Dear experts,

I would like to create an average surface template of fMRI activation for two groups, and then determine areas of low cerebrovascular reactivity in my disease group, create a ROI, and extract the cortical thickness in this region and see how it compares to a control group by translating this ROI onto the control surface template. Do you have any tips or suggestions on how this workflow should be done?

I've currently been able to create an average surface for both groups, and I know how to create labels using tksurfer and to extract cortical thickness using mri_anatomical_stats. Is it possible however to create an ROI by only considering areas of low CVR/low activation in my disease group and calculating cortical thickness for this area, and then visualize it somehow and then translate this label onto the control group and doing the same? 

I know it's a lot of questions, but going through the tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_tktools) it seems that I wasn't able to find exactly what I'm looking for. 

Thank you for your help,

Arsenije