Hippocampus mask unavailable/incompatible

[naji-s]

Describe the bug
I am trying to create left and right Hippocampi masks that would be compatible with Clinica's adni-to-bids (and then to CAPS) converter. Unfortunately though it seems like t1-linear processing is mixed with a cropping that is to my knowledge uses the template ref_cropped_template.nii.gz based on

clinica/clinica/pydra/t1_linear/t1_linear.py

Line 11 in 37da1cb

from clinica.pydra.tasks import download_mni_template_2009c, download_ref_template

I have also made a bug issue in clinica-dl here:
aramis-lab/clinicadl#537

And including it for clarity, since the original use of masks as part of data prepration is suggested there

My question is that can masks (taken from TamplateFlow be cropped using the reference tempalte I outlined above and they end up being compatible with CAPS data processed through Clinica?

[github-actions]

This issue is considered stale because it has not received further activity for the last 14 days. You may remove the inactive label or add a comment, otherwise it will be closed after the next 14 days.