A 3D Digital Brain Atlas System Based On Talairach-Tournoux Atlas

3D digital brain atlases are convenient and useful tools in neuroanatomy that can provide neurosurgeons valuable references during the planning of intervention. Since a printed atlas book can not fulfill the requirements, many groups work on the development of 3D digital brain atlases.To generate a digital brain atlas, we need to segment and extract brain structures from images of an individual brain. However, many of the brain structures can hardly be accurately segmented if only according to the content of them. The goal of this thesis is to develop an experiment flatform, which focuses on the basic methods about labeling, extraction, segmentation and visualization brain structures in MR images by leveraging the anatomic information and topological structure in standard atlas.We chose the Talairach-Tournoux atlas as the standard atlas, since it is widely used by neurosurgical research community. We transferred the atlas and MR images into the same coordinate frame based on anatomic knowledge, and adapted a piecewise affine transformation according to space information in Talairach coordinate frame and MR images.We used Thin-plate Splines (TPS) in the nonlinear registration of images and atlas. In our experiments, corpus callosum and thalamus are presented as examples. Experimental results show TPS is fast, effective, and stable. We also designed a semiautomatic method to get markers in TPS matching, and the experiment results show this method is convenient and feasible.After the segmentation of corpus callosum and thalamus, we used two shape-based interpolation methods. Both of the methods based on distance transform and based on morphology can get reasonable results, but the former approach is more convenient.We also visualized corpus callosum and thalamus in 3D, during which Marching cubes algorithm and Ray casting algorithm are performed.In this thesis, we explored the basic approaches of realizing digital 3D brain atlas and developed a research flatform based on standard atlas. Finally we discussed possible directions for extensions.