Assessing the sequelae of a focal CNS injury across the entire neuroaxis holds great potential to better understand the temporal and spatial distributed pathophysiological changes. Currently, voxel-based analysis is either performed at the level of the spinal cord or brain. As a result, most imaging studies fail to implement and analyse the interactions between remote areas across the CNS. In this study, a new probabilistic-atlas including brain and cervical spinal cord (SC) was used for the simultaneous, fully automated and multi-parametric analysis in SPM framework. This approach was validated by assessing trauma-induced changes in SCI patients and compared with findings from analytical tools assessing the brain and cord separately.