A method for correcting registration misalignment in magnetic resonance perfusion images includes receiving a time series of magnetic resonance images of an anatomical organ, each image comprising a plurality of intensities defined on an N-dimensional domain of points, performing a first group-wise registration of all images in the time series of images using a pair-wise registration as an initialization, detecting a misaligned image from the group-wise registration by analyzing a total variation of intensity differences between consecutive images, and correcting the misaligned image by optimizing a second group-wise energy function over registration parameters of the misaligned image.