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