In patients with chronic spinal cord injury, imaging of the spinal cord and brain above the level of the lesion provides evidence of neural degeneration; however, the spatial and temporal patterns of progression and their relation to clinical outcomes are uncertain. New interventions targeting acute spinal cord injury have entered clinical trials but neuroimaging outcomes as responsive markers of treatment have yet to be established. We aim to use MRI to assess neuronal degeneration above the level of the lesion after acute spinal cord injury. In our prospective longitudinal study, we enroll patients with acute traumatic spinal cord injury and healthy controls. We assess patients clinically and by MRI at baseline, 2 months, 6 months, and 12 months 24 months and 60 months, and controls by MRI at the same timepoints. We assess atrophy in white and brain matter and we use cross-sectional spinal cord area measurements to assess atrophy at cervical level C2/C3. We use myelin-sensitive magnetisation transfer (MT) and longitudinal relaxation rate (R1) maps to assess microstructural changes associated with myelin. We also assess associations between MRI parameters and clinical improvement.