Systems and methods predict functional and cognitive recovery of a person after the person has experienced a brain injury such as traumatic brain injury, cerebrovascular disease, and stroke. A computer system includes a database that stores multimodal data of the person recovering from a brain injury and a computer that analyzes the multimodal data over multiple intervals that span several months of time. The computer executes longitudinal heterogeneous trajectory analysis on the multimodal data and executes separation of heterogeneous groups that include good recovery potential of the brain injury, moderate recovery potential of the brain injury, and poor recovery potential of the brain injury. Based on the longitudinal heterogeneous trajectory analysis and the separation of the heterogeneous groups, the computer predicts functional recovery of the person from the brain injury.