

[AlexVCaron]

Maybe one day we'll be able to fuse the containers, but for now, let's keep it like that. Add a short paragraph to the description in the meta referring to the conversion module.