The brain network is the function of a structurally and functionally organized complex system. Its structure and activity analysis is one of the most significant challenges. The graph based techniques of brain complex networks have been successfully used in various types of image and medical data analysis. In this survey paper, we focus on a comprehensive study of the analytical methods for complex brain network based on graph theory. This review paper is intended to provide automated brain disease diagnosis based on functional and diffusional MRI modalities. Furthermore, we discuss subjective and objective quality evaluations of complex brain networks, important tools for automated brain disease diagnosis, challenging issues and future research directions in this increasingly evolving research field.