The Low-Dimensional Neural Architecture of Cognitive Complexity Is Related to Activity in Medial Thalamic Nuclei

Thalamocortical architectures for flexible cognition and efficient learning

The brain exhibits a remarkable ability to learn and execute context-appropriate behaviors. How it achieves such flexibility, without sacrificing learning efficiency, is an important open question. Neuroscience, psychology, and engineering suggest that reusing and repurposing computations are part of the answer. Here, we review evidence that thalamocortical architectures may have evolved to facilitate these objectives of flexibility and efficiency by coordinating distributed computations. Recent work suggests that distributed prefrontal cortical networks compute with flexible codes, and that the mediodorsal thalamus provides regularization to promote efficient reuse. Thalamocortical interactions resemble hierarchical Bayesian computations, and their network implementation can be related to existing gating, synchronization, and hub theories of thalamic function. By reviewing recent findings and providing a novel synthesis, we highlight key research horizons integrating computation, cognition, and systems neuroscience.

Mediodorsal thalamus and ventral pallidum contribute to subcortical regulation of the default mode network

Humans and other animals readily transition from externally to internally focused attention, and these transitions are accompanied by activation of the default mode network (DMN). The DMN was considered a cortical network, yet recent evidence suggests subcortical structures are also involved. We investigated the role of ventral pallidum (VP) and mediodorsal thalamus (MD) in DMN regulation in tree shrew, a close relative of primates. Electrophysiology and deep learning-based classification of behavioral states revealed gamma oscillations in VP and MD coordinated with gamma in anterior cingulate (AC) cortex during DMN states. Cross-frequency coupling between gamma and delta oscillations was higher during DMN than other behaviors, underscoring the engagement of MD, VP and AC. Our findings highlight the importance of VP and MD in DMN regulation, extend homologies in DMN regulation among mammals, and underline the importance of thalamus and basal forebrain to the regulation of DMN.

Reconfigurations of cortical manifold structure during reward-based motor learning

Adaptive motor behavior depends on the coordinated activity of multiple neural systems distributed across the brain. While the role of sensorimotor cortex in motor learning has been well established, how higher-order brain systems interact with sensorimotor cortex to guide learning is less well understood. Using functional MRI, we examined human brain activity during a reward-based motor task where subjects learned to shape their hand trajectories through reinforcement feedback. We projected patterns of cortical and striatal functional connectivity onto a low-dimensional manifold space and examined how regions expanded and contracted along the manifold during learning. During early learning, we found that several sensorimotor areas in the dorsal attention network exhibited increased covariance with areas of the salience/ventral attention network and reduced covariance with areas of the default mode network (DMN). During late learning, these effects reversed, with sensorimotor areas now exhibiting increased covariance with DMN areas. However, areas in posteromedial cortex showed the opposite pattern across learning phases, with its connectivity suggesting a role in coordinating activity across different networks over time. Our results establish the neural changes that support reward-based motor learning and identify distinct transitions in the functional coupling of sensorimotor to transmodal cortex when adapting behavior.

Thalamic contributions to the state and contents of consciousness

Consciousness can be conceptualized as varying along at least two dimensions: the global state of consciousness and the content of conscious experience. Here, we highlight the cellular and systems-level contributions of the thalamus to conscious state and then argue for thalamic contributions to conscious content, including the integrated, segregated, and continuous nature of our experience. We underscore vital, yet distinct roles for core- and matrix-type thalamic neurons. Through reciprocal interactions with deep-layer cortical neurons, matrix neurons support wakefulness and determine perceptual thresholds, whereas the cortical interactions of core neurons maintain content and enable perceptual constancy. We further propose that conscious integration, segregation, and continuity depend on the convergent nature of corticothalamic projections enabling dimensionality reduction, a thalamic reticular nucleus-mediated divisive normalization-like process, and sustained coherent activity in thalamocortical loops, respectively. Overall, we conclude that the thalamus plays a central topological role in brain structures controlling conscious experience.

Dynamics of brain-muscle networks reveal effects of age and somatosensory function on gait

Walking is a complex motor activity that requires coordinated interactions between the sensory and motor systems. We used mobile EEG and EMG to investigate the brain-muscle networks involved in gait control during overground walking in young people, older people, and individuals with Parkinson's disease. Dynamic interactions between the sensorimotor cortices and eight leg muscles within a gait cycle were assessed using multivariate analysis. We identified three distinct brain-muscle networks during a gait cycle. These networks include a bilateral network, a left-lateralized network activated during the left swing phase, and a right-lateralized network active during the right swing. The trajectories of these networks are contracted in older adults, indicating a reduction in neuromuscular connectivity with age. Individuals with the impaired tactile sensitivity of the foot showed a selective enhancement of the bilateral network, possibly reflecting a compensation strategy to maintain gait stability. These findings provide a parsimonious description of interindividual differences in neuromuscular connectivity during gait.

Abnormal higher-order network interactions in Parkinson's disease visual hallucinations

Visual hallucinations in Parkinson's disease can be viewed from a systems-level perspective, whereby dysfunctional communication between brain networks responsible for perception predisposes a person to hallucinate. To this end, abnormal functional interactions between higher-order and primary sensory networks have been implicated in the pathophysiology of visual hallucinations in Parkinson's disease, however the precise signatures remain to be determined. Dimensionality reduction techniques offer a novel means for simplifying the interpretation of multidimensional brain imaging data, identifying hierarchical patterns in the data that are driven by both within- and between-functional network changes. Here, we applied two complementary non-linear dimensionality reduction techniques-diffusion-map embedding and t-distributed stochastic neighbour embedding (t-SNE)-to resting state functional MRI data, in order to characterize the altered functional hierarchy associated with susceptibility to visual hallucinations. Our study involved 77 people with Parkinson's disease (31 with hallucinations; 46 without hallucinations) and 19 age-matched healthy control subjects. In patients with visual hallucinations, we found compression of the unimodal-heteromodal gradient consistent with increased functional integration between sensory and higher order networks. This was mirrored in a traditional functional connectivity analysis, which showed increased connectivity between the visual and default mode networks in the hallucinating group. Together, these results suggest a route by which higher-order regions may have excessive influence over earlier sensory processes, as proposed by theoretical models of hallucinations across disorders. By contrast, the t-SNE analysis identified distinct alterations in prefrontal regions, suggesting an additional layer of complexity in the functional brain network abnormalities implicated in hallucinations, which was not apparent in traditional functional connectivity analyses. Together, the results confirm abnormal brain organization associated with the hallucinating phenotype in Parkinson's disease and highlight the utility of applying convergent dimensionality reduction techniques to investigate complex clinical symptoms. In addition, the patterns we describe in Parkinson's disease converge with those seen in other conditions, suggesting that reduced hierarchical differentiation across sensory-perceptual systems may be a common transdiagnostic vulnerability in neuropsychiatric disorders with perceptual disturbances.

