A practical evaluation of measures derived from compressed sensing diffusion spectrum imaging

Diffusion Spectrum Imaging (DSI) using dense Cartesian sampling of q-space has been shown to provide important advantages for modeling complex white matter architecture. However, its adoption has been limited by the lengthy acquisition time required. Sparser sampling of q-space combined with compressed sensing (CS) reconstruction techniques has been proposed as a way to reduce the scan time of DSI acquisitions. However prior studies have mainly evaluated CS-DSI in post-mortem or non-human data. At present, the capacity for CS-DSI to provide accurate and reliable measures of white matter anatomy and microstructure in the living human brain remains unclear. We evaluated the accuracy and inter-scan reliability of 6 different CS-DSI schemes that provided up to 80% reductions in scan time compared to a full DSI scheme. We capitalized on a dataset of 26 participants who were scanned over eight independent sessions using a full DSI scheme. From this full DSI scheme, we subsampled images to create a range of CS-DSI images. This allowed us to compare the accuracy and inter-scan reliability of derived measures of white matter structure (bundle segmentation, voxel-wise scalar maps) produced by the CS-DSI and the full DSI schemes. We found that CS-DSI estimates of both bundle segmentations and voxel-wise scalars were nearly as accurate and reliable as those generated by the full DSI scheme. Moreover, we found that the accuracy and reliability of CS-DSI was higher in white matter bundles that were more reliably segmented by the full DSI scheme. As a final step, we replicated the accuracy of CS-DSI in a prospectively acquired dataset (n = 20, scanned once). Together, these results illustrate the utility of CS-DSI for reliably delineating in vivo white matter architecture in a fraction of the scan time, underscoring its promise for both clinical and research applications.

Stress affects navigation strategies in immersive virtual reality

There are known individual differences in both the ability to learn the layout of novel environments and the flexibility of strategies for navigating known environments. However, it is unclear how navigational abilities are impacted by high-stress scenarios. Here we used immersive virtual reality (VR) to develop a novel behavioral paradigm to examine navigation under dynamically changing situations. We recruited 48 participants (24 female; ages 17-32) to navigate a virtual maze (7.5 m × 7.5 m). Participants learned the maze by moving along a fixed path past the maze's landmarks (paintings). Subsequently, participants experienced either a non-stress condition, or a high-stress condition tasking them with navigating the maze. In the high-stress condition, their initial path was blocked, the environment was darkened, threatening music was played, fog obstructed more distal views of the environment, and participants were given a time limit of 20 s with a countdown timer displayed at the top of their screen. On trials where the path was blocked, we found self-reported stress levels and distance traveled increased while trial completion rate decreased (as compared to non-stressed control trials). On unblocked stress trials, participants were less likely to take a shortcut and consequently navigated less efficiently compared to control trials. Participants with more trait spatial anxiety reported more stress and navigated less efficiently. Overall, our results suggest that navigational abilities change considerably under high-stress conditions.

Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts

Active reinforcement learning enables dynamic prediction and control, where one should not only maximize rewards but also minimize costs such as of inference, decisions, actions, and time. For an embodied agent such as a human, decisions are also shaped by physical aspects of actions. Beyond the effects of reward outcomes on learning processes, to what extent can modeling of behavior in a reinforcement-learning task be complicated by other sources of variance in sequential action choices? What of the effects of action bias (for actions per se) and action hysteresis determined by the history of actions chosen previously? The present study addressed these questions with incremental assembly of models for the sequential choice data from a task with hierarchical structure for additional complexity in learning. With systematic comparison and falsification of computational models, human choices were tested for signatures of parallel modules representing not only an enhanced form of generalized reinforcement learning but also action bias and hysteresis. We found evidence for substantial differences in bias and hysteresis across participants-even comparable in magnitude to the individual differences in learning. Individuals who did not learn well revealed the greatest biases, but those who did learn accurately were also significantly biased. The direction of hysteresis varied among individuals as repetition or, more commonly, alternation biases persisting from multiple previous actions. Considering that these actions were button presses with trivial motor demands, the idiosyncratic forces biasing sequences of action choices were robust enough to suggest ubiquity across individuals and across tasks requiring various actions. In light of how bias and hysteresis function as a heuristic for efficient control that adapts to uncertainty or low motivation by minimizing the cost of effort, these phenomena broaden the consilient theory of a mixture of experts to encompass a mixture of expert and nonexpert controllers of behavior.

