Diverse cognitive processes set different demands on locally segregated and globally integrated brain activity. However, it remains unclear how resting brains configure their functional organization to balance the demands on network segregation and integration to best serve cognition. Here, we use an eigenmode-based approach to identify hierarchical modules in functional brain networks, and quantify the functional balance between network segregation and integration. In a large sample of healthy young adults (n=991), we combine the whole-brain resting state functional magnetic resonance imaging (fMRI) data with a mean-filed model on the structural network derived from diffusion tensor imaging and demonstrate that resting brain networks are on average close to a balanced state. This state allows for a balanced time dwelling at segregated and integrated configurations, and highly flexible switching between them. Furthermore, we employ structural equation modelling to estimate general and domain-specific cognitive phenotypes from nine tasks, and demonstrate that network segregation, integration and their balance in resting brains predict individual differences in diverse cognitive phenotypes. More specifically, stronger integration is associated with better general cognitive ability, stronger segregation fosters crystallized intelligence and processing speed, and individuals tendency towards balance supports better memory. Our findings provide a comprehensive and deep understanding of the brains functioning principles in supporting diverse functional demands and cognitive abilities, and advance modern network neuroscience theories of human cognition.
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