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Hi Wen, It is a bit difficult to understand from your description, but I think your second model is testing a different hypothesis than you think. Can you send snapshots of the design matrices and contrasts that you're comparing from the 2 models? Thanks, Jeanette On Thu, Aug 14, 2014 at 4:18 PM, Leslie Cao <[log in to unmask]> wrote: > Dear FSL experts, > I have a question about ANOVA group effect. We have two groups and each > subject has two sessions. First I followed the instructions on FSL wiki *ANOVA: > 2-groups, 2-levels per subject (2-way Mixed Effect ANOVA), *so I got > session effect and interaction from first step and averaged the 2 measures > within-subject and ran a 2 group mean comparison on these data in a 3 level > analysis approach. Another method I just ran one ANOVA with group main > effect modeled, to avoid rank-deficiency with the EVs, I dropped one > subject-specific mean in each group. I was expecting similar results from > both methods.The interaction and session effects are pretty similar, > however, the group difference I got using first approach and group main > effect in the second ANOVA are totally different. The second group effect > is much stronger but appear to be suspicious. So is there a explanation > that the second approach might be giving wrong group main effects? > Thanks, > Wen >