Diffusion MRI head motion correction methods are highly accurate but impacted by denoising and sampling scheme

Head motion correction is particularly challenging in diffusion-weighted MRI (dMRI) scans due to the dramatic changes in image contrast at different gradient strengths and directions. Head motion correction is typically performed using a Gaussian Process model implemented in FSL's Eddy. Recently, the 3dSHORE-based SHORELine method was introduced that does not require shell-based acquisitions, but it has not been previously benchmarked. Here we perform a comprehensive evaluation of both methods on realistic simulations of a software fiber phantom that provides known ground-truth head motion. We demonstrate that both methods perform remarkably well, but that performance can be impacted by sampling scheme and the extent of head motion and the denoising strategy applied before head motion correction. Furthermore, we find Eddy benefits from denoising the data first with MP-PCA. In sum, we provide the most extensive known benchmarking of dMRI head motion correction, together with extensive simulation data and a reproducible workflow. PRACTITIONER POINTS: Both Eddy and SHORELine head motion correction methods performed quite well on a large variety of simulated data. Denoising with MP-PCA can improve head motion correction performance when Eddy is used. SHORELine effectively corrects motion in non-shelled diffusion spectrum imaging data.

Non-invasive monitoring of cardiac contractility: Trans-radial electrical bioimpedance velocimetry (TREV)

We describe methods and software resources for a bioimpedance measurement technique, 'trans-radial electrical bioimpedance velocimetry' (TREV) that allows for the non-invasive monitoring of relative cardiac contractility and stroke volume. After reviewing the relationship between the measurement and cardiac contractility, we describe the general recording methodology, which requires impedance measurements of the forearm. We provide open-source Jupyter-based software (operable on most computers) for deriving cardiac contractility from the impedance measurements. The software includes tools for removing variance associated with heart rate and respiration. We demonstrate the ability of this bioimpedance measurement for tracking beat-to-beat changes of contractility in a maximal grip force production task. Critically, the results demonstrate both a reactive increase in contractility with force production, and suggest there is a learned increase in contractility prior to grip onset, consistent with anticipatory allostatic autonomic regulation mediated by sympathetic inotropy. The method and software should be of broad utility for investigations of event-related cardiac dynamics in psychophysical studies.

ReeBundle: A Method for Topological Modeling of White Matter Pathways Using Diffusion MRI

Tractography can generate millions of complex curvilinear fibers (streamlines) in 3D that exhibit the geometry of white matter pathways in the brain. Common approaches to analyzing white matter connectivity are based on adjacency matrices that quantify connection strength but do not account for any topological information. A critical element in neurological and developmental disorders is the topological deterioration and irregularities in streamlines. In this paper, we propose a novel Reeb graph-based method "ReeBundle" that efficiently encodes the topology and geometry of white matter fibers. Given the trajectories of neuronal fiber pathways (neuroanatomical bundle), we re-bundle the streamlines by modeling their spatial evolution to capture geometrically significant events (akin to a fingerprint). ReeBundle parameters control the granularity of the model and handle the presence of improbable streamlines commonly produced by tractography. Further, we propose a new Reeb graph-based distance metric that quantifies topological differences for automated quality control and bundle comparison. We show the practical usage of our method using two datasets: (1) For International Society for Magnetic Resonance in Medicine (ISMRM) dataset, ReeBundle handles the morphology of the white matter tract configurations due to branching and local ambiguities in complicated bundle tracts like anterior and posterior commissures; (2) For the longitudinal repeated measures in the Cognitive Resilience and Sleep History (CRASH) dataset, repeated scans of a given subject acquired weeks apart lead to provably similar Reeb graphs that differ significantly from other subjects, thus highlighting ReeBundle's potential for clinical fingerprinting of brain regions.

Interhemispheric Structural Connectivity Underlies Motor Recovery after Stroke

OBJECTIVE

Although ample evidence highlights that the ipsilesional corticospinal tract (CST) plays a crucial role in motor recovery after stroke, studies on cortico-cortical motor connections remain scarce and provide inconclusive results. Given their unique potential to serve as structural reserve enabling motor network reorganization, the question arises whether cortico-cortical connections may facilitate motor control depending on CST damage.

METHODS

Diffusion spectrum imaging (DSI) and a novel compartment-wise analysis approach were used to quantify structural connectivity between bilateral cortical core motor regions in chronic stroke patients. Basal and complex motor control were differentially assessed.

RESULTS

Both basal and complex motor performance were correlated with structural connectivity between bilateral premotor areas and ipsilesional primary motor cortex (M1) as well as interhemispheric M1 to M1 connectivity. Whereas complex motor skills depended on CST integrity, a strong association between M1 to M1 connectivity and basal motor control was observed independent of CST integrity especially in patients who underwent substantial motor recovery. Harnessing the informational wealth of cortico-cortical connectivity facilitated the explanation of both basal and complex motor control.

