The present article gives an analytical overview of the current state of processing problems and visualization of magnetic resonance imaging (MRI). It is presented the expediency of combining of instrumental means, presented in various open-source programs and scientific publications in recent years, into a single program-tool complex solving in full problems of pre-processing and filtering data, directed precision thematic segmentation and analysis of images, forming the feature space, recognition of the situation, 3D modeling, and visualization. The complex is designed for expert decision support of doctors-researchers in the process of carrying out scientific experiments. Support is based on the application of new methods of brain area texture analysis, effective metrics, and advanced means of cognitive computer graphics. An important feature of the complex must be the interactive operating mode of the doctor-researcher with MRI data, which can be provided by applying high-performance computing with software support of hardware accelerators.