afni.nimh.nih.gov

You only need to use a zeroed sub-brick for the third sub-brick passed to make this work. 3dThreetoRGB can take 3 datasets as input, each with a single sub-brick. In other words, the "Three" of 3dThreetoRGB should be set to zero. So create a zero sub-brick dataset somewhere with the same dimensions as the other two sub-bricks. 3dcalc -a 'dataset1[0]' -expr '0' will work. You could also use the Draw Dataset plug-in to make a zero copy.