INTERPRETATION

We demonstrate for the first time that distinct aspects of cortical structural reserve enable basal and complex motor control after stroke. In particular, recovery of basal motor control may be supported via an alternative route through contralesional M1 and non-crossing fibers of the contralesional CST. Our findings help to explain previous conflicting interpretations regarding the functional role of the contralesional M1 and highlight the potential of cortico-cortical structural connectivity as a future biomarker for motor recovery post-stroke. ANN NEUROL 2023;94:785-797.

Within-subject reproducibility varies in multi-modal, longitudinal brain networks

Network neuroscience provides important insights into brain function by analyzing complex networks constructed from diffusion Magnetic Resonance Imaging (dMRI), functional MRI (fMRI) and Electro/Magnetoencephalography (E/MEG) data. However, in order to ensure that results are reproducible, we need a better understanding of within- and between-subject variability over long periods of time. Here, we analyze a longitudinal, 8 session, multi-modal (dMRI, and simultaneous EEG-fMRI), and multiple task imaging data set. We first confirm that across all modalities, within-subject reproducibility is higher than between-subject reproducibility. We see high variability in the reproducibility of individual connections, but observe that in EEG-derived networks, during both rest and task, alpha-band connectivity is consistently more reproducible than connectivity in other frequency bands. Structural networks show a higher reliability than functional networks across network statistics, but synchronizability and eigenvector centrality are consistently less reliable than other network measures across all modalities. Finally, we find that structural dMRI networks outperform functional networks in their ability to identify individuals using a fingerprinting analysis. Our results highlight that functional networks likely reflect state-dependent variability not present in structural networks, and that the type of analysis should depend on whether or not one wants to take into account state-dependent fluctuations in connectivity.

Decision heuristics in contexts integrating action selection and execution

Heuristics can inform human decision making in complex environments through a reduction of computational requirements (accuracy-resource trade-off) and a robustness to overparameterisation (less-is-more). However, tasks capturing the efficiency of heuristics typically ignore action proficiency in determining rewards. The requisite movement parameterisation in sensorimotor control questions whether heuristics preserve efficiency when actions are nontrivial. We developed a novel action selection-execution task requiring joint optimisation of action selection and spatio-temporal skillful execution. State-appropriate choices could be determined by a simple spatial heuristic, or by more complex planning. Computational models of action selection parsimoniously distinguished human participants who adopted the heuristic from those using a more complex planning strategy. Broader comparative analyses then revealed that participants using the heuristic showed combined decisional (selection) and skill (execution) advantages, consistent with a less-is-more framework. In addition, the skill advantage of the heuristic group was predominantly in the core spatial features that also shaped their decision policy, evidence that the dimensions of information guiding action selection might be yoked to salient features in skill learning.

Habituation of the stress response multiplex to repeated cold pressor exposure

Humans show remarkable habituation to aversive events as reflected by changes of both subjective report and objective measures of stress. Although much experimental human research focuses on the effects of stress, relatively little is known about the cascade of physiological and neural responses that contribute to stress habituation. The cold pressor test (CPT) is a common method for inducing acute stress in human participants in the laboratory; however, there are gaps in our understanding of the global state changes resulting from this stress-induction technique and how these responses change over multiple exposures. Here, we measure the stress response to repeated CPT exposures using an extensive suite of physiologic measures and state-of-the-art analysis techniques. In two separate sessions on different days, participants underwent five 90 s CPT exposures of both feet and five warm water control exposures, while electrocardiography (ECG), impedance cardiography, continuous blood pressure, pupillometry, scalp electroencephalography (EEG), salivary cortisol and self-reported pain assessments were recorded. A diverse array of adaptive responses are reported that vary in their temporal dynamics within each exposure as well as habituation across repeated exposures. During cold-water exposure there was a cascade of changes across several cardiovascular measures (elevated heart rate (HR), cardiac output (CO) and Mean Arterial Pressure (MAP) and reduced left ventricular ejection time (LVET), stroke volume (SV) and high-frequency heart rate variability (HF)). Increased pupil dilation was observed, as was increased power in low-frequency bands (delta and theta) across frontal EEG electrode sites. Several cardiovascular measures also habituated over repeated cold-water exposures (HR, MAP, CO, SV, LVET) as did pupil dilation and alpha frequency activity across the scalp. Anticipation of cold water induced stress effects in the time-period immediately prior to exposure, indexed by increased pupil size and cortical disinhibition in the alpha and beta frequency bands across central scalp sites. These results provide comprehensive insight into the evolution of a diverse array of stress responses to an acute noxious stressor, and how these responses adaptively contribute to stress habituation.

