The module clinica.utils.mri_registration only contains a single function convert_flirt_transformation_to_mrtrix_transformation which is only used in a single place in the code base:
[x] I propose that we delete this useless module and move the function to clinica.pipelines.dwi.connectome.utils.
[x] Since it is used as a Nipype interface, it would be great to implement the corresponding adapter in clinica.pipelines.dwi.connectome.tasks.
[x] Finally, it would be awesome to implement some unit tests for it since they are currently missing.
Hints for the unit testing:
The function is basically doing a subprocess call, so we could refactor a bit to have a helper function building and returning the command that should be run (that would be easy to test).
Then, by monkey patching check_software and os.system we could test the behavior of the function without running the underlying MRTrix command.
Description
The module
clinica.utils.mri_registrationonly contains a single functionconvert_flirt_transformation_to_mrtrix_transformationwhich is only used in a single place in the code base:https://github.com/aramis-lab/clinica/blob/7d2819a9db4a7e06d829e606a1714c854ef912fb/clinica/pipelines/dwi/connectome/pipeline.py#L353
Steps
clinica.pipelines.dwi.connectome.utils.clinica.pipelines.dwi.connectome.tasks.Hints for the unit testing: The function is basically doing a subprocess call, so we could refactor a bit to have a helper function building and returning the command that should be run (that would be easy to test). Then, by monkey patching
check_softwareandos.systemwe could test the behavior of the function without running the underlying MRTrix command.