Propofol Disrupts the Functional Core-Matrix Architecture of the Thalamus in Humans

Research into the role of thalamocortical circuits in anesthesia-induced unconsciousness is difficult due to anatomical and functional complexity. Prior neuroimaging studies have examined either the thalamus as a whole or focused on specific subregions, overlooking the distinct neuronal subtypes like core and matrix cells. We conducted a study of heathy volunteers and functional magnetic resonance imaging during conscious baseline, deep sedation, and recovery. We advanced the functional gradient mapping technique to delineate the functional geometry of thalamocortical circuits, within a framework of the unimodal-transmodal functional axis of the cortex. We observed a significant shift in this geometry during unconsciousness, marked by the dominance of unimodal over transmodal geometry. This alteration was closely linked to the spatial variations in the density of matrix cells within the thalamus. This research bridges cellular and systems-level understanding, highlighting the crucial role of thalamic core-matrix functional architecture in understanding the neural mechanisms of states of consciousness.

Subcortical influences on the topology of cortical networks align with functional processing hierarchies

fMRI of the human brain reveals spatiotemporal patterns of functional connectivity (FC), forming distinct cortical networks. Lately, subcortical contributions to these configurations are receiving renewed interest, but investigations rarely focus explicitly on their effects on cortico-cortical FC. Here, we employ a straightforward multivariable approach and graph-theoretic tools to assess subcortical impact on topological features of cortical networks. Given recent evidence showing that structures like the thalamus and basal ganglia integrate input from multiple networks, we expect increased segregation between cortical networks after removal of subcortical effects on their FC patterns. We analyze resting state data of young and healthy participants (male and female; N = 100) from the human connectome project. We find that overall, the cortical network architecture becomes less segregated, and more integrated, when subcortical influences are accounted for. Underlying these global effects are the following trends: 'Transmodal' systems become more integrated with the rest of the network, while 'unimodal' networks show the opposite effect. For single nodes this hierarchical organization is reflected by a close correspondence with the spatial layout of the principal gradient of FC (Margulies et al., 2016). Lastly, we show that the limbic system is significantly less coherent with subcortical influences removed. The findings are validated in a (split-sample) replication dataset. Our results provide new insight regarding the interplay between subcortex and cortical networks, by putting the integrative impact of subcortex in the context of macroscale patterns of cortical organization.

Functional neuroimaging as a catalyst for integrated neuroscience

Functional magnetic resonance imaging (fMRI) enables non-invasive access to the awake, behaving human brain. By tracking whole-brain signals across a diverse range of cognitive and behavioural states or mapping differences associated with specific traits or clinical conditions, fMRI has advanced our understanding of brain function and its links to both normal and atypical behaviour. Despite this headway, progress in human cognitive neuroscience that uses fMRI has been relatively isolated from rapid advances in other subdomains of neuroscience, which themselves are also somewhat siloed from one another. In this Perspective, we argue that fMRI is well-placed to integrate the diverse subfields of systems, cognitive, computational and clinical neuroscience. We first summarize the strengths and weaknesses of fMRI as an imaging tool, then highlight examples of studies that have successfully used fMRI in each subdomain of neuroscience. We then provide a roadmap for the future advances that will be needed to realize this integrative vision. In this way, we hope to demonstrate how fMRI can help usher in a new era of interdisciplinary coherence in neuroscience.

The 1/f-like behavior of neural field spectra are a natural consequence of noise driven brain dynamics

Consistent observations across recording modalities, experiments, and neural systems find neural field spectra with 1/f-like scaling, eliciting many alternative theories to explain this universal phenomenon. We show that a general dynamical system with stochastic drive and minimal assumptions generates 1/f-like spectra consistent with the range of values observed in vivo, without requiring a specific biological mechanism or collective critical behavior.

The impact of the human thalamus on brain-wide information processing

The thalamus is a small, bilateral structure in the diencephalon that integrates signals from many areas of the CNS. This critical anatomical position allows the thalamus to influence whole-brain activity and adaptive behaviour. However, traditional research paradigms have struggled to attribute specific functions to the thalamus, and it has remained understudied in the human neuroimaging literature. Recent advances in analytical techniques and increased accessibility to large, high-quality data sets have brought forth a series of studies and findings that (re-)establish the thalamus as a core region of interest in human cognitive neuroscience, a field that otherwise remains cortico-centric. In this Perspective, we argue that using whole-brain neuroimaging approaches to investigate the thalamus and its interaction with the rest of the brain is key for understanding systems-level control of information processing. To this end, we highlight the role of the thalamus in shaping a range of functional signatures, including evoked activity, interregional connectivity, network topology and neuronal variability, both at rest and during the performance of cognitive tasks.

Altered thalamic volume in patients with mild autonomous cortisol secretion: a structural brain MRI study

PURPOSE

To compare thalamic volume and cognitive functions of patients with mild autonomous cortisol secretion (MACS) with control subjects and patients with overt Cushing's syndrome (CS).

METHODS

In this cross-sectional study, volumes of regions of interest were assessed using 3 T magnetic resonance imaging and a voxel-based morphometry approach in 23 patients with MACS, 21 patients with active CS, 27 patients with CS in remission, and 21 control subjects. Cognitive functions were assessed using validated questionnaires.

RESULTS

Patients with MACS had smaller left thalamic (F = 3.8, p = 0.023), left posterior thalamic (F = 4.9, p = 0.01), left medial thalamic (F = 4.7, p = 0.028), and right lateral thalamic (F = 4.1, p = 0.025) volumes than control subjects. Patients with active CS also had smaller left thalamic (F = 3.8, p = 0.044), left posterior thalamic (F = 4.9, p = 0.007), left medial thalamic (F = 4.7, p = 0.006), and right lateral thalamic (F = 4.1, p = 0.042) volumes compared to controls. Patients with CS in remission had smaller left medial (F = 4.7, p = 0.030) and right lateral thalamic (F = 4.1, p = 0.028) volumes than controls. Neuropsychological tests showed no difference between the groups.

CONCLUSION

MACS may decrease thalamic volume.

