Robin,
> If I my end goal is to the the stats + residuals for the bottom 10 slices. Can I make a "fake" dataset,
> containing 20 slices: first 10 are bottom slices that I'm interested in and the next 10 could be from the
> middle of the brain, just to trick MVM to think that the model/stats are correct?
Yes, that should be fine. Alternatively, in this case, you can temporarily comment out those few lines in 3dMVM.R that performs model checking, and then run 3dMVM on those first and last 10 slices.
Gang