A method of analyzing structure of a network of vessels in a medical image, comprising:receiving the medical image depicting the network of vessels;obtaining a mask of the network of vessels in the image; andgenerating a non-forest graph mapping a plurality of paths of vessels in the network to directed paths in the graph, with each edge in the graph either directed to indicate a known direction of flow in the corresponding vessel, or undirected to indicate a lack of knowledge of direction of flow in the corresponding vessel, and with all directed edges in a path directed in a same direction as the path.