An agent-based modeling system for predicting and/or analyzing brain behavior is provided. The system includes a computer processor configured to define nodes and edges that interconnect the nodes. The edges are defined by physiological interactions and/or anatomical connections. The computer processor further defines rules and/or model parameters that define a functional behavior of the nodes and edges. The computer processor assigns the nodes to respective brain regions, and the rules and/or model parameters are defined by observed physiological interaction of the nodes that are functionally and/or structurally connected by said edges of brain regions to thereby provide an agent-based brain model (ABBM) for predicting and/or analyzing brain behavior.