Hi, 

I have a question about the paired-diff.fsgd file listed on the freesurfer wiki. I have 3 groups and 2 time points. How is the subject1pair computed? 
GroupDescriptorFile 1
Class Main
Variables Age
Input subject1pair   Main 30
Input subject2pair   Main 40
Input subject3pair   Main 50
Input subject4pair   Main 60