Medical image registration is a key step of image processing and analysis and the first problem of medical image fusion to be solved. In this paper, we focus on magnetic resonance images registration for preoperative and postoperative of deep brain stimulation for the Parkinson's disease. First of all, mutual distance is brought into the mutual information in this paper, realize the two groups of MR slices (for both preoperative and postoperative) mapping, and then 3D images are reconstructed from the corresponding MR slices. Finally, we use Powell algorithm to register 3D images. After the 3D images is registered, we can analyze the relative position between planted electrode (postoperative) and the subthalamic nucleus (preoperative), and measure the quality of deep brain stimulation scientifically.