I tried searching for this question on the mailing list but couldn't get an
answer. Hence, I am posting this here again.

I ran the freesurfer analysis and got cortical thickness map for my group.
I want to build an adjacency matrix by finding the correlation between the
cortical thickness of various ROIs on an atlas (Either the
default freesurfer atlas or AAL atlas).
1) How can I map the cortical thickness map to freesurfer template volume
so that I can average the cortical thickness in the ROI to build the
connectivity matrix?
2) Instead of mapping to freesurfer template, if I have to use AAL atlas
can I simply map the cortical thickness map to MNI template and use AAL
atlas in MNI template to carry out step (1). If yes, how should I go about
doing that?

I would appreciate any response.

Thanks

Regards!