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Hello Dr. Christian Gaser and CAT team, I have estimated cortical thickness in ROIs identified from several atlases (i.e., AAL and Neuromorphometrics atlases) using the CAT toolbox. And I found mean cortical thickness for subcortical areas, including the amygdala, hippocampus, and basal ganglia, though some subcortical areas were not estimated (as 'NaN' output). As far as I know, as cortical thickness is calculated by the distance between GM-WM (inner surface) and CSF-GM (outer surface) boundaries, it is thus impossible to estimate the cortical thickness in subcortical areas using Freesurfer. I think that the PBT method (to estimate cortical thickness) of the CAT may cause the cortical thickness in some subcortical areas. Is it right? I just wonder if I can use these thickness values of subcortical areas for my study or just ignore/remove those of subcortical areas. Thank you in advance! Best, Wi Hoon