We present two new clustering algorithms for medical image segmentation based on the multimodal image registration and the information bottleneck method. In these algorithms, the histogram bins of two registered multimodal 3D-images are clustered by minimizing the loss of mutual information between them. Thus, the clustering of histogram bins is driven by the preservation of the shared information between the images, extracting from each image the structures that are more relevant to the other one. In the first algorithm, we segment only one image at a time, while in the second both images are simultaneously segmented. Experiments show the good behavior of the presented algorithms, especially the simultaneous clustering.