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:

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0

________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield 
[shane.schofi...@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 ?

DT_RECON has been completed in Freesurfer.

Thank you.

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