Systems and methods for mapping neuronal circuitry in accordance with embodiments of the invention are illustrated. One embodiment includes a method for generating a neuronal shape graph, including obtaining functional brain imaging data from an imaging device, where the functional brain imaging data includes a time-series of voxels describing neuronal activation over time in a patient's brain, lowering the dimensionality of the functional brain imaging data to a set of points, where each point represents the brain state at a particular time in the timeseries, binning the points into a plurality of bins, clustering the binned points, and generating a shape graph from the clustered points, where nodes in the shape graph represent a brain state and edges between the nodes represent transitions between brain states.