[Freesurfer] vertex-wise cortical thickness and whole brain labeling

Hi Douglas and all,

I have used the ‘recon-all’ command to segment the gray matter of 140 subjects. I have three questions:

(1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ‘mri_surf2surf’?

(2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes?

(3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this?

Thank you very much!

Qiongmin Ma