An automatic segmentation and classification method of magnetic resonance image of human brain based on a computerized brain atlas-TT atlas is introduced in this paper. The algorithm could be divided into two steps. Firstly, the object brain dataset is registered with the TT atlas by a 3D image matching method. With the help of anatomy structure information of the computerized atlas, the brain image is segmented and classified coarsely. Secondly, the segmentation result is taken as the input of a fuzzy cluster segmentation. In order to use the anatomic structure information directly, a new fuzzy cluster method with a shape factor is introduced, the method is mostly and automatically except selection of some intrinsic point pairs for global linear matching method in the first step.