Spinal cord injury (SCI) triggers a cascade of neurodegenerative and compensatory changes across the neuroaxis. Rehabilitative training has been shown to improve clinical outcome following SCI. However, the spatial and temporal patterns of neurodegenerative processes follow a complicated trajectory over 2-years. Previous studies have already shown trauma-induced neurodegenerative processes and highlight the relationships amongst these in the cord and brain. Here, we investigate the trajectories of neurodegenerative changes that occur over a period of 5 years post-SCI.