[Freesurfer] registration of gene expression images

Hi all, I have some images (2-d (single slice)) from mouse brains which show gene expression data from in-situ hybridization from several different mice. I would like to align each of these images with one another. Does anyone know of a really good tool for that sort of thing? Ideally I am looking to perform a 6-parameter transform of these images to bring them all into the same space. I know mri_robust_register does something similar for structural images of the human brain. Does anyone know of a good tool for this kind of thing? I thought someone in the freesurfer world might know. All the best and thanks for the help, Jared