The article presents the hypothesis that the structure of human knowledge can be reflected in the structure of human consciousness, which in turn can manifest itself in a corresponding representation on the cerebral cortex. The appropriate mathematical techniques is described, based on the use of a matrix of mutual influence, which makes it possible to visualize the structure of human knowledge in the subject area on which the experts are interviewed. Based on this data an interaction matrix is built, which can make it possible to build predictive mathematical models of thinking. For these purposes it is proposed to conduct a series of experiments to study the activity of the network brain using MEG sensors and fMRI data, interviewing subjects using a matrix of mutual influences, and then analyze the collected data in order to find correlations between the “structure of human knowledge” and the “structure of the map of ontologies on the cerebral cortex”. In this article, we will try to outline algorithms for the practical implementation of experiments to test the idea of building an ontology map on the cerebral cortex, as well as methods for implementing some other projects based on the matrix of mutual influence.