Network modeling of dynamic brain interactions predicts emergence of neural information that supports human cognitive behavior.

How cognitive task behavior is generated by brain network interactions is a central question in neuroscience. Answering this question calls for the development of novel analysis tools that can firstly capture neural signatures of task information with high spatial and temporal precision (the "where and when") and then allow for empirical testing of alternative network models of brain function that link information to behavior (the "how"). We outline a novel network modeling approach suited to this purpose that is applied to noninvasive functional neuroimaging data in humans. We first dynamically decoded the spatiotemporal signatures of task information in the human brain by combining MRI-individualized source electroencephalography (EEG) with multivariate pattern analysis (MVPA). A newly developed network modeling approach-dynamic activity flow modeling-then simulated the flow of task-evoked activity over more causally interpretable (relative to standard functional connectivity [FC] approaches) resting-state functional connections (dynamic, lagged, direct, and directional). We demonstrate the utility of this modeling approach by applying it to elucidate network processes underlying sensory-motor information flow in the brain, revealing accurate predictions of empirical response information dynamics underlying behavior. Extending the model toward simulating network lesions suggested a role for the cognitive control networks (CCNs) as primary drivers of response information flow, transitioning from early dorsal attention network-dominated sensory-to-response transformation to later collaborative CCN engagement during response selection. These results demonstrate the utility of the dynamic activity flow modeling approach in identifying the generative network processes underlying neurocognitive phenomena.

Functionality of arousal-regulating brain circuitry at rest predicts human cognitive abilities.

Arousal state is regulated by subcortical neuromodulatory nuclei, such as locus coeruleus, which send wide-reaching projections to cortex. Whether higher-order cortical regions have the capacity to recruit neuromodulatory systems to aid cognition is unclear. Here, we hypothesized that select cortical regions activate the arousal system, which, in turn, modulates large-scale brain activity, creating a functional circuit predicting cognitive ability. We utilized the Human Connectome Project 7T functional magnetic resonance imaging dataset (n = 149), acquired at rest with simultaneous eye tracking, along with extensive cognitive assessment for each subject. First, we discovered select frontoparietal cortical regions that drive large-scale spontaneous brain activity specifically via engaging the arousal system. Second, we show that the functionality of the arousal circuit driven by bilateral posterior cingulate cortex (associated with the default mode network) predicts subjects' cognitive abilities. This suggests that a cortical region that is typically associated with self-referential processing supports cognition by regulating the arousal system.

Acute psychosocial stress modulates neural and behavioral substrates of cognitive control.

Acute psychosocial stress affects learning, memory, and attention, but the evidence for the influence of stress on the neural processes supporting cognitive control remains mixed. We investigated how acute psychosocial stress influences performance and neural processing during the Go/NoGo task-an established cognitive control task. The experimental group underwent the Trier Social Stress Test (TSST) acute stress induction, whereas the control group completed personality questionnaires. Then, participants completed a functional magnetic resonance imaging (fMRI) Go/NoGo task, with self-report, blood pressure and salivary cortisol measurements of induced stress taken intermittently throughout the experimental session. The TSST was successful in eliciting a stress response, as indicated by significant Stress > Control between-group differences in subjective stress ratings and systolic blood pressure. We did not identify significant differences in cortisol levels, however. The stress induction also impacted subsequent Go/NoGo task performance, with participants who underwent the TSST making fewer commission errors on trials requiring the most inhibitory control (NoGo Green) relative to the control group, suggesting increased vigilance. Univariate analysis of fMRI task-evoked brain activity revealed no differences between stress and control groups for any region. However, using multivariate pattern analysis, stress and control groups were reliably differentiated by activation patterns contrasting the most demanding NoGo trials (i.e., NoGo Green trials) versus baseline in the medial intraparietal area (mIPA, affiliated with the dorsal attention network) and subregions of the cerebellum (affiliated with the default mode network). These results align with prior reports linking the mIPA and the cerebellum to visuomotor coordination, a function central to cognitive control processes underlying goal-directed behavior. This suggests that stressor-induced hypervigilance may produce a facilitative effect on response inhibition which is represented neurally by the activation patterns of cognitive control regions.

