Selecting regions of interest (ROI) of the medical images is an important task in medical image processing. Manual selection of ROIs serves as the main method for single images and it has a high accuracy. However, it will become infeasible to manually segment ROIs on a large number of images. Observing this problem, this paper proposes a fast and accurate segmentation method to obtain ROIs on a batch of medical images. Firstly, we segment the standard brain image St which has not been injected with tracer. Secondly, we use a B-Spline elastic registration method to get the inverse-registration parameters. Thirdly, we get the template image Te with the registration parameters. Finally, we search the target region by template matching. Experimental results show that the proposed method performs well on medical image segmentation. © 2017, Society for Imaging Science and Technology.