Spinal cord injury (Sci) leads to widespread neurodegeneration across the neuroaxis. We explored trajectories of surface morphology, demyelination and iron concentration within the basal gangliathalamic circuit over 2 years post-SCI. This allowed us to explore the predictive value of neuroimaging biomarkers and determine their suitability as surrogate markers for interventional trials. changes in markers of surface morphology, myelin and iron concentration of the basal ganglia and thalamus were estimated from 182 MRI datasets acquired in 17 SCI patients and 21 healthy controls at baseline (1-month post injury for patients), after 3, 6, 12, and 24 months. Using regression models, we investigated group difference in linear and non-linear trajectories of these markers. Baseline quantitative MRI parameters were used to predict 24-month clinical outcome. Surface area contracted in the motor (i.e. lower extremity) and pulvinar thalamus, and striatum; and expanded in the motor thalamus and striatum in patients compared to controls over 2-years. In parallel, myelin-sensitive markers decreased in the thalamus, striatum, and globus pallidus, while iron-sensitive markers decreased within the left caudate. Baseline surface area expansions within the striatum (i.e. motor caudate) predicted better lower extremity motor score at 2-years. Extensive extrapyramidal neurodegenerative and reorganizational changes across the basal ganglia-thalamic circuitry occur early after Sci and progress over time; their magnitude being predictive of functional recovery. these results demonstrate a potential role of extrapyramidal plasticity during functional recovery after Sci. Spinal cord injury (SCI) leads to permanent functional deficits below the level of injury. Neurorehabilitation can foster sensorimotor recovery, but often only partial improvements can be achieved. Recovery is paralleled by a cascade of progressive neurodegenerative changes affecting the pyramidal, sensory and limbic system 1,2 ; its magnitude predicting functional recovery 1,2. In addition, compensatory changes within the extrapyramidal system might contribute to recovery as shown in the non-human primate model of SCI 3,4. For example, impaired information flow within the basal ganglia-thalamic circuit 5 and the motor cortex 6 was associated with abnormal activation patterns and increased functional connectivity in pallido-thalamocortical loops 6. However, in SCI patients, the role of the extrapyramidal system in sensorimotor recovery is understudied 7. To characterize structural trajectories of surface area and microstructural parameters, we modelled the MRI measures in terms of linear rate of change (reflecting degeneration/plasticity) and non-linear rate of change (reflecting acceleration/deceleration). In particularly, T1-weighted volumes were used to track trajectories of vertex-wise surface area contractions and expansions of the basal ganglia and thalamic subnuclei over 2-years. Myelin-sensitive magnetization transfer saturation (MT) and longitudinal relaxation ra...