afni.nimh.nih.gov

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]
<[afni.nimh.nih.gov];

You can also align the centers of the eigenvectors and FA datasets before creating your RGB datasets.