Disclosed herein are a method and a system for creating a registered image that integrates the information of CT and CBCT images. With the present method and system, medical practitioners can precisely transform the information of CT image-based treatment plan into the CBCT image so as to accurately control the dosage and location of a radiation therapy. Accordingly, also disclosed herein are methods of treating a cancer in the subject with the aid of the method and/or system of the present disclosure.