afni.nimh.nih.gov

Sorry, got my terminology mixed up there - you're right, it's better if I tell you what I'm trying to do.
I have two maps - each a 3D NIFTI where each voxel has a certain value and I'm trying to calculate how similar these two maps are in terms of the correlation between their voxel values (i.e. value of each voxel in map A vs value of each voxel in map B).