The intrinsic functional architecture of the brain and its alterations due to cognitive engagement, ageing and diseases are nodal topics in neuroscience, attracting considerable attention from many disciplines of scientific investigation. Complex network theory offers powerful tools to investigate brain connectivity disclosing the structure of the human brain functional network. Here we put forward a number of methods to investigate the network of brain areas coupled by their functional coordination without introducing exogenous thresholds. In this way we overcame the problem of having a fully connected network and found the intrinsic structure of the functional architecture of the brain.
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