[ENH] Update registration subworkflows and modules

[anroy1]

Type of improvement

• Documentation
• Development tools (e.g. linter, formatter, etc.)
• Development container
• Global update (please specify)
• Other (please specify)

Describe your improvement

subworkflow/registration:

• add synthregistration optionality to subworkflow
• add specific test for synthregistration

modules/synthregistration:

• change output structure to tuple transfo_image containing both transforms
• add python package access.

module/convert:

• add optionality to affine conversion. If no affine is provided, skips conversion. Synthmorph output include affine initialization in its deform output.
• change output order

Checklist before requesting a review

• Ensure the syntax is correct (EditorConfig and Prettier must pass)
• Run the test suites if your changes affect any module
• Regenerate the Poetry lock file if you have updated the dependencies
• Ensure the documentation is up-to-date

[arnaudbore]

LGTM but needs some consistency with version. Sometimes Freesurfer 7.4 / 7.4.1
Is there a way to extract version from one bin instead of hardcoded it ?

[gagnonanthony]

There is a version flag for mri_convert, we could use it like this to fetch freesurfer's version: mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/' @anroy1 @arnaudbore

[anroy1]

In this case, in the case of synthregistration, there is an official synthmorph only container, therefore not allowing to extract version with mri_convert. But synthmorph:3, which we use here, starts at freesurfer:7.4.1 (i believe, but not 100% ure)