you can refer to this post:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31297.html

-- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

On 9/12/13 9:04 AM, "Anita van Loenhoud" <acvanloenhoud@gmail.commailto:acvanloenhoud@gmail.com> wrote:

Hi FreeSurfers,

I'm doing an analysis with two groups: patients and controls. When I look at "Does the average thickness differ between 1 (patients) and 2 (controls)?", I can see blue (negative) and red (positive) correlations. I know that it means that in some cases, the patients have a higher cortical thickness compared to the controls, and in others it's the other way around. But which is which?

Since most of the clusters are blue, I assume that blue means: patients have a lower cortical thickness compared to controls, and red means: patients have a higher cortical thickness compared to controls. Is this correct?

How does FreeSurfer decide which group to use as the 'reference group' (i.e. the group to which the other group is compared)?

Thanks,

Anita