A segmentation method comprises clustering spatial, intensity and volumetric shape index to automatically segment a medical lesion. The algorithm has the following steps: (1) calculating volumetric shape index (SI) for each voxel in the image; (2) combining the SI features with the intensity range and the spatial position (x, y, z) to form a 5-dimensional feature vector set; (3) grouping the 5-dimensional feature vector set into clusters; (4) employing a modified expectation-maximization algorithm (EM) considering not only spatial but also shape features on an intensity mode map from the clustering algorithm to merge the neighbouring regions or modes. The joint spatial-intensity-shape feature provides rich information for the segmentation of the anatomic structures of interest, such as lesions or tumours.