A method and system for brain tumor segmentation in multi-spectral 3D MRI images is disclosed. A trained probabilistic boosting tree (PBT) classifier is used to determine, for each voxel in a multi-spectral 3D MR image sequence, a probability that the voxel is part of a brain tumor. The brain tumor is then segmented in the multi-spectral 3D MRI image sequence using graph cuts segmentation based on the probabilities determined using the trained PBT classifier and intensities of the voxels in the multi-spectral 3D MR image sequence.