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What is Image Registration and How is it helpful in targeting specific brain structures? What are the procedures involved in atlas based segmentation schemes and How is this important in image guided neurosurgical procedures? This book will cover mathematical concepts involved in image alignment and spatial transformations of 3D MR Images. As textbooks provide necessary tools to understand basic signal and image processing concepts and applications, this is a valuable reference book for scientists, and an essential source for upper-level undergraduate and graduate students to understand deep aspects of image registration and segmentation in MR Images. A special scheme of inter-subject registration is also presented which aids in locating subcortical and cerebellar structures in patients suffering from multiple diseases. Both subjective and objective analysis is provided to validate segmentation results.