Understanding complex systems such as the human brain requires characterization of the system's architecture across multiple levels of organization-from neurons, to local circuits, to brain regions, and ultimately large-scale brain networks. Here we focus on characterizing the human brain's large-scale network organization, as it provides an overall framework for the organization of all other levels. We developed a highly principled approach to identify cortical network communities at the level of functional systems, calibrating our community detection algorithm using extremely well-established sensory and motor systems as guides. Building on previous network partitions, we replicated and expanded upon well-known and recently-identified networks, including several higher-order cognitive networks such as a left-lateralized language network. We expanded these cortical networks to subcortex, revealing 358 highly-organized subcortical parcels that take part in forming whole-brain functional networks. Notably, the identified subcortical parcels are similar in number to a recent estimate of the number of cortical parcels (360). This whole-brain network atlas-released as an open resource for the neuroscience community-places all brain structure s across both cortex and subcortex into a single large-scale functional framework, with the potential to facilitate a variety of studies investigating large-scale functional networks in health and disease.

Resting-state functional connectivity (FC) has helped reveal the intrinsic network organization of the human brain, yet its relevance to cognitive task activations has been unclear. Uncertainty remains despite evidence that resting-state FC patterns are highly similar to cognitive task activation patterns. Identifying the distributed processes that shape localized cognitive task activations may help reveal why resting-state FC is so strongly related to cognitive task activations. We found that estimating task-evoked activity flow (the spread of activation amplitudes) over resting-state FC networks allows prediction of cognitive task activations in a large-scale neural network model. Applying this insight to empirical functional MRI data, we found that cognitive task activations can be predicted in held-out brain regions (and held-out individuals) via estimated activity flow over resting-state FC networks. This suggests that task-evoked activity flow over intrinsic networks is a large-scale mechanism explaining the relevance of resting-state FC to cognitive task activations.

The frontoparietal control network (FPCN) plays a central role in executive control. It has been predominantly viewed as a unitary domain general system. Here, we examined patterns of FPCN functional connectivity (FC) across multiple conditions of varying cognitive demands, to test for FPCN heterogeneity. We identified two distinct subsystems within the FPCN based on hierarchical clustering and machine learning classification analyses of within-FPCN FC patterns. These two FPCN subsystems exhibited distinct patterns of FC with the default network (DN) and the dorsal attention network (DAN). FPCN exhibited stronger connectivity with the DN than the DAN, whereas FPCN exhibited the opposite pattern. This twofold FPCN differentiation was observed across four independent datasets, across nine different conditions (rest and eight tasks), at the level of individual-participant data, as well as in meta-analytic coactivation patterns. Notably, the extent of FPCN differentiation varied across conditions, suggesting flexible adaptation to task demands. Finally, we used meta-analytic tools to identify several functional domains associated with the DN and DAN that differentially predict activation in the FPCN subsystems. These findings reveal a flexible and heterogeneous FPCN organization that may in part emerge from separable DN and DAN processing streams. We propose that FPCN may be preferentially involved in the regulation of introspective processes, whereas FPCN may be preferentially involved in the regulation of visuospatial perceptual attention.

Cognition and behavior emerge from brain network interactions, such that investigating causal interactions should be central to the study of brain function. Approaches that characterize statistical associations among neural time series-functional connectivity (FC) methods-are likely a good starting point for estimating brain network interactions. Yet only a subset of FC methods ("effective connectivity") are explicitly designed to infer causal interactions from statistical associations. Here we incorporate best practices from diverse areas of FC research to illustrate how FC methods can be refined to improve inferences about neural mechanisms, with properties of causal neural interactions as a common ontology to facilitate cumulative progress across FC approaches. We further demonstrate how the most common FC measures (correlation and coherence) reduce the set of likely causal models, facilitating causal inferences despite major limitations. Alternative FC measures are suggested to immediately start improving causal inferences beyond these common FC measures.

Resting-state functional connectivity (FC) has helped reveal the intrinsic network organization of the human brain, yet its relevance to cognitive task activations has been unclear. Uncertainty remains despite evidence that resting-state FC patterns are highly similar to cognitive task activation patterns. Identifying the distributed processes that shape localized cognitive task activations may help reveal why resting-stateFC is so strongly related to cognitive task activations. We found that estimating task-evoked activity flow (the spread of activation amplitudes) over resting-state FC networks allows prediction of cognitive task activations in a large-scale neural network model. Applying this insight to empirical functional MRI data, we found that cognitive task activations can be predicted in held-out brain regions (and held-out individuals via estimated activity flow over resting-state FC networks. This suggests that task-evoked activity flow over intrinsic networks is a large-scale mechanism explaining the relevance of resting-state FC to cognitive task activations.