Vigilance associates with the low-dimensional structure of fMRI data

The human brain exhibits rich dynamics that reflect ongoing functional states. Patterns in fMRI data, detected in a data-driven manner, have uncovered recurring configurations that relate to individual and group differences in behavioral, cognitive, and clinical traits. However, resolving the neural and physiological processes that underlie such measurements is challenging, particularly without external measurements of brain state. A growing body of work points to underlying changes in vigilance as one driver of time-windowed fMRI connectivity states, calculated on the order of tens of seconds. Here we examine the degree to which the low-dimensional spatial structure of instantaneous fMRI activity is associated with vigilance levels, by testing whether vigilance-state detection can be carried out in an unsupervised manner based on individual BOLD time frames. To investigate this question, we first reduce the spatial dimensionality of fMRI data, and apply Gaussian Mixture Modeling to cluster the resulting low-dimensional data without any a priori vigilance information. Our analysis includes long-duration task and resting-state scans that are conducive to shifts in vigilance. We observe a close alignment between low-dimensional fMRI states (data-driven clusters) and measurements of vigilance derived from concurrent electroencephalography (EEG) and behavior. Whole-brain coactivation analysis revealed cortical anti-correlation patterns that resided primarily during higher behavioral- and EEG-defined levels of vigilance, while cortical activity was more often spatially uniform in states corresponding to lower vigilance. Overall, these findings indicate that vigilance states may be detected in the low-dimensional structure of fMRI data, even within individual time frames.

Functional geometry of the cortex encodes dimensions of consciousness

Consciousness is a multidimensional phenomenon, but key dimensions such as awareness and wakefulness have been described conceptually rather than neurobiologically. We hypothesize that dimensions of consciousness are encoded in multiple neurofunctional dimensions of the brain. We analyze cortical gradients, which are continua of the brain's overarching functional geometry, to characterize these neurofunctional dimensions. We demonstrate that disruptions of human consciousness - due to pharmacological, neuropathological, or psychiatric causes - are associated with a degradation of one or more of the major cortical gradients depending on the state. Network-specific reconfigurations within the multidimensional cortical gradient space are associated with behavioral unresponsiveness of various etiologies, and these spatial reconfigurations correlate with a temporal disruption of structured transitions of dynamic brain states. In this work, we therefore provide a unifying neurofunctional framework for multiple dimensions of human consciousness in both health and disease.

Microscale multicircuit brain stimulation: Achieving real-time brain state control for novel applications

Neurological and psychiatric disorders typically result from dysfunction across multiple neural circuits. Most of these disorders lack a satisfactory neuromodulation treatment. However, deep brain stimulation (DBS) has been successful in a limited number of disorders; DBS typically targets one or two brain areas with single contacts on relatively large electrodes, allowing for only coarse modulation of circuit function. Because of the dysfunction in distributed neural circuits - each requiring fine, tailored modulation - that characterizes most neuropsychiatric disorders, this approach holds limited promise. To develop the next generation of neuromodulation therapies, we will have to achieve fine-grained, closed-loop control over multiple neural circuits. Recent work has demonstrated spatial and frequency selectivity using microstimulation with many small, closely-spaced contacts, mimicking endogenous neural dynamics. Using custom electrode design and stimulation parameters, it should be possible to achieve bidirectional control over behavioral outcomes, such as increasing or decreasing arousal during central thalamic stimulation. Here, we discuss one possible approach, which we term microscale multicircuit brain stimulation (MMBS). We discuss how machine learning leverages behavioral and neural data to find optimal stimulation parameters across multiple contacts, to drive the brain towards desired states associated with behavioral goals. We expound a mathematical framework for MMBS, where behavioral and neural responses adjust the model in real-time, allowing us to adjust stimulation in real-time. These technologies will be critical to the development of the next generation of neurostimulation therapies, which will allow us to treat problems like disorders of consciousness and cognition.

Thalamocortical contributions to cognitive task activity

Thalamocortical interaction is a ubiquitous functional motif in the mammalian brain. Previously (Hwang et al., 2021), we reported that lesions to network hubs in the human thalamus are associated with multi-domain behavioral impairments in language, memory, and executive functions. Here, we show how task-evoked thalamic activity is organized to support these broad cognitive abilities. We analyzed functional magnetic resonance imaging (MRI) data from human subjects that performed 127 tasks encompassing a broad range of cognitive representations. We first investigated the spatial organization of task-evoked activity and found a basis set of activity patterns evoked to support processing needs of each task. Specifically, the anterior, medial, and posterior-medial thalamus exhibit hub-like activity profiles that are suggestive of broad functional participation. These thalamic task hubs overlapped with network hubs interlinking cortical systems. To further determine the cognitive relevance of thalamic activity and thalamocortical functional connectivity, we built a data-driven thalamocortical model to test whether thalamic activity can be used to predict cortical task activity. The thalamocortical model predicted task-specific cortical activity patterns, and outperformed comparison models built on cortical, hippocampal, and striatal regions. Simulated lesions to low-dimensional, multi-task thalamic hub regions impaired task activity prediction. This simulation result was further supported by profiles of neuropsychological impairments in human patients with focal thalamic lesions. In summary, our results suggest a general organizational principle of how the human thalamocortical system supports cognitive task activity.

It's about time: Linking dynamical systems with human neuroimaging to understand the brain

Most human neuroscience research to date has focused on statistical approaches that describe stationary patterns of localized neural activity or blood flow. While these patterns are often interpreted in light of dynamic, information-processing concepts, the static, local, and inferential nature of the statistical approach makes it challenging to directly link neuroimaging results to plausible underlying neural mechanisms. Here, we argue that dynamical systems theory provides the crucial mechanistic framework for characterizing both the brain's time-varying quality and its partial stability in the face of perturbations, and hence, that this perspective can have a profound impact on the interpretation of human neuroimaging results and their relationship with behavior. After briefly reviewing some key terminology, we identify three key ways in which neuroimaging analyses can embrace a dynamical systems perspective: by shifting from a local to a more global perspective, by focusing on dynamics instead of static snapshots of neural activity, and by embracing modeling approaches that map neural dynamics using "forward" models. Through this approach, we envisage ample opportunities for neuroimaging researchers to enrich their understanding of the dynamic neural mechanisms that support a wide array of brain functions, both in health and in the setting of psychopathology.

