A method for automatic mismatch correction is presented. The method includes identifying a feature of interest in a reference image volume and a target image volume. Furthermore, the method includes computing a cost matrix based on one or more pairs of image slices in the reference image volume and the target image volume. The method also includes identifying one or more longest common matching regions in the reference image volume and the target image volume based on the computed cost matrix. In addition, the method includes aligning the reference image volume and the target image volume based on the identified one or more longest common matching regions. A non-transitory computer readable medium including one or more tangible media, where the one or more tangible media include code adapted to perform the method for automatic mismatch correction is also presented. Systems and non-transitory computer readable medium configured to perform the method for automatic mismatch correction of image volumes are also presented.