Amanda,
> 1. If I understand correctly, I need to use a covariate file because there are more than 3 groups, correct?
Yes, that's correct.
> 2. If so, are you coding group membership in the covariate file or contrasts?
Through a covariate file using option -covariates.
> 3. If you are coding contrasts, will 3dMEMA then just run pairwise comparisons or will it also give me an omnibus effect?
Check out this web page: [
afni.nimh.nih.gov]
Gang