I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7.

When comparing the cortical thickness results obtained from FS6 and FS7, I found that FS 7 results are much smaller than the FS6 ones. On average, about 13%-21% decrease in the subject's average cortical thickness. Specifically, on a cohort of images from GE scanners, the average cortical thickness from FS6 is 2.5mm, but from FS7 is less than 2.0mm. 

According to some published papers, I think 2.5mm as the average cortical thickness is more accurate than 2.0mm. 

Have you encountered this issue or question before? Do you think I should keep using FS6? Please give me your advice. Thank you!

John.