In this paper, we propose a coding method to improve compression efficiency for MR image. This can be achieved by combining coding scheme and segmentation scheme which removes noisy background region, which is meaningless for diagnosis in the MR image. In segmentation algoritm, we use full-resolution wavelet transform to extract features of regions in image and Kohonen self-organizing map to classify the features. The subsequent wavelet coder encodes only diagnostically significant foreground regions refering to segmentation map. Our proposed algorithm provides about 15% of bit rate reduction when compared with the same coder which is not combined with segmentation scheme. And the proposed scheme shows better reconstructed image quality than JPEG at the same compression ratio.