Sophia,
You have a pretty simple and straightforward model, and either 3dMVM or 3dLME should work fine with your data structure. Even simple t-tests with 3dttest++ would work in your case if you know how to set it up.
> I ran a group analysis (i.e., repeated measure) for each group, using FSL (GRF corrected for multiple comparisons,
> cluster-level thresholding Z > 2.3, p < 0.05).
Just curious: How did you run the analysis in FSL? If you perform the analysis for each group separately, that would be a simple paired t-test.
Gang