Hi, Freesurfer Users.

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!