Chronic Traumatic Encephalopathy (CTE) is a neurodegenerative disease associated with exposure to repetitive head impacts. This study aims to characterize the differing clinical presentations of CTE using MR Spectroscopy and Diffusion Tensor Imaging. Unsupervised Learning was first used to divide a cohort of former NFL players into sub-groups based on the degree of mood/behavior symptoms and cognitive impairment relative to controls. The neurometabolite concentrations and measures of diffusivity were then compared between the sub-groups. Athletes with increased mood/behavior symptoms showed alterations reflective of neuroinflammation, whereas the cognitive impairment sub-group showed more neuronal and structural alterations.