You can use the wmparc, which includes ROIs of the WM underlying each cortical area, right below the grey-white boundary surface. These are the relevant tutorials:
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Shane Schofield [shane.schofield@yahoo.com] Sent: Friday, August 11, 2017 2:03 AM To: Freesurfer Support List Subject: [Freesurfer] Mean diffusivity on cortex?
Hi DTI Experts,
Is it sensible to do comparisons of MD on the cortex surface like a normal cortical thickness comparisons between group? If the answer is yes, are there recommended on smoothing ?