See the group analysis tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0

The tutorial uses age and gender, but you can add any other variables you want 
to the design matrix.

________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Liu Y [liuy8...@gmail.com]
Sent: Wednesday, March 29, 2017 9:03 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] correlation between cortical thickness and cognitive 
measure

Dear Experts,
Is there any instruction to analyze  correlation between cortical thickness and 
cognitive measure?
Thanks,
Yawu
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