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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Liu Y [liuy8866@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