Brain Atlasing: Design Principles, Methods, Tools and Applications

Abstract

We recently witness unprecedented big brain projects. Our contribution to these global, brain-related efforts is to create adult human brain atlases and develop atlas-based applications. The objectives of this work are to provide a concise general overview of our brain atlas efforts in terms of design principles, methods, tools and applications; to differentiate our efforts from the existing big brain atlas projects; and to summarize a potential usefulness of our brain atlases in the BRAIN Initiative. We have created so far 34 brain atlases applied in education, research and clinical applications. Dedicated atlas-based solutions have been proposed and developed for stereotactic and functional neurosurgery, stroke image analysis, scan interpretation, brain cancer, and human brain mapping in neurosurgery. The latest generation of our brain atlases has been constructed from in vivo imaging by employing multiple magnetic resonance (MR) 3 and 7 Tesla, and high resolution computed tomography (CT) scans of the same brain (male) specimen. The brain (and some head and neck) model has been subdivided into about 3,000 three-dimensional components, including the cerebrum, cerebellum, brainstem, spinal cord, white matter, deep gray nuclei, ventricles, intracranial arteries, intracranial veins, dural sinuses, white matter tracts, visual system, cranial nerves, extracranial arteries, extracranial veins, head muscles, pharynx, glands, cervical vertebrae, skull, and skin. We address design principles, brain atlas definition and characterization from anatomic and computer graphics perspectives, techniques, tools, and functionality. In contrast to the ongoing initiatives, our approach is guided by research, clinical and market perspectives, is top-down and holistic. The latest brain atlas is potentially useful in the BRAIN Initiative as a reference for enormous amounts of data to be generated, a framework for result integration and interpretation, a potential 4D “Wikipedia” for the community, a vehicle to present and disseminate the discoveries from science to medicine to public, and an education tool reducing a difficulty barrier.