Hi Damien, it should be group1 - group2. You can look in the QDEC output directory for the contrast folder. In there is a C.dat file with the matrix. The design matrix is Xg.dat in the output folder.
doug


On 5/26/13 8:32 AM, Damien MARIE wrote:
Dear FreeSurfer experts,

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,

Damien Marie - Doctorant / PhD student
E-mail: damien.marie@u-bordeaux2.fr
Phone: +33 (0)5 57 82 09 39
Homepage: www.gin.cnrs.fr/spip.php?article23&lang=en
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