Causally informed activity flow models provide mechanistic insight into network-generated cognitive activations.

Brain activity flow models estimate the movement of task-evoked activity over brain connections to help explain network-generated task functionality. Activity flow models have been shown to accurately generate task-evoked brain activations across a wide variety of brain regions and task conditions. However, these models have had limited explanatory power, given known issues with causal interpretations of the standard functional connectivity measures used to parameterize activity flow models. We show here that functional/effective connectivity (FC) measures grounded in causal principles facilitate mechanistic interpretation of activity flow models. We progress from simple to complex FC measures, with each adding algorithmic details reflecting causal principles. This reflects many neuroscientists' preference for reduced FC measure complexity (to minimize assumptions, minimize compute time, and fully comprehend and easily communicate methodological details), which potentially trades off with causal validity. We start with Pearson correlation (the current field standard) to remain maximally relevant to the field, estimating causal validity across a range of FC measures using simulations and empirical fMRI data. Finally, we apply causal-FC-based activity flow modeling to a dorsolateral prefrontal cortex region (DLPFC), demonstrating distributed causal network mechanisms contributing to its strong activation during a working memory task. Notably, this fully distributed model is able to account for DLPFC working memory effects traditionally thought to rely primarily on within-region (i.e., not distributed) recurrent processes. Together, these results reveal the promise of parameterizing activity flow models using causal FC methods to identify network mechanisms underlying cognitive computations in the human brain.

Dorsal attention network activity during perceptual organization is distinct in schizophrenia and predictive of cognitive disorganization.

Visual shape completion is a canonical perceptual organization process that integrates spatially distributed edge information into unified representations of objects. People with schizophrenia show difficulty in discriminating completed shapes, but the brain networks and functional connections underlying this perceptual difference remain poorly understood. Also unclear is whether brain network differences in schizophrenia occur in related illnesses or vary with illness features transdiagnostically. To address these topics, we scanned (functional magnetic resonance imaging, fMRI) people with schizophrenia, bipolar disorder, or no psychiatric illness during rest and during a task in which they discriminated configurations that formed or failed to form completed shapes (illusory and fragmented condition, respectively). Multivariate pattern differences were identified on the cortical surface using 360 predefined parcels and 12 functional networks composed of such parcels. Brain activity flow mapping was used to evaluate the likely involvement of resting-state connections for shape completion. Illusory/fragmented task activation differences ('modulations') in the dorsal attention network (DAN) could distinguish people with schizophrenia from the other groups (AUCs > .85) and could transdiagnostically predict cognitive disorganization severity. Activity flow over functional connections from the DAN could predict secondary visual network modulations in each group, except in schizophrenia. The secondary visual network was strongly and similarly modulated in each group. Task modulations were dispersed over more networks in patients compared to controls. In summary, DAN activity during visual perceptual organization is distinct in schizophrenia, symptomatically relevant, and potentially related to improper attention-related feedback into secondary visual areas.

Global connectivity fingerprints predict the domain generality of multiple-demand regions.

A set of distributed cognitive control networks are known to contribute to diverse cognitive demands, yet it is unclear how these networks gain this domain-general capacity. We hypothesized that this capacity is largely due to the particular organization of the human brain's intrinsic network architecture. Specifically, we tested the possibility that each brain region's domain generality is reflected in its level of global (hub-like) intrinsic connectivity as well as its particular global connectivity pattern ("connectivity fingerprint"). Consistent with prior work, we found that cognitive control networks exhibited domain generality as they represented diverse task context information covering sensory, motor response, and logic rule domains. Supporting our hypothesis, we found that the level of global intrinsic connectivity (estimated with resting-state functional magnetic resonance imaging [fMRI]) was correlated with domain generality during tasks. Further, using a novel information fingerprint mapping approach, we found that each cognitive control region's unique rule response profile("information fingerprint") could be predicted based on its unique intrinsic connectivity fingerprint and the information content in regions outside cognitive control networks. Together, these results suggest that the human brain's intrinsic network architecture supports its ability to represent diverse cognitive task information largely via the location of multiple-demand regions within the brain's global network organization.

