Hi Freesurfer experts, When I perform the statistical analysis, I am very confused with the following questions:
My experimental design includes 3 discrete factors: diagnosis with two levels (A, B); genotype with two levels (G, T); gender (F, M), and two covariates. So I can get 8 classes: AGF, AGM, ATF,ATM, BGF, BGM, BTF, BTM. 1) I want to perform 2 (diagnosis)* 2(genotype) interaction analysis with regressing out the effect of gender and two covariates, but I don't know the rules for setting the contrasts for the interaction. The contrast matrix I used is: 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0.25 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 is it correct? If it is correct, how to explain the results, for example, what does the positive (or negative) clusters stand for? Or the clusters showed in the t-test statistical map are the regions that have the significant interaction? 2) When I perform the main effect of dignosis, is the following matrix I used correct? 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 (I think it regressed out the effect of genotype and gender, that is it takes the genotype as a covariable) Or I should create another fsgd file, that has 4 classes: AF, AM, BF, BM. And I can use the matrix (0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0) to perform the main effect of diagnosis. which one is right? Any help will be very appreciated. Best wishes, Meng
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