Hi Karl,

the thickness is defined using both surfaces, so I don't think it makes sense to talk about "white matter thickness" or "pial thickness". It is the distance between the two.

cheers Bruce On Wed, 23 Mar 2011, Liukarl wrote:

Hello, Freesurfer experts:

I am using the mris_anatomical_stats to extract the average cortical thickness: mris_anatomical_stats -l lh.cortex.label -f subject1.txt subject1 lh

the output is number of vertices = 127190 total surface area = 84246 mm^2 total gray matter volume = 257279 mm^3 average cortical thickness = 2.628 mm +- 0.698 mm average integrated rectified mean curvature = 0.158 average integrated rectified Gaussian curvature = 0.146 folding index = 6266 intrinsic curvature index = 403.9

My question is whether the average cortical thickness here is from white matter surface or pial surface? How can I get the pial surface average thickness? Our goal is to use average cortical thickness as a covariate to examine the possible local thickness difference, like in the prefrontal lobe. Which average cortical thickness, pial or white, is a better fit in our case?

Thanks in advance

Karl