Widefield optical imaging enables longitudinal capturing of the large-scale network activity of the cerebral cortex in awake behaving animals. Utilizing this technique, we investigate how the brain's functional network structure is altered following injury. Cortical activity in transgenic calcium reporter mice expressing GCaMP6s is recorded in two sessions, prior and after inducing the injury. As a quantitative network measure, 'communicability' which is indicative of how easily the information flows between nodes in a network via both direct and indirect paths, is considered. Compared to control subjects, results confirm altered functional network structure after the injury. Links that significantly contribute to the altered connectivity after the injury are spatially localized. It is shown that spectral clustering applied to the communicability networks is capable of distinguishing trials associated with pre-and post-injury sessions, suggesting that this approach can be used as an effective way to track changes in brain networks following the injury, and potentially, towards recovery.