> What are the main effect F-tests comparing in 3dANOVA and
> GroupAna? Are the main effect F-tests given by 3dANOVA and
> GroupAna tests of a given factor vs baseline?
The main effect of a factor tests whethere there is any difference across all the levels of the factor. If you modeled the baseline with a parameter greater than -1 in option -polort in 3dDeconvolve, all the regressor coefficients are contrasts against baseline by default.
Gang