I'm not sure exactly what you're trying to do, but we have the program 3dThreetoRGB that creates an RGB file from three input sub-brick volumes. The example here shows how to create a DTI FA encoded primary eigenvector image (that may be the same kind of dataset you are working with):
[
afni.nimh.nih.gov]
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afni.nimh.nih.gov];
You can also align the centers of the eigenvectors and FA datasets before creating your RGB datasets.