Tractography is a method that finds fiber tracts within a sample (e.g. a mouse brain), which allows users to better understand how different regions and structures of the brain are connected. The only animal magnetic resonance imaging (MRI) centre in Manitoba does not have the software to perform tractography on their images. This severely limits the variation of studies that can be performed in the centre. The goal of this project was to develop a robust tractography analysis method for the centre. The designed tractography analysis method was tested on known phantoms (objects which are meant to mimic tissue) such as celery, and then on animal brain samples from various mouse models of multiple sclerosis and Alzheimer's disease. The first test of the tractography analysis method was to determine if the tracts within the corpus collosum in the brain of mice differ between mouse models. Tracts in the corpus callosum were measured using the developed tractography analysis method.Single factor ANOVA found no differences between the tractography parameters in tracts of the corpora callosa in a mouse model of multiple sclerosis (MS) and the corresponding wildtype mouse, nor between a mouse model of Alzheimer's disease (AD) and its corresponding wildtype mouse. The tractography analysis method was successfully developed and is now ready for use in more complex models.