This paper proposed an automated segmentation algorithm for MR brain images through the complementary use of T1-weighted, T2-weighted, and PD images. The proposed segmentation algorithm is composed of 3 steps. The first step involves the extraction of cerebrum images by placing a cerebrum mask over the three input images. In the second step, outstanding clusters that represent the inner tissues of the cerebrum are chosen from among the 3-dimensional (3D) clusters. The 3D clusters are determined by intersecting densely distributed parts of a 2D histogram in 3D space formed using three optimal scale images. The optimal scale image results from applying scale-space filtering to each 2D histogram and a searching graph structure. As a result, the optimal scale image can accurately describe the shape of the densely distributed pixel parts in the 2D histogram. In the final step, the cerebrum images are segmented by the FCM (Fuzzy c-means) algorithm using the outstanding cluster center value as the initial center value. The ability of the proposed segmentation algorithm to calculate the cluster center value accurately then compensates for the current limitation of the FCM algorithm, which is unduly restricted by the initial center value used. In addition, the proposed algorithm, which includes a multi spectral analysis, can achieve better segmentation results than a single spectral analysis.