Invalid streamlines when transforming tractogram

[levje]

System (complete the following information, else the issue will be closed):

Describe the bug
Maybe this is due to my limited knowledge on the matter, but in the REGISTRATION_TRACTOGRAM module, we run scil_tractogram_apply_transform.py. Let's say that my output tractogram contains invalid streamlines. From the current implementation of the module, I can only use --cut_invalid.

However, if I don't want to cut the invalid streamlines in scil_tractogram_apply_transform.py, the module fails. Wouldn't it be more complete to allow for --keep_invalid and/or --remove_invalid to be configured?

Also, why is scil_tractogram_remove_invalid.py used right after if we're already taking care of the invalid streamlines in scil_tractogram_apply_transform.py?

Screenshots
Error I get:

Additional context
Add any other context about the problem here.

[AlexVCaron]

Hi @levje ! Thank you very much for the issue. You're in luck, I'm working on registration right now, because there are a few interaction problems between modules.

I will take a look at this module. By memory, the transformation script doesn't have all the features of remove_invalid. Maybe this has changed since, I'll look into it. Either way, I'll fix it so you can use your desired post-processing method (or none) after the transformation.

[AlexVCaron]

This is answered in #175, latest commit

[AlexVCaron]

Sould already be answered in main