> For the 3MEMA format, do you list all the files under the same set? How would it know who is in which group?

If you code your subjects via the following fashion:

grp2 grp3
grp1 0 0
grp2 1 0
grp3 0 1

you should assign "0 0" for any subject in group1, "1 0" for group2, and "0 1" for group3. Also you need to label the two columns as something like group2-group1 and group3-group1, respectively.

> Also how is this method different from doing 3 separate 3dMEMAs , one for grp1 vs grp2, one for grp1 vs grp3, and one for grp2 vs grp 3?

Not exactly the same, but very similar to each other. The reason is that a contrast in a model with all the three groups is tested with the residuals across all the three groups, instead of two as in the contrast between those two groups.

Gang