I processed a bunch of subjects using recon-all, but now I would like to get labels from aparc.a2009s.annot from each subject in MNI space in nii from, the problem is that the annotation file (lh and rh) is in subject native space. I have a grey matter mask in MNI from each subject and my goal is to have each label from aparc.a2009s.annot to fit that mask.

How can I do this?

Thank you,

Daiana