The Functional Relevance of Task-State Functional Connectivity.

Resting-state functional connectivity has provided substantial insight into intrinsic brain network organization, yet the functional importance of task-related change from that intrinsic network organization remains unclear. Indeed, such task-related changes are known to be small, suggesting they may have only minimal functional relevance. Alternatively, despite their small amplitude, these task-related changes may be essential for the ability of the human brain to adaptively alter its functionality via rapid changes in inter-regional relationships. We used activity flow mapping-an approach for building empirically derived network models-to quantify the functional importance of task-state functional connectivity (above and beyond resting-state functional connectivity) in shaping cognitive task activations in the (female and male) human brain. We found that task-state functional connectivity could be used to better predict independent fMRI activations across all 24 task conditions and all 360 cortical regions tested. Further, we found that prediction accuracy was strongly driven by individual-specific functional connectivity patterns, while functional connectivity patterns from other tasks (task-general functional connectivity) still improved predictions beyond resting-state functional connectivity. Additionally, since activity flow models simulate how task-evoked activations (which underlie behavior) are generated, these results may provide mechanistic insight into why prior studies found correlations between task-state functional connectivity and individual differences in behavior. These findings suggest that task-related changes to functional connections play an important role in dynamically reshaping brain network organization, shifting the flow of neural activity during task performance.SIGNIFICANCE STATEMENT Human cognition is highly dynamic, yet the functional network organization of the human brain is highly similar across rest and task states. We hypothesized that, despite this overall network stability, task-related changes from the intrinsic (resting-state) network organization of the brain strongly contribute to brain activations during cognitive task performance. Given that cognitive task activations emerge through network interactions, we leveraged connectivity-based models to predict independent cognitive task activations using resting-state versus task-state functional connectivity. This revealed that task-related changes in functional network organization increased prediction accuracy of cognitive task activations substantially, demonstrating their likely functional relevance for dynamic cognitive processes despite the small size of these task-related network changes.

A Whole-Brain and Cross-Diagnostic Perspective on Functional Brain Network Dysfunction.

A wide variety of mental disorders have been associated with resting-state functional network alterations, which are thought to contribute to the cognitive changes underlying mental illness. These observations appear to support theories postulating large-scale disruptions of brain systems in mental illness. However, existing approaches isolate differences in network organization without putting those differences in a broad, whole-brain perspective. Using a graph distance approach-connectome-wide similarity-we found that whole-brain resting-state functional network organization is highly similar across groups of individuals with and without a variety of mental diseases. This similarity was observed across autism spectrum disorder, attention-deficit hyperactivity disorder, and schizophrenia. Nonetheless, subtle differences in network graph distance were predictive of diagnosis, suggesting that while functional connectomes differ little across health and disease, those differences are informative. These results suggest a need to reevaluate neurocognitive theories of mental illness, with a role for subtle functional brain network changes in the production of an array of mental diseases. Such small network alterations suggest the possibility that small, well-targeted alterations to brain network organization may provide meaningful improvements for a variety of mental disorders.

Developing control-theoretic objectives for large-scale brain dynamics and cognitive enhancement.

The development of technologies for brain stimulation provides a means for scientists and clinicians to directly actuate the brain and nervous system. Brain stimulation has shown intriguing potential in terms of modifying particular symptom clusters in patients and behavioral characteristics of subjects. The stage is thus set for optimization of these techniques and the pursuit of more nuanced stimulation objectives, including the modification of complex cognitive functions such as memory and attention. Control theory and engineering will play a key role in the development of these methods, guiding computational and algorithmic strategies for stimulation. In particular, realizing this goal will require new development of frameworks that allow for controlling not only brain activity, but also latent dynamics that underlie neural computation and information processing. In the current opinion, we review recent progress in brain stimulation and outline challenges and potential research pathways associated with exogenous control of cognitive function.

Flexible Coordinator and Switcher Hubs for Adaptive Task Control.

