This paper presents the approaches and methods for modeling and analysis of the open human cerebral cortex IRthermo maps. The main goal of the development is to solve fundamental problems: the selection of reliable informative features, which allow detecting abnormalities of the brain, to classify its types, and to delineate its boundaries. The created analytical tools are also directed to the studying fundamental problems related to the mechanisms of autoregulation and compensation in the brain. The described methods and approaches were tested on the real medical history.