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The ultimate goal of this paper is to develop a novel personalized comprehensive computer aided diagnostic (CAD) system for precise diagnosis of autism spectrum disorder (ASD) based on the 3D shape analysis of the cerebral cortex (Cx), To achieve the main goal of the proposed system, we used structural MRI modality (sMRI) to be able to extract the shape features of the brain cortex. After segmenting the brain cortex from sMRI, we used a spherical harmonics analysis to measure the surface complexity, in addition to studying surface curvatures. Finally, a multi-stage deep network based on several autoencoders and softmax classifiers is constructed to provide the final global diagnosis. The presented CAD system was tested on several datasets, achieving an average accuracy of 92.15%. In addition to its global diagnostic accuracy, the local diagnostic accuracies of the most significant areas also demonstrated …