Hi Knut, if you have a glm analysis, set up a contrast for group1 vs 0 and group2 vs 0. This will create gamma.mgh files that are the mean thicknesses for each group. You can then compute the mean: fscalc group1/gamma.mgh add group2/gamma.mgh div 2 -o group.mean.mgh Then compute the percent difference: fscalc group1/gamma.mgh sub group2/gamma.mgh div group.mean.mgh mul 100 -o pctdiff.mgh

doug

On 10/17/2012 08:24 AM, Knut J Bjuland wrote:

Hi

Is it possible to generate surface maps for the percent difference in cortical thickness between 2 groups within with Freesurfer 5.1? Could you please give link to how to use Matlab to compute the differences as described in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07433.html?

Cheers Knut J

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