# 2x2 anova with multiple comparisons correction

I am trying to run a repeat measures 2x2 anova and correct for multiple comparisons all in one, a la 3dttest++ -ClustSim. Is there any functionality to do this yet? I am using 3dANOVA3 to run the anova.

If not, which method is best for permutation testing to correct for multiple comparisons in a repeat measure 2x2 ANOVA in afni?

For a 2 x 2 repeated-measures design, you can break it into multiple one-sample or paired t-tests, and then run 3dttest++ multiple times.

How would this work in calculating F-scores?

For a 2 x 2 structure, the F-test for the interaction between factors A and B is essentially equivalent to the t-test (A1B1-A1B2)-(A2B1-A2B2) or (A1B1-A2B1)-(A1B2-A2B2). Even better, you get more information from the t-test than F because t-test directly provides the sign/directionality for the associated effect; for example, a positive t-value shows A1B1-A1B2 > A2B1-A2B2 and A1B1-A2B1 > A1B2-A2B2.

The same goes with the two main effects.

Thank you!

I’m sorry I don’t quite understand, actually. I am not familiar with this notation for t-tests: does (A1B1-A2B1)-(A1B2-A2B2), for example, mean I do the subtraction of A1B1-A2B1 and the subtraction A1B2-A2B2 for each subject and the run a paired sample t-test between the resultant maps? Or do I need to run ttests instead of subtractions? I’m unsure how it could be the latter, since that would only leave me with two maps for the final ttest.

I should note that all factors and levels are within subject. Every subject did all factors and all levels.

Final Q: in which of these ttests should I run multiple compairson correcting permutation tests? Running on all of them seems wrong, but so does running it on jus the final ttest.