Subcortical-cortical dynamical states of the human brain and their breakdown in stroke

The mechanisms controlling dynamical patterns in spontaneous brain activity are poorly understood. Here, we provide evidence that cortical dynamics in the ultra-slow frequency range (<0.01–0.1 Hz) requires intact cortical-subcortical communication. Using functional magnetic resonance imaging (fMRI) at rest, we identify Dynamic Functional States (DFSs), transient but recurrent clusters of cortical and subcortical regions synchronizing at ultra-slow frequencies. We observe that shifts in cortical clusters are temporally coincident with shifts in subcortical clusters, with cortical regions flexibly synchronizing with either limbic regions (hippocampus/amygdala), or subcortical nuclei (thalamus/basal ganglia). Focal lesions induced by stroke, especially those damaging white matter connections between basal ganglia/thalamus and cortex, provoke anomalies in the fraction times, dwell times, and transitions between DFSs, causing a bias toward abnormal network integration. Dynamical anomalies observed 2 weeks after stroke recover in time and contribute to explaining neurological impairment and long-term outcome.

Favaretto et al. show that the brain rapidly alternates between transient connectivity patterns, with cortical regions flexibly synchronizing with two groups of subcortical regions, and that this dynamic is abnormal in stroke patients.

Cost function for low-dimensional manifold topology assessment

In reduced-order modeling, complex systems that exhibit high state-space dimensionality are described and evolved using a small number of parameters. These parameters can be obtained in a data-driven way, where a high-dimensional dataset is projected onto a lower-dimensional basis. A complex system is then restricted to states on a low-dimensional manifold where it can be efficiently modeled. While this approach brings computational benefits, obtaining a good quality of the manifold topology becomes a crucial aspect when models, such as nonlinear regression, are built on top of the manifold. Here, we present a quantitative metric for characterizing manifold topologies. Our metric pays attention to non-uniqueness and spatial gradients in physical quantities of interest, and can be applied to manifolds of arbitrary dimensionality. Using the metric as a cost function in optimization algorithms, we show that optimized low-dimensional projections can be found. We delineate a few applications of the cost function to datasets representing argon plasma, reacting flows and atmospheric pollutant dispersion. We demonstrate how the cost function can assess various dimensionality reduction and manifold learning techniques as well as data preprocessing strategies in their capacity to yield quality low-dimensional projections. We show that improved manifold topologies can facilitate building nonlinear regression models.

Neural excursions from manifold structure explain patterns of learning during human sensorimotor adaptation

Humans vary greatly in their motor learning abilities, yet little is known about the neural mechanisms that underlie this variability. Recent neuroimaging and electrophysiological studies demonstrate that large-scale neural dynamics inhabit a low-dimensional subspace or manifold, and that learning is constrained by this intrinsic manifold architecture. Here, we asked, using functional MRI, whether subject-level differences in neural excursion from manifold structure can explain differences in learning across participants. We had subjects perform a sensorimotor adaptation task in the MRI scanner on 2 consecutive days, allowing us to assess their learning performance across days, as well as continuously measure brain activity. We find that the overall neural excursion from manifold activity in both cognitive and sensorimotor brain networks is associated with differences in subjects' patterns of learning and relearning across days. These findings suggest that off-manifold activity provides an index of the relative engagement of different neural systems during learning, and that subject differences in patterns of learning and relearning are related to reconfiguration processes occurring in cognitive and sensorimotor networks.

Network Analysis of Time Series: Novel Approaches to Network Neuroscience

In the last two decades, there has been an explosion of interest in modeling the brain as a network, where nodes correspond variously to brain regions or neurons, and edges correspond to structural or statistical dependencies between them. This kind of network construction, which preserves spatial, or structural, information while collapsing across time, has become broadly known as "network neuroscience." In this work, we provide an alternative application of network science to neural data: network-based analysis of non-linear time series and review applications of these methods to neural data. Instead of preserving spatial information and collapsing across time, network analysis of time series does the reverse: it collapses spatial information, instead preserving temporally extended dynamics, typically corresponding to evolution through some kind of phase/state-space. This allows researchers to infer a, possibly low-dimensional, "intrinsic manifold" from empirical brain data. We will discuss three methods of constructing networks from nonlinear time series, and how to interpret them in the context of neural data: recurrence networks, visibility networks, and ordinal partition networks. By capturing typically continuous, non-linear dynamics in the form of discrete networks, we show how techniques from network science, non-linear dynamics, and information theory can extract meaningful information distinct from what is normally accessible in standard network neuroscience approaches.

Focal neural perturbations reshape low-dimensional trajectories of brain activity supporting cognitive performance

The emergence of distributed patterns of neural activity supporting brain functions and behavior can be understood by study of the brain's low-dimensional topology. Functional neuroimaging demonstrates that brain activity linked to adaptive behavior is constrained to low-dimensional manifolds. In human participants, we tested whether these low-dimensional constraints preserve working memory performance following local neuronal perturbations. We combined multi-session functional magnetic resonance imaging, non-invasive transcranial magnetic stimulation (TMS), and methods translated from the fields of complex systems and computational biology to assess the functional link between changes in local neural activity and the reshaping of task-related low dimensional trajectories of brain activity. We show that specific reconfigurations of low-dimensional trajectories of brain activity sustain effective working memory performance following TMS manipulation of local activity on, but not off, the space traversed by these trajectories. We highlight an association between the multi-scale changes in brain activity underpinning cognitive function.

Injury to thalamocortical projections following traumatic brain injury results in attractor dynamics for cortical networks

Major theories of consciousness predict that complex electroencephalographic (EEG) activity is required for consciousness, yet it is not clear how such activity arises in the corticothalamic system. The thalamus is well-known to control cortical excitability via interlaminar projections, but whether thalamic input is needed for complexity is not known. We hypothesized that the thalamus facilitates complex activity by adjusting synaptic connectivity, thereby increasing the availability of different configurations of cortical neurons (cortical "states"), as well as the probability of state transitions. To test this hypothesis, we characterized EEG activity from prefrontal cortex (PFC) in traumatic brain injury (TBI) patients with and without injuries to thalamocortical projections, measured with diffusion tensor imaging (DTI). We found that injury to thalamic projections (especially from the mediodorsal thalamus) was strongly associated with unconsciousness and delta-band EEG activity. Using advanced signal processing techniques, we found that lack of thalamic input led to 1.) attractor dynamics for cortical networks with a tendency to visit the same states, 2.) a reduced repertoire of possible states, and 3.) high predictability of transitions between states. These results imply that complex PFC activity associated with consciousness depends on thalamic input. Our model implies that restoration of cortical connectivity is a critical function of the thalamus after brain injury. We draw a critical connection between thalamic input and complex cortical activity associated with consciousness.

Dopamine depletion and subcortical dysfunction disrupt cortical synchronization and metastability affecting cognitive function in Parkinson's disease

Parkinson's disease (PD) is primarily characterized by the loss of dopaminergic cells and atrophy in subcortical regions. However, the impact of these pathological changes on large-scale dynamic integration and segregation of the cortex are not well understood. In this study, we investigated the effect of subcortical dysfunction on cortical dynamics and cognition in PD. Spatiotemporal dynamics of the phase interactions of resting-state blood-oxygen-level-dependent signals in 159 PD patients and 152 normal control (NC) individuals were estimated. The relationships between subcortical atrophy, subcortical-cortical fiber connectivity impairment, cortical synchronization/metastability, and cognitive performance were then assessed. We found that cortical synchronization and metastability in PD patients were significantly decreased. To examine whether this is an effect of dopamine depletion, we investigated 45 PD patients both ON and OFF dopamine replacement therapy, and found that cortical synchronization and metastability are significantly increased in the ON state. The extent of cortical synchronization and metastability in the OFF state reflected cognitive performance and mediates the difference in cognitive performance between the PD and NC groups. Furthermore, both the thalamic volume and thalamocortical fiber connectivity had positive relationships with cortical synchronization and metastability in the dopaminergic OFF state, and mediate the difference in cortical synchronization between the PD and NC groups. In addition, thalamic volume also reflected cognitive performance, and cortical synchronization/metastability mediated the relationship between thalamic volume and cognitive performance in PD patients. Together, these results highlight that subcortical dysfunction and reduced dopamine levels are responsible for decreased cortical synchronization and metastability, further affecting cognitive performance in PD. This might lead to biomarkers being identified that can predict if a patient is at risk of developing dementia.

Nonlinear reconfiguration of network edges, topology and information content during an artificial learning task

Here, we combine network neuroscience and machine learning to reveal connections between the brain's network structure and the emerging network structure of an artificial neural network. Specifically, we train a shallow, feedforward neural network to classify hand-written digits and then used a combination of systems neuroscience and information-theoretic tools to perform 'virtual brain analytics' on the resultant edge weights and activity patterns of each node. We identify three distinct phases of network reconfiguration across learning, each of which are characterized by unique topological and information-theoretic signatures. Each phase involves aligning the connections of the neural network with patterns of information contained in the input dataset or preceding layers (as relevant). We also observe a process of low-dimensional category separation in the network as a function of learning. Our results offer a systems-level perspective of how artificial neural networks function-in terms of multi-stage reorganization of edge weights and activity patterns to effectively exploit the information content of input data during edge-weight training-while simultaneously enriching our understanding of the methods used by systems neuroscience.

The ascending arousal system promotes optimal performance through mesoscale network integration in a visuospatial attentional task

Previous research has shown that the autonomic nervous system provides essential constraints over ongoing cognitive function. However, there is currently a relative lack of direct empirical evidence for how this interaction manifests in the brain at the macroscale level. Here, we examine the role of ascending arousal and attentional load on large-scale network dynamics by combining pupillometry, functional MRI, and graph theoretical analysis to analyze data from a visual motion-tracking task with a parametric load manipulation. We found that attentional load effects were observable in measures of pupil diameter and in a set of brain regions that parametrically modulated their BOLD activity and mesoscale network-level integration. In addition, the regional patterns of network reconfiguration were correlated with the spatial distribution of the α2a adrenergic receptor. Our results further solidify the relationship between ascending noradrenergic activity, large-scale network integration, and cognitive task performance.

Low-Dimensional Dynamics of Brain Activity Associated with Manual Acupuncture in Healthy Subjects

Acupuncture is one of the oldest traditional medical treatments in Asian countries. However, the scientific explanation regarding the therapeutic effect of acupuncture is still unknown. The much-discussed hypothesis it that acupuncture’s effects are mediated via autonomic neural networks; nevertheless, dynamic brain activity involved in the acupuncture response has still not been elicited. In this work, we hypothesized that there exists a lower-dimensional subspace of dynamic brain activity across subjects, underpinning the brain’s response to manual acupuncture stimulation. To this end, we employed a variational auto-encoder to probe the latent variables from multichannel EEG signals associated with acupuncture stimulation at the ST36 acupoint. The experimental results demonstrate that manual acupuncture stimuli can reduce the dimensionality of brain activity, which results from the enhancement of oscillatory activity in the delta and alpha frequency bands induced by acupuncture. Moreover, it was found that large-scale brain activity could be constrained within a low-dimensional neural subspace, which is spanned by the “acupuncture mode”. In each neural subspace, the steady dynamics of the brain in response to acupuncture stimuli converge to topologically similar elliptic-shaped attractors across different subjects. The attractor morphology is closely related to the frequency of the acupuncture stimulation. These results shed light on probing the large-scale brain response to manual acupuncture stimuli.

Dynamic Transitions between Neural States Are Associated with Flexible Task Switching during a Memory Task

Flexible behavior requires switching between different task conditions. It is known that such task switching is associated with costs in terms of slowed RT, reduced accuracy, or both. The neural correlates of task switching have usually been studied by requiring participants to switch between distinct task conditions that recruit different brain networks. Here, we investigated the transition of neural states underlying switching between two opposite memory-related processes (i.e., memory retrieval and memory suppression) in a memory task. We investigated 26 healthy participants who performed a think/no-think task while being in the fMRI scanner. Behaviorally, we show that it was more difficult for participants to suppress unwanted memories when a no-think was preceded by a think trial instead of another no-think trial. Neurally, we demonstrate that think-no-think switches were associated with an increase in control-related and a decrease in memory-related brain activity. Neural representations of task condition, assessed by decoding accuracy, were lower immediately after task switching compared with the nonswitch transitions, suggesting a switch-induced delay in the neural transition toward the required task condition. This suggestion is corroborated by an association between condition-specific representational strength and condition-specific performance in switch trials. Taken together, we provided neural evidence from the time-resolved decoding approach to support the notion that carryover of the previous task set activation is associated with the switching cost, leading to less successful memory suppression.

Flexible brain transitions between hierarchical network segregation and integration associated with cognitive performance during a multisource interference task

Cognition involves locally segregated and globally integrated processing. This process is hierarchically organized and linked to evidence from hierarchical modules in brain networks. However, researchers have not clearly determined how flexible transitions between these hierarchical processes are associated with cognitive behavior. Here, we designed a multisource interference task (MSIT) and introduced the nested-spectral partition (NSP) method to detect hierarchical modules in brain functional networks. By defining hierarchical segregation and integration across multiple levels, we showed that the MSIT requires higher network segregation in the whole brain and most functional systems but generates higher integration in the control system. Meanwhile, brain networks have more flexible transitions between segregated and integrated configurations in the task state. Crucially, higher functional flexibility in the resting state, less flexibility in the task state and more efficient switching of the brain from resting to task states were associated with better task performance. Our hierarchical modular analysis was more effective at detecting alterations in functional organization and the phenotype of cognitive performance than graph-based network measures at a single level.

The ascending arousal system shapes neural dynamics to mediate awareness of cognitive states

Models of cognitive function typically focus on the cerebral cortex and hence overlook functional links to subcortical structures. This view does not consider the role of the highly-conserved ascending arousal system's role and the computational capacities it provides the brain. We test the hypothesis that the ascending arousal system modulates cortical neural gain to alter the low-dimensional energy landscape of cortical dynamics. Here we use spontaneous functional magnetic resonance imaging data to study phasic bursts in both locus coeruleus and basal forebrain, demonstrating precise time-locked relationships between brainstem activity, low-dimensional energy landscapes, network topology, and spatiotemporal travelling waves. We extend our analysis to a cohort of experienced meditators and demonstrate locus coeruleus-mediated network dynamics were associated with internal shifts in conscious awareness. Together, these results present a view of brain organization that highlights the ascending arousal system's role in shaping both the dynamics of the cerebral cortex and conscious awareness.

Lost Dynamics and the Dynamics of Loss: Longitudinal Compression of Brain Signal Variability is Coupled with Declines in Functional Integration and Cognitive Performance

Reduced moment-to-moment blood oxygen level-dependent (BOLD) signal variability has been consistently linked to advanced age and poorer cognitive performance, showing potential as a functional marker of brain aging. To date, however, this promise has rested exclusively on cross-sectional comparisons. In a sample of 74 healthy adults, we provide the first longitudinal evidence linking individual differences in BOLD variability, age, and performance across multiple cognitive domains over an average period of 2.5 years. As expected, those expressing greater loss of BOLD variability also exhibited greater decline in cognition. The fronto-striato-thalamic system emerged as a core neural substrate for these change-change associations. Preservation of signal variability within regions of the fronto-striato-thalamic system also cohered with preservation of functional integration across regions of this system, suggesting that longitudinal maintenance of "local" dynamics may require across-region communication. We therefore propose this neural system as a primary target in future longitudinal studies on the neural substrates of cognitive aging. Given that longitudinal change-change associations between brain and cognition are notoriously difficult to detect, the presence of such an association within a relatively short follow-up period bolsters the promise of brain signal variability as a viable, experimentally sensitive probe for studying individual differences in human cognitive aging.

Learning brain dynamics for decoding and predicting individual differences

Insights from functional Magnetic Resonance Imaging (fMRI), as well as recordings of large numbers of neurons, reveal that many cognitive, emotional, and motor functions depend on the multivariate interactions of brain signals. To decode brain dynamics, we propose an architecture based on recurrent neural networks to uncover distributed spatiotemporal signatures. We demonstrate the potential of the approach using human fMRI data during movie-watching data and a continuous experimental paradigm. The model was able to learn spatiotemporal patterns that supported 15-way movie-clip classification (∼90%) at the level of brain regions, and binary classification of experimental conditions (∼60%) at the level of voxels. The model was also able to learn individual differences in measures of fluid intelligence and verbal IQ at levels comparable to that of existing techniques. We propose a dimensionality reduction approach that uncovers low-dimensional trajectories and captures essential informational (i.e., classification related) properties of brain dynamics. Finally, saliency maps and lesion analysis were employed to characterize brain-region/voxel importance, and uncovered how dynamic but consistent changes in fMRI activation influenced decoding performance. When applied at the level of voxels, our framework implements a dynamic version of multivariate pattern analysis. Our approach provides a framework for visualizing, analyzing, and discovering dynamic spatially distributed brain representations during naturalistic conditions.

The BigBrainWarp toolbox for integration of BigBrain 3D histology with multimodal neuroimaging

Neuroimaging stands to benefit from emerging ultrahigh-resolution 3D histological atlases of the human brain; the first of which is 'BigBrain'. Here, we review recent methodological advances for the integration of BigBrain with multi-modal neuroimaging and introduce a toolbox, 'BigBrainWarp', that combines these developments. The aim of BigBrainWarp is to simplify workflows and support the adoption of best practices. This is accomplished with a simple wrapper function that allows users to easily map data between BigBrain and standard MRI spaces. The function automatically pulls specialised transformation procedures, based on ongoing research from a wide collaborative network of researchers. Additionally, the toolbox improves accessibility of histological information through dissemination of ready-to-use cytoarchitectural features. Finally, we demonstrate the utility of BigBrainWarp with three tutorials and discuss the potential of the toolbox to support multi-scale investigations of brain organisation.

Characterizing the Network Architecture of Emotion Regulation Neurodevelopment

The ability to regulate emotions is key to goal attainment and well-being. Although much has been discovered about neurodevelopment and the acquisition of emotion regulation, very little of this work has leveraged information encoded in whole-brain networks. Here we employed a network neuroscience framework to parse the neural underpinnings of emotion regulation skill acquisition, while accounting for age, in a sample of children and adolescents (N = 70, 34 female, aged 8-17 years). Focusing on three key network metrics-network differentiation, modularity, and community number differences between active regulation and a passive emotional baseline-we found that the control network, the default mode network, and limbic network were each related to emotion regulation ability while controlling for age. Greater network differentiation in the control and limbic networks was related to better emotion regulation ability. With regards to network community structure (modularity and community number), more communities and more crosstalk between modules (i.e., less modularity) in the control network were associated with better regulatory ability. By contrast, less crosstalk (i.e., greater modularity) between modules in the default mode network was associated with better regulatory ability. Together, these findings highlight whole-brain connectome features that support the acquisition of emotion regulation in youth.

Increased segregation of structural brain networks underpins enhanced broad cognitive abilities of cognitive training

A major challenge in the cognitive training field is inducing broad, far-transfer training effects. Thus far, little is known about the neural mechanisms underlying broad training effects. Here, we tested a set of competitive hypotheses regarding the role of brain integration versus segregation underlying the broad training effect. We retrospectively analyzed data from a randomized controlled trial comparing neurocognitive effects of vision-based speed of processing training (VSOP) and an active control consisting of mental leisure activities (MLA) in older adults with MCI. We classified a subset of participants in the VSOP as learners, who showed improvement in executive function and episodic memory. The other participants in the VSOP (i.e., VSOP non-learners) and a subset of participants in the MLA (i.e., MLA non-learners) served as controls. Structural brain networks were constructed from diffusion tensor imaging. Clustering coefficients (CCs) and characteristic path lengths were computed as measures of segregation and integration, respectively. Learners showed significantly greater global CCs after intervention than controls. Nodal CCs were selectively enhanced in cingulate cortex, parietal regions, striatum, and thalamus. Among VSOP learners, those with more severe baseline neurodegeneration had greater improvement in segregation after training. Our findings suggest broad training effects are related to enhanced segregation in selective brain networks, providing insight into cognitive training related neuroplasticity.

Associations between subregional thalamic volume and brain pathology in autosomal dominant Alzheimer's disease

Histopathological reports suggest that subregions of the thalamus, which regulates multiple physiological and cognitive processes, are not uniformly affected by Alzheimer's disease. Despite this, structural neuroimaging studies often consider the thalamus as a single region. Identification of in vivo Alzheimer's-dependent volumetric changes in thalamic subregions may aid the characterization of early nuclei-specific neurodegeneration in Alzheimer's disease. Here, we leveraged access to the largest single-mutation cohort of autosomal-dominant Alzheimer's disease to test whether cross-sectional abnormalities in subregional thalamic volumes are evident in non-demented mutation carriers (n = 31), compared to non-carriers (n = 36), and whether subregional thalamic volume is associated with age, markers of brain pathology and cognitive performance. Using automatic parcellation we examined the thalamus in six subregions (anterior, lateral, ventral, intralaminar, medial, and posterior) and their relation to age and brain pathology (amyloid and tau), as measured by PET imaging. No between-group differences were observed in the volume of the thalamic subregions. In carriers, lower volume in the medial subregion was related to increased cortical amyloid and entorhinal tau burden. These findings suggest that thalamic Alzheimer's-related volumetric reductions are not uniform even in preclinical and prodromal stages of autosomal-dominant Alzheimer's disease and therefore, this structure should not be considered as a single, unitary structure in Alzheimer's disease research.

Voxel-Based State Space Modeling Recovers Task-Related Cognitive States in Naturalistic fMRI Experiments

Complex natural tasks likely recruit many different functional brain networks, but it is difficult to predict how such tasks will be represented across cortical areas and networks. Previous electrophysiology studies suggest that task variables are represented in a low-dimensional subspace within the activity space of neural populations. Here we develop a voxel-based state space modeling method for recovering task-related state spaces from human fMRI data. We apply this method to data acquired in a controlled visual attention task and a video game task. We find that each task induces distinct brain states that can be embedded in a low-dimensional state space that reflects task parameters, and that attention increases state separation in the task-related subspace. Our results demonstrate that the state space framework offers a powerful approach for modeling human brain activity elicited by complex natural tasks.

Thalamocortical excitability modulation guides human perception under uncertainty

Knowledge about the relevance of environmental features can guide stimulus processing. However, it remains unclear how processing is adjusted when feature relevance is uncertain. We hypothesized that (a) heightened uncertainty would shift cortical networks from a rhythmic, selective processing-oriented state toward an asynchronous ("excited") state that boosts sensitivity to all stimulus features, and that (b) the thalamus provides a subcortical nexus for such uncertainty-related shifts. Here, we had young adults attend to varying numbers of task-relevant features during EEG and fMRI acquisition to test these hypotheses. Behavioral modeling and electrophysiological signatures revealed that greater uncertainty lowered the rate of evidence accumulation for individual stimulus features, shifted the cortex from a rhythmic to an asynchronous/excited regime, and heightened neuromodulatory arousal. Crucially, this unified constellation of within-person effects was dominantly reflected in the uncertainty-driven upregulation of thalamic activity. We argue that neuromodulatory processes involving the thalamus play a central role in how the brain modulates neural excitability in the face of momentary uncertainty.

An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization

Adolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from childhood to young adulthood. By projecting high-dimensional connectomes into compact manifold spaces, we identified a marked expansion of structural connectomes, with strongest effects in transmodal regions during adolescence. Findings reflected increased within-module connectivity together with increased segregation, indicating increasing differentiation of higher-order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Statistical learning of cortical and subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up. Our findings demonstrate that connectome manifold learning can bridge the conceptual and empirical gaps between macroscale network reconfigurations, microscale processes, and cognitive outcomes in adolescent development.

Topographic gradients of intrinsic dynamics across neocortex

The intrinsic dynamics of neuronal populations are shaped by both microscale attributes and macroscale connectome architecture. Here we comprehensively characterize the rich temporal patterns of neural activity throughout the human brain. Applying massive temporal feature extraction to regional haemodynamic activity, we systematically estimate over 6000 statistical properties of individual brain regions' time-series across the neocortex. We identify two robust spatial gradients of intrinsic dynamics, one spanning a ventromedial-dorsolateral axis and dominated by measures of signal autocorrelation, and the other spanning a unimodal-transmodal axis and dominated by measures of dynamic range. These gradients reflect spatial patterns of gene expression, intracortical myelin and cortical thickness, as well as structural and functional network embedding. Importantly, these gradients are correlated with patterns of meta-analytic functional activation, differentiating cognitive versus affective processing and sensory versus higher-order cognitive processing. Altogether, these findings demonstrate a link between microscale and macroscale architecture, intrinsic dynamics, and cognition.

Diffuse neural coupling mediates complex network dynamics through the formation of quasi-critical brain states

The biological mechanisms that allow the brain to balance flexibility and integration remain poorly understood. A potential solution may lie in a unique aspect of neurobiology, which is that numerous brain systems contain diffuse synaptic connectivity. Here, we demonstrate that increasing diffuse cortical coupling within a validated biophysical corticothalamic model traverses the system through a quasi-critical regime in which spatial heterogeneities in input noise support transient critical dynamics in distributed subregions. The presence of quasi-critical states coincides with known signatures of complex, adaptive brain network dynamics. Finally, we demonstrate the presence of similar dynamic signatures in empirical whole-brain human neuroimaging data. Together, our results establish that modulating the balance between local and diffuse synaptic coupling in a thalamocortical model subtends the emergence of quasi-critical brain states that act to flexibly transition the brain between unique modes of information processing.

