Stereotactic digital brain atlas was developed from the complete serial histological section of the brain of Japanese. Further, the methods of making averaged brain surface model from neuroimages of many healthy volunteers by use of the self-organizing deformable model, mapping with parameterization that preserves the area and angle of patches of brain surface and also estimating the internal structures of a patient brain by deforming a standard brain atlas by the finite element model were developed. Using our stereotactic atlas of Japanese brain, we analyzed the relationship between the simulation of the current field around DBS lead and the target neural structure; namely, the relationships between the therapeutic effect and abnormal current field of DBS which involves short circuit, between the tolerance to DBS and the lead positioning in the internal pallidum of dystonia and between the long-term effect and the lead positioning in the subthalamic nucleus of Parkinson’s disease.