afni.nimh.nih.gov

You could use this type of approach:

[afni.nimh.nih.gov]

Or use 3dcalc in a similar way to having multiple ROIs on the same map. Threshold the images for significance where anything significant is set to 1 in each overlay. Then do something along the lines of:

3dcalc -a firstOverlay+tlrc -b secondOverlay+tlrc -c thirdOverlay+tlrc -prefix combined -expr '1*a + 2*b + 3*c'

Then you can have the AFNI viewer code 1, 2, and 3 as different colors.