This book is a complete reference that guides researchers to solve the simulation problem from the very basic level up of brain structure up to simulation level. It takes into consideration how to deal with DICOM medical images from scratch. The suitable medical image for brain modeling is the Diffusion Tensor MRI (DTI). Converting DTI images into meaningful scalar indexes for further processing is also discussed in details. Enhancing images using different image processing techniques is also discussed. Clustering brain images into White Matter (WM), Gray Matter (GM) and CSF fluid is also discussed as preprocessing for brain images before the modeling of its electrical activities. Finally, finite element model for reaction diffusion equation is discussed in details. Matlab codes for implementation are also included in the book.