I think there is an example on the wiki in the ROI analysis section.  See

http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI

After you run aparcstats2table, you can run mri_glmfit with --table aparcstatstable instead of --y. The output folder will have tables with lists of ROIs and p-values

Hey FreeSurfer experts, 

Does anyone know the steps i have to perform if I want to conduct surface based thickness analysis using GLM but with ROI approach. Thank you very much. 

Best, 

Paul

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