Functional connectivity (FC) studies have identified at least two large-scale neural systems that constitute cognitive control networks, the frontoparietal network (FPN) and cingulo-opercular network (CON). Control networks are thought to support goal-directed cognition and behavior. It was previously shown that the FPN flexibly shifts its global connectivity pattern according to task goal, consistent with a "flexible hub" mechanism for cognitive control. Our aim was to build on this finding to develop a functional cartography (a multimetric profile) of control networks in terms of dynamic network properties. We quantified network properties in (male and female) humans using a high-control-demand cognitive paradigm involving switching among 64 task sets. We hypothesized that cognitive control is enacted by the FPN and CON via distinct but complementary roles reflected in network dynamics. Consistent with a flexible "coordinator" mechanism, FPN connections were varied across tasks, while maintaining within-network connectivity to aid cross-region coordination. Consistent with a flexible "switcher" mechanism, CON regions switched to other networks in a task-dependent manner, driven primarily by reduced within-network connections to other CON regions. This pattern of results suggests FPN acts as a dynamic, global coordinator of goal-relevant information, while CON transiently disbands to lend processing resources to other goal-relevant networks. This cartography of network dynamics reveals a dissociation between two prominent cognitive control networks, suggesting complementary mechanisms underlying goal-directed cognition.SIGNIFICANCE STATEMENT Cognitive control supports a variety of behaviors requiring flexible cognition, such as rapidly switching between tasks. Furthermore, cognitive control is negatively impacted in a variety of mental illnesses. We used tools from network science to characterize the implementation of cognitive control by large-scale brain systems. This revealed that two systems, the frontoparietal (FPN) and cingulo-opercular (CON) networks, have distinct but complementary roles in controlling global network reconfigurations. The FPN exhibited properties of a flexible coordinator (orchestrating task changes), while CON acted as a flexible switcher (switching specific regions to other systems to lend processing resources). These findings reveal an underlying distinction in cognitive processes that may be applicable to clinical, educational, and machine learning work targeting cognitive flexibility.

Combining Multiple Functional Connectivity Methods to Improve Causal Inferences.

Cognition and behavior emerge from brain network interactions, suggesting that causal interactions should be central to the study of brain function. Yet, approaches that characterize relationships among neural time series-functional connectivity (FC) methods-are dominated by methods that assess bivariate statistical associations rather than causal interactions. Such bivariate approaches result in substantial false positives because they do not account for confounders (common causes) among neural populations. A major reason for the dominance of methods such as bivariate Pearson correlation (with functional MRI) and coherence (with electrophysiological methods) may be their simplicity. Thus, we sought to identify an FC method that was both simple and improved causal inferences relative to the most popular methods. We started with partial correlation, showing with neural network simulations that this substantially improves causal inferences relative to bivariate correlation. However, the presence of colliders (common effects) in a network resulted in false positives with partial correlation, although this was not a problem for bivariate correlations. This led us to propose a new combined FC method (combinedFC) that incorporates simple bivariate and partial correlation FC measures to make more valid causal inferences than either alone. We release a toolbox for implementing this new combinedFC method to facilitate improvement of FC-based causal inferences. CombinedFC is a general method for FC and can be applied equally to resting-state and task-based paradigms.

Brain network mechanisms of visual shape completion.

Visual shape completion recovers object shape, size, and number from spatially segregated edges. Despite being extensively investigated, the process's underlying brain regions, networks, and functional connections are still not well understood. To shed light on the topic, we scanned (fMRI) healthy adults during rest and during a task in which they discriminated pac-man configurations that formed or failed to form completed shapes (illusory and fragmented condition, respectively). Task activation differences (illusory-fragmented), resting-state functional connectivity, and multivariate patterns were identified on the cortical surface using 360 predefined parcels and 12 functional networks composed of such parcels. Brain activity flow mapping (ActFlow) was used to evaluate the likely involvement of resting-state connections for shape completion. We identified 36 differentially-active parcels including a posterior temporal region, PH, whose activity was consistent across 95% of observers. Significant task regions primarily occupied the secondary visual network but also incorporated the frontoparietal, dorsal attention, default mode, and cingulo-opercular networks. Each parcel's task activation difference could be modeled via its resting-state connections with the remaining parcels (r=.62, p<10-9), suggesting that such connections undergird shape completion. Functional connections from the dorsal attention network were key in modelling task activation differences in the secondary visual network. Dorsal attention and frontoparietal connections could also model activations in the remaining networks. Taken together, these results suggest that shape completion relies upon a sparsely distributed but densely interconnected network coalition that is centered in the secondary visual network, coordinated by the dorsal attention network, and inclusive of at least three other networks.

