New imaging techniques, such as pharmacological magnetic resonance imaging (phMRI) permit measurement of in vivo changes in the brain after drug administration. However, there are numerous challenges when trying to apply this technique to commonly used animal models of disease, such as the mouse. This capstone project focuses on some of the data analysis issues faced when trying to analyze high-resolution mouse phMRI data. Many of the problems encountered were due to the small size of the mouse brain in comparison to the human brain and the fact that most available MRI software is designed for human data. This work is part of a larger project designed to measure changes in the mouse brain after alcohol administration.