Generative Embeddings of Brain Collective Dynamics Using Variational Autoencoders

We consider the problem of encoding pairwise correlations between coupled dynamical systems in a low-dimensional latent space based on few distinct observations. We use variational autoencoders (VAEs) to embed temporal correlations between coupled nonlinear oscillators that model brain states in the wake-sleep cycle into a two-dimensional manifold. Training a VAE with samples generated using two different parameter combinations results in an embedding that encodes the repertoire of collective dynamics, as well as the topology of the underlying connectivity network. We first follow this approach to infer the trajectory of brain states measured from wakefulness to deep sleep from the two end points of this trajectory; then, we show that the same architecture was capable of representing the pairwise correlations of generic Landau-Stuart oscillators coupled by complex network topology.

The thalamus integrates the macrosystems of the brain to facilitate complex, adaptive brain network dynamics

The human brain is a complex, adaptive system comprised of billions of cells with trillions of connections. The interactions between the elements of the system oppose this seemingly limitless capacity by constraining the system's dynamic repertoire, enforcing distributed neural states that balance integration and differentiation. How this trade-off is mediated by the brain, and how the emergent, distributed neural patterns give rise to cognition and awareness, remains poorly understood. Here, I argue that the thalamus is well-placed to arbitrate the interactions between distributed neural assemblies in the cerebral cortex. Different classes of thalamocortical connections are hypothesized to promote either feed-forward or feedback processing modes in the cerebral cortex. This activity can be conceptualized as emerging dynamically from an evolving attractor landscape, with the relative engagement of distinct distributed circuits providing differing constraints over the manner in which brain state trajectories change over time. In addition, inputs to the distinct thalamic populations from the cerebellum and basal ganglia, respectively, are proposed to differentially shape the attractor landscape, and hence, the temporal evolution of cortical assemblies. The coordinated engagement of these neural macrosystems is then shown to share key characteristics with prominent models of cognition, attention and conscious awareness. In this way, the crucial role of the thalamus in mediating the distributed, multi-scale network organization of the central nervous system can be related to higher brain function.

A multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain

The vast net of fibres within and underneath the cortex is optimised to support the convergence of different levels of brain organisation. Here, we propose a novel coordinate system of the human cortex based on an advanced model of its connectivity. Our approach is inspired by seminal, but so far largely neglected models of cortico-cortical wiring established by postmortem anatomical studies and capitalises on cutting-edge in vivo neuroimaging and machine learning. The new model expands the currently prevailing diffusion magnetic resonance imaging (MRI) tractography approach by incorporation of additional features of cortical microstructure and cortico-cortical proximity. Studying several datasets and different parcellation schemes, we could show that our coordinate system robustly recapitulates established sensory-limbic and anterior-posterior dimensions of brain organisation. A series of validation experiments showed that the new wiring space reflects cortical microcircuit features (including pyramidal neuron depth and glial expression) and allowed for competitive simulations of functional connectivity and dynamics based on resting-state functional magnetic resonance imaging (rs-fMRI) and human intracranial electroencephalography (EEG) coherence. Our results advance our understanding of how cell-specific neurobiological gradients produce a hierarchical cortical wiring scheme that is concordant with increasing functional sophistication of human brain organisation. Our evaluations demonstrate the cortical wiring space bridges across scales of neural organisation and can be easily translated to single individuals.

Temporal embedding and spatiotemporal feature selection boost multi-voxel pattern analysis decoding accuracy

BACKGROUND

In fMRI decoding, temporal embedding of spatial features of the brain allows the incorporation of brain activity dynamics into the multivariate pattern classification process, and provides enriched information about stimulus-specific response patterns and potentially improved prediction accuracy.

NEW METHOD

This study investigates the possibility of enhancing the classification performance by exploring temporal embedding, to identify the optimum combination of spatiotemporal features based on their classification performance. We investigated the importance of spatiotemporal feature selection using a slow event-related design adapted from the classic Haxby study (Haxby et al., 2001). Data were collected using a multiband fMRI sequence with temporal resolution of 0.568 s.

COMPARISON WITH EXISTING METHODS

A wide range of spatiotemporal observations were created as various combinations of spatiotemporal features. Using both random forest, and support vector machine, classifiers prediction accuracies for these combinations were then compared with the single spatial multivariate pattern approach that uses only a single temporal observation.

RESULTS

Our findings showed that, on average, spatiotemporal feature selection improved prediction accuracy. Moreover, the random forest algorithm outperformed the support vector machine and benefitted from temporal information to a greater extent.

CONCLUSIONS

As expected, the most influential temporal durations were found to be around the peak of the hemodynamic response function, a few seconds after the stimuli onset until -4 s after the peak of the hemodynamic response function. The superiority of spatiotemporal feature selection over single time-point spatial approaches invites future work to design optimal approaches that incorporate spatiotemporal dependencies into feature selection for decoding.

Topographic organization of the human subcortex unveiled with functional connectivity gradients

Brain atlases are fundamental to understanding the topographic organization of the human brain, yet many contemporary human atlases cover only the cerebral cortex, leaving the subcortex a terra incognita. We use functional MRI (fMRI) to map the complex topographic organization of the human subcortex, revealing large-scale connectivity gradients and new areal boundaries. We unveil four scales of subcortical organization that recapitulate well-known anatomical nuclei at the coarsest scale and delineate 27 new bilateral regions at the finest. Ultrahigh field strength fMRI corroborates and extends this organizational structure, enabling the delineation of finer subdivisions of the hippocampus and the amygdala, while task-evoked fMRI reveals a subtle subcortical reorganization in response to changing cognitive demands. A new subcortical atlas is delineated, personalized to represent individual differences and used to uncover reproducible brain-behavior relationships. Linking cortical networks to subcortical regions recapitulates a task-positive to task-negative axis. This new atlas enables holistic connectome mapping and characterization of cortico-subcortical connectivity.

Reductions in task positive neural systems occur with the passage of time and are associated with changes in ongoing thought

Cognition is dynamic and involves both the maintenance of and transitions between neurocognitive states. While recent research has identified some of the neural systems involved in sustaining task states, it is less well understood how intrinsic influences on cognition emerge over time. The current study uses fMRI and Multi-Dimensional Experience Sampling (MDES) to chart how cognition changes over time from moments in time when external attention was established. We found that the passage of time was associated with brain regions associated with external attention decreasing in activity over time. Comparing this pattern of activity to defined functional hierarchies of brain organization, we found that it could be best understood as movement away from systems involved in task performance. Moments where the participants described their thoughts as off-task showed a significant similarity to the task-negative end of the same hierarchy. Finally, the greater the similarity of a participant's neural dynamics to this hierarchy the faster their rate of increasing off-task thought over time. These findings suggest topographical changes in neural processing that emerge over time and those seen during off-task thought can both be understood as a common shift away from neural motifs seen during complex task performance.