Task-evoked activity quenches neural correlations and variability across cortical areas.

Many large-scale functional connectivity studies have emphasized the importance of communication through increased inter-region correlations during task states. In contrast, local circuit studies have demonstrated that task states primarily reduce correlations among pairs of neurons, likely enhancing their information coding by suppressing shared spontaneous activity. Here we sought to adjudicate between these conflicting perspectives, assessing whether co-active brain regions during task states tend to increase or decrease their correlations. We found that variability and correlations primarily decrease across a variety of cortical regions in two highly distinct data sets: non-human primate spiking data and human functional magnetic resonance imaging data. Moreover, this observed variability and correlation reduction was accompanied by an overall increase in dimensionality (reflecting less information redundancy) during task states, suggesting that decreased correlations increased information coding capacity. We further found in both spiking and neural mass computational models that task-evoked activity increased the stability around a stable attractor, globally quenching neural variability and correlations. Together, our results provide an integrative mechanistic account that encompasses measures of large-scale neural activity, variability, and correlations during resting and task states.

Heterogeneity within the frontoparietal control network and its relationship to the default and dorsal attention networks.

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). FPCNA exhibited stronger connectivity with the DN than the DAN, whereas FPCNB 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 FPCNA may be preferentially involved in the regulation of introspective processes, whereas FPCNB may be preferentially involved in the regulation of visuospatial perceptual attention.

A cortical hierarchy of localized and distributed processes revealed via dissociation of task activations, connectivity changes, and intrinsic timescales.

Many studies have identified the role of localized and distributed cognitive functionality by mapping either local task-related activity or distributed functional connectivity (FC). However, few studies have directly explored the relationship between a brain region's localized task activity and its distributed task FC. Here we systematically evaluated the differential contributions of task-related activity and FC changes to identify a relationship between localized and distributed processes across the cortical hierarchy. We found that across multiple tasks, the magnitude of regional task-evoked activity was high in unimodal areas, but low in transmodal areas. In contrast, we found that task-state FC was significantly reduced in unimodal areas relative to transmodal areas. This revealed a strong negative relationship between localized task activity and distributed FC across cortical regions that was associated with the previously reported principal gradient of macroscale organization. Moreover, this dissociation corresponded to hierarchical cortical differences in the intrinsic timescale estimated from resting-state fMRI and region myelin content estimated from structural MRI. Together, our results contribute to a growing literature illustrating the differential contributions of a hierarchical cortical gradient representing localized and distributed cognitive processes.

Predicting dysfunctional age-related task activations from resting-state network alterations.

Alzheimer's disease (AD) is linked to changes in fMRI task activations and fMRI resting-state functional connectivity (restFC), which can emerge early in the illness timecourse. These fMRI correlates of unhealthy aging have been studied in largely separate subfields. Taking inspiration from neural network simulations, we propose a unifying mechanism wherein restFC alterations associated with AD disrupt the flow of activations between brain regions, leading to aberrant task activations. We apply this activity flow model in a large sample of clinically normal older adults, which was segregated into healthy (low-risk) and at-risk subgroups based on established imaging (positron emission tomography amyloid) and genetic (apolipoprotein) AD risk factors. Modeling the flow of healthy activations over at-risk AD connectivity effectively transformed the healthy aged activations into unhealthy (at-risk) aged activations. This enabled reliable prediction of at-risk AD task activations, and these predicted activations were related to individual differences in task behavior. These results support activity flow over altered intrinsic functional connections as a mechanism underlying Alzheimer's-related dysfunction, even in very early stages of the illness. Beyond these mechanistic insights, this approach raises clinical potential by enabling prediction of task activations and associated cognitive dysfunction in individuals without requiring them to perform in-scanner cognitive tasks.