The role of corticospinal and extrapyramidal pathways in motor impairment after stroke

Anisotropy of descending motor pathways has repeatedly been linked to the severity of motor impairment following stroke-related damage to the corticospinal tract. Despite promising findings consistently tying anisotropy of the ipsilesional corticospinal tract to motor outcome, anisotropy is not yet utilized as a biomarker for motor recovery in clinical practice as several methodological constraints hinder a conclusive understanding of degenerative processes in the ipsilesional corticospinal tract and compensatory roles of other descending motor pathways. These constraints include estimating anisotropy in voxels with multiple fibre directions, sampling biases and confounds due to ageing-related atrophy. The present study addressed these issues by combining diffusion spectrum imaging with a novel compartmentwise analysis approach differentiating voxels with one dominant fibre direction (one-directional voxels) from voxels with multiple fibre directions. Compartmentwise anisotropy for bihemispheric corticospinal and extrapyramidal tracts was compared between 25 chronic stroke patients, 22 healthy age-matched controls, and 24 healthy young controls and its associations with motor performance of the upper and lower limbs were assessed. Our results provide direct evidence for Wallerian degeneration along the entire length of the ipsilesional corticospinal tract reflected by decreased anisotropy in descending fibres compared with age-matched controls, while ageing-related atrophy was observed more ubiquitously across compartments. Anisotropy of descending ipsilesional corticospinal tract voxels showed highly robust correlations with various aspects of upper and lower limb motor impairment, highlighting the behavioural relevance of Wallerian degeneration. Moreover, anisotropy measures of two-directional voxels within bihemispheric rubrospinal and reticulospinal tracts were linked to lower limb deficits, while anisotropy of two-directional contralesional rubrospinal voxels explained gross motor performance of the affected hand. Of note, the relevant extrapyramidal structures contained fibres crossing the midline, fibres potentially mitigating output from brain stem nuclei, and fibres transferring signals between the extrapyramidal system and the cerebellum. Thus, specific parts of extrapyramidal pathways seem to compensate for impaired gross arm and leg movements incurred through stroke-related corticospinal tract lesions, while fine motor control of the paretic hand critically relies on ipsilesional corticospinal tract integrity. Importantly, our findings suggest that the extrapyramidal system may serve as a compensatory structural reserve independent of post-stroke reorganization of extrapyramidal tracts. In summary, compartment-specific anisotropy of ipsilesional corticospinal tract and extrapyramidal tracts explained distinct aspects of motor impairment, with both systems representing different pathophysiological mechanisms contributing to motor control post-stroke. Considering both systems in concert may help to develop diffusion imaging biomarkers for specific motor functions after stroke.

Reinforcement learning with associative or discriminative generalization across states and actions: fMRI at 3 T and 7 T

The model-free algorithms of "reinforcement learning" (RL) have gained clout across disciplines, but so too have model-based alternatives. The present study emphasizes other dimensions of this model space in consideration of associative or discriminative generalization across states and actions. This "generalized reinforcement learning" (GRL) model, a frugal extension of RL, parsimoniously retains the single reward-prediction error (RPE), but the scope of learning goes beyond the experienced state and action. Instead, the generalized RPE is efficiently relayed for bidirectional counterfactual updating of value estimates for other representations. Aided by structural information but as an implicit rather than explicit cognitive map, GRL provided the most precise account of human behavior and individual differences in a reversal-learning task with hierarchical structure that encouraged inverse generalization across both states and actions. Reflecting inference that could be true, false (i.e., overgeneralization), or absent (i.e., undergeneralization), state generalization distinguished those who learned well more so than action generalization. With high-resolution high-field fMRI targeting the dopaminergic midbrain, the GRL model's RPE signals (alongside value and decision signals) were localized within not only the striatum but also the substantia nigra and the ventral tegmental area, including specific effects of generalization that also extend to the hippocampus. Factoring in generalization as a multidimensional process in value-based learning, these findings shed light on complexities that, while challenging classic RL, can still be resolved within the bounds of its core computations.

Combining Repetition Suppression and Pattern Analysis Provides New Insights into the Role of M1 and Parietal Areas in Skilled Sequential Actions

How does the brain change during learning? In functional magnetic resonance imaging (fMRI) studies, both multivariate pattern analysis (MVPA) and repetition suppression (RS) have been used to detect changes in neuronal representations. In the context of motor sequence learning, the two techniques have provided discrepant findings: pattern analysis showed that only premotor and parietal regions, but not primary motor cortex (M1), develop a representation of trained sequences. In contrast, RS suggested trained sequence representations in all these regions. Here, we applied both analysis techniques to a five-week finger sequence training study, in which participants executed each sequence twice before switching to a different sequence. Both RS and pattern analysis indicated learning-related changes for parietal areas, but only RS showed a difference between trained and untrained sequences in M1. A more fine-grained analysis, however, revealed that the RS effect in M1 reflects a fundamentally different process than in parietal areas. On the first execution, M1 represents especially the first finger of each sequence, likely reflecting preparatory processes. This effect dramatically reduces during the second execution. In contrast, parietal areas represent the identity of a sequence, