Have you seen the spmmouse extension (designed to run in spm5)? http://www.wbic.cam.ac.uk/~sjs80/spmmouse.html
It comes with a mouse brain template and a nice tutorial with an example data set. It seems to run well to modify spm to work on a mouse scale. It also has the functionality to allow you to create your own template but this requires the matlab image processing tool box. I have just acquired the toolbox and am now trying (but currently failing) to get this to work to create a rat brain. (am a bit of a matlab novice so am not sure if the problem lies with the spm mouse or the image processing toobox installation at the moment).