Deformation based morphometry is used to detect differences in in-vivo Magnetic Resonance Image (MRI) of the mouse brain obtained from two transgenic strains: TASTPM mice that over-express proteins associated with Alzheimer's disease, and wild-type mice. MRI was carried out at four time points. We compare two different methods to detect group differences in the longitudinal and cross-sectional data. Both methods are based on non-rigid registration of the images to a mouse brain atlas. The whole brain volume measurements on 27 TASTPM and wild-type animals are reproducible to within 0.4% of whole brain volume. The agreement between different methods for measuring volumes in a serial study is shown. The ability to quantify changes in growth between strains in whole brain, hippocampus and cerebral cortex is demonstrated.