Are you doing this inside or outside of FSFAST? If outside you would register your fmri to the anatomical with bbregister, then use mri_vol2surf to map it to the surface, then surf2surf to map it to fsaverage, then smooth, then mri_glmfit to test for a differnece between groups, then mri_glmfit-sim to get clusters. One of the cluster outputs will be "ocn" file. This is a segmentation-like surface structure. To get the mean thickness in each cluster, you would run mris_preproc to get a stack of thickness maps in fsaverage space, then run something like

mri_segstats --i lh.thickness.stack.mgh --seg ocn.mgh --exlucdeid 0 --avgwf cluster.thickness.stack.dat

cluster.thickness.stack.dat will have a row for each subject and a column for each cluster

On 04/10/2018 12:06 PM, Arsenije Subotic wrote:

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_tkt...) it seems that I wasn't able to find exactly what I'm looking for.

Thank you for your help,

Arsenije

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