Exploring brain-behavior relationships in the N-back task.

Working memory (WM) function has traditionally been investigated in terms of two dimensions: within-individual effects of WM load, and between-individual differences in task performance. In human neuroimaging studies, the N-back task has frequently been used to study both. A reliable finding is that activation in frontoparietal regions exhibits an inverted-U pattern, such that activity tends to decrease at high load levels. Yet it is not known whether such U-shaped patterns are a key individual differences factor that can predict load-related changes in task performance. The current study investigated this question by manipulating load levels across a much wider range than explored previously (N â€‹= â€‹1-6), and providing a more comprehensive examination of brain-behavior relationships. In a sample of healthy young adults (n â€‹= â€‹57), the analysis focused on a distinct region of left lateral prefrontal cortex (LPFC) identified in prior work to show a unique relationship with task performance and WM function. In this region it was the linear slope of load-related activity, rather than the U-shaped pattern, that was positively associated with individual differences in target accuracy. Comprehensive supplemental analyses revealed the brain-wide selectivity of this pattern. Target accuracy was also independently predicted by the global resting-state connectivity of this LPFC region. These effects were robust, as demonstrated by cross-validation analyses and out-of-sample prediction, and also critically, were primarily driven by the high-load conditions. Together, the results highlight the utility of high-load conditions for investigating individual differences in WM function.

Estimation and validation of individualized dynamic brain models with resting state fMRI.

A key challenge for neuroscience is to develop generative, causal models of the human nervous system in an individualized, data-driven manner. Previous initiatives have either constructed biologically-plausible models that are not constrained by individual-level human brain activity or used data-driven statistical characterizations of individuals that are not mechanistic. We aim to bridge this gap through the development of a new modeling approach termed Mesoscale Individualized Neurodynamic (MINDy) modeling, wherein we fit nonlinear dynamical systems models directly to human brain imaging data. The MINDy framework is able to produce these data-driven network models for hundreds to thousands of interacting brain regions in just 1-3 â€‹min per subject. We demonstrate that the models are valid, reliable, and robust. We show that MINDy models are predictive of individualized patterns of resting-state brain dynamical activity. Furthermore, MINDy is better able to uncover the mechanisms underlying individual differences in resting state activity than functional connectivity methods.

Transcranial alternating current stimulation attenuates BOLD adaptation and increases functional connectivity.

Transcranial alternating current stimulation (tACS) is used as a noninvasive tool for cognitive enhancement and clinical applications. The physiological effects of tACS, however, are complex and poorly understood. Most studies of tACS focus on its ability to entrain brain oscillations, but our behavioral results in humans and extracellular recordings in nonhuman primates support the view that tACS at 10 Hz also affects brain function by reducing sensory adaptation. Our primary goal in the present study is to test this hypothesis using blood oxygen level-dependent (BOLD) imaging in human subjects. Using concurrent functional magnetic resonance imaging (fMRI) and tACS, and a motion adaptation paradigm developed to quantify BOLD adaptation, we show that tACS significantly attenuates adaptation in the human motion area (hMT+). In addition, an exploratory analysis shows that tACS increases functional connectivity of the stimulated hMT+ with the rest of the brain and the dorsal attention network in particular. Based on field estimates from individualized head models, we relate these changes to the strength of tACS-induced electric fields. Specifically, we report that functional connectivity (between hMT+ and any other region of interest) increases in proportion to the field strength in the region of interest. These findings add support for the claim that weak 10-Hz currents applied to the scalp modulate both local and global measures of brain activity.NEW & NOTEWORTHY Concurrent transcranial alternating current stimulation (tACS) and functional MRI show that tACS affects the human brain by attenuating adaptation and increasing functional connectivity in a dose-dependent manner. This work is important for our basic understanding of what tACS does, but also for therapeutic applications, which need insight into the full range of ways in which tACS affects the brain.

Mapping the human brain's cortical-subcortical functional network organization.

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 structures 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.