A medical image processing system includes a memory and a processor coupled to each other. The processor accesses and executes instructions which memory stores to perform the following: obtaining a plurality of brain MR images corresponding to a subject, wherein the brain MR images corresponds to a subject brain space; accessing a DBS targets atlas corresponding to a specific stimulation area; transforming the DBS targets atlas from a MNI brain space to the subject brain space based on a DARTEL algorithm; marking at least one coordinate having a largest Voxel value in the brain MR images based on the transformed DBS targets atlas; and storing the brain MR images being targeted with the at least one coordinate into a predetermined format corresponding to a guiding device so that the guiding device displays the brain MR images being targeted with the at least one coordinate for guidance in DBS procedure.