Understanding the organization of the human brain is the fundamental prerequisite for appreciating the neural dysfunctions underlying neurological or psychiatric disorders. One major challenge in this context is the presence of multiple organizational aspects, in particular the regional differentiation in structure and function on one hand and the integration by inter-regional connectivity on the other. We here review these fundamental distinctions and introduce current methods for mapping regional specialization. The main focus of this review is to provide an overview over the different concepts and methods for assessing connections and interactions in the brain, in particular anatomical, functional and effective connectivity. In this context, we focus less on technical details and more on the comparative description of strengths and weaknesses of different aspects of connectivity as well as different methods for examining a particular aspect. This overview closes by raising several open questions on the conceptual and empirical relationship between different approaches towards understanding brain structure, function and connectivity.
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