The Buffalo Neuroimaging Analysis Center assesses brains of living humans with magnetic resonance imaging (MRI) data compiled from healthy controls and persons with neurological diseases. In neuroscience research with MRI, a connectome is the inter-connectivity of brain regions according to white matter tracts and the functional relationships of activity between structures. Multiple sclerosis (MS) is a neurodegenerative disease affecting myelin, white matter tracts, and grey matter. Lesions in the brain caused by MS may disrupt the healthy, natural function of underlying white matter tracts and the relationship of activity between brain regions. Complex protocols to process and analyze connectome data in healthy controls have been developed by the Human Connectome Project (HCP) research consortium fostered by the National Institutes of Health. However, these protocols require adaptation so that they may be applied to connectome data collected from persons with MS. We are designing protocols according to HCP guidelines to accurately reconstruct images of structural and functional connectivity in brains of people with MS. This processing involves many steps drawing from many neuroscience softwares and includes correcting for distortions from movement, eddy currents, and differences in the magnetic susceptibilities of brain regions, removing outlying tissue and bone and extracting only the brain, aligning and registering images for comparison, file type conversions, estimating fibre orientations, and applying probabilistic tractography over deterministic tractography to estimate more than one fibre and orientation per base three-dimensional space. Each step requires careful monitoring. More accurate representations of the effects of these lesions and how they interrupt white matter tracts and functional connectivity in the brain by connectome mapping will help us better understand the pathophysiological mechanisms associated with neuropsychological and neuropsychiatric dysfunction in MS.