In recent years, a number of new products introduced to the global market combine intelligent robotics, artificial intelligence and smart interfaces to provide powerful tools to support professional decision making. However, while brain disease diagnosis from the brain scan images is supported by imaging robotics, the data analysis to form a medical diagnosis is performed solely by highly trained medical professionals. Recent advances in medical imaging techniques, artificial intelligence, machine learning and computer vision present new opportunities to build intelligent decision support tools to aid the diagnostic process, increase the disease detection accuracy, reduce error, automate the monitoring of patient's recovery, and discover new knowledge about the disease cause and its treatment. This article introduces the topic of medical diagnosis of brain diseases from the MRI based images. We describe existing, multi-modal imaging techniques of the brain's soft tissue and describe in detail how are the resulting images are analyzed by a radiologist to form a diagnosis. Several comparisons between the best results of classifying natural scenes and medical image analysis illustrate the challenges of applying existing image processing techniques to the medical image analysis domain. The survey of medical image processing methods also identified several knowledge gaps, the need for automation of image processing analysis, and the identification of the brain structures in the medical images that differentiate healthy tissue from a pathology. This survey is grounded in the cases of brain tumor analysis and the traumatic brain injury diagnoses, as these two case studies illustrate the vastly different approaches needed to define, extract, and synthesize meaningful information from multiple MRI image sets for a diagnosis. Finally, the article summarizes artificial intelligence frameworks that are built as multi-stage, hybrid, hierarchical information processing work-flows and the benefits of applying these models for medical diagnosis to build intelligent physician's aids with knowledge transparency, expert knowledge embedding, and increased analytical quality.