[New module] Freesurfer registration/convert

[anroy1]

Describe your changes

Add the synthbet option to preproc_t1Warp conversion module - designed initially to convert freesurfer registration warp (affine and deform) to ants-itk. Then decided to generalize the module for all cases possible. Receives one affine matrix, one deform warp, source and target images for orientation (and freesurfer licence) and outputs converted affine and deform.

List test packages used by your module

• freeurfer.zip
• freesurfer_relice.zip
• freesurfer_transforms.zip

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.

To Do

[AlexVCaron]

Excellent work, all functionalities are there ! There is a little work to be done on syntax. To be consistent, you should stick with a naming convention. Either use affine or linear everywhere when you are talking about the affine/linear part, and drop init when talking about the input or output transforms.

Once adressed, LGTM !

[arnaudbore]

GTG

[AlexVCaron]

Great job @anroy1 ! LGTM 🚀