I have been trying to align Harvard-Oxford atlas to the template that comes with FreeSurfer (know as Bert’s brain). However, there are some problems to deal with. The first one is related to space. In the case of Harvard-Oxford, it has been built in MNI152, and Bert’s brain is in native space. The other issue has to do with the coordinates orientation. In Harvard-Oxford, it uses RAS, and in Bert’s brain uses LAS. On top of that, it looks like both are in different scales. So, I was wondering if there is a way to overlay the Harvard-Oxford atlas on Bert’s brain?
Thanks for any help or guidance on this case.