Stroke is a leading cause of death and disability worldwide. However, the misalignment between multi-contrast MR images bring difficulties in identifying the lesions. We propose an automatic framework including affine and deformation transformation for multi-contrast stroke images registration. In the framework, a new inverse operation is proposed to maintain the topology of images and a background suppression loss function is designed to optimize background predictions. The method achieves the best Dice score of 0.826 compared to 5 state-of-the-art methods. Moreover, our method is about 17 times faster than the most competitive method SyN when testing on a same CPU.
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