I was using VBM for group analysis but I am now working with FreeSurfer 5.3 which is pretty new for me. I have to compare two groups but I'm confused about the results and I have a coupe of questions about that. 

How can we select contrasts? I mean Qdec propose this with Cortical Thickness for example:

" Does the average thickness differ between group 1 and group 2 ? ". Thus I was thinking that when I choose this question, the result will correspond to the contrast " group 1 - group 2 " but I'm not sure since the results presented then looks like corresponding to the inverse, the contrast " group 2 - group 1 ".

Anyway I have to check both contrasts.

1) How identify the contrast presented?

2) How select the contrast?

Best regards,