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_tktools) > > it seems that I wasn't able to find exactly what I'm looking for. > > > Thank you for your help, > > Arsenije > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
