This paper presents an automatic approach which classifies structural Magnetic Resonance images into pathological or healthy controls. A classification model was trained to find the boundaries that allow to separate the study groups. The method uses the deformation values from a set of regions, automatically identified as relevant, in a process that selects the statistically significant regions of a t-test under the restriction that this significance must be spatially coherent within a neighborhood of 5 voxels. The proposed method was assessed to distinguish healthy controls from schizophrenia patients. Classification results showed accuracy between 74% and 89%, depending on the stage of the disease and number of training samples