Measuring the cortical thickness for a specific region using Freesurfer

Software Support
1

Hi,

I want to extract cortical thickness values at an MNI coordinate for several subjects.
I have run recon-all for all subjects.
I open T1.mgz and lh.pial in Freeview. For lh.pial, I add the lh.thickness file in overlay. In the Cursor panel, I enter the MNI coordinates I want and Freeview displays a value for cortical thickness.
I would like to know if this is the real value of cortical thickness in this specific region (or vertex) and how it’s calculated (average of the distance between CFS/GM interface and GM/WM interface, and GM/WM interface and CFS/GM interface).

Thank you very much for your help.
Fanny

2

FreeSurfer computes thickness at every node as the average of two distances - the minimum distance from each node on the pial surface to the smoothwm surface and, the opposite direction, from each node on the smoothwm surface to the closest vertex on the pial surface.

3

Thank you for your reply.