Graph theory
Graph theory uses a matrix to characterize covariance between regions, which is then transformed into a network map. The problem with graph theory analysis is that network mapping is heavily influenced by "a priori" brain region and connectivity (nodes and edges). This places the researcher at risk of cherry-picking regions and connections according to their own preconceived theories. However, graph theory analysis is still considered extremely valuable, as it is the only method that gives pair-wise relationships between nodes.