The tremendous pace of development in brain imaging technologies has revolutionized our ability to investigate brain structure and function. Techniques are now available to capture features of anatomy and function at both molecular and whole-brain scales, mapping neuronal dynamics and gene expression as well as growth and degenerative processes that span multiyear time scales. The number of brain imaging investigations is also increasing exponentially. A major goal of these studies is to analyze how the dynamically changing brain varies across age, gender, disease, across multiple imaging modalities, and in large human populations. To tackle these questions, many laboratories are using sophisticated algorithms for brain image analysis. Engineering approaches drawn from computer vision, image analysis, computer graphics, and artificial intelligence research fields are required to manipulate, analyze, and communicate brain data. Novel image analysis algorithms continue to uncover new patterns of altered structure and function in individuals and clinical populations, and mathematical strategies are being developed to relate these patterns to clinical, demographic, and genetic parameters.
In this chapter, we review current challenges in brain image analysis, focusing on the main algorithms, their technical foundations, and their scientific and clinical applications. The approaches include methods for automated registration and segmentation, anatomical parameterization and modeling, tissue classification and shape analysis, and pathology detection in individuals or groups. Algorithms are also described for generating digital brain atlases. Atlases are fundamental to brain image analysis, as they offer a powerful framework to synthesize the results of disparate imaging studies. Built from one or more representations of the brain, atlases are annotated representations of anatomy in a 3D coordinate system. They serve as standardized templates on which other brain maps can be overlaid, for subsequent comparison and integration. To align new imaging data with an atlas, a variety of registration algorithms may be employed (see also Chapter 8 for other applications). Once registered, brain maps can be pooled across subjects and combined mathematically and statistically. As such, atlases provide a standardized 3D coordinate system to express observations from different individuals and a framework for interlaboratory communication.
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