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At voxels where the masks differed, there would be
no information to talk about group differences with
anyway. To compare 2 groups at some voxel, one
needs information about both groups there, meaning
that voxel must be common to both masks.
Really, think that there should be only 1 mask (for
all subjects in all groups).
Note that you also want a common mask to apply
any multiple comparison correction.