Diffusion magnetic resonance imaging (dMRI) is a non-invasive imaging technique capable of characterizing the diffusion properties of water molecules in vivo and detecting microstructural changes in brain tissue. It provides new tools to investigate the integrity of brain white matter. Although dMRI is widely used in clinical studies, and has become a common method in clinical radiology, it is infrequently used in preclinical brain imaging studies on small animal models. In this paper, we implemented computational methods for small animal dMRI. First, a high-resolution dMRI template for rat was constructed. Secondly, voxel-based analysis and tract-based spatial statistics methods for small animal dMRI were implemented. Last but not least, the deterministic and probabilistic tractography methods for small animal imaging were implemented. The implementation of these methods will facilitate the applications of dMRI in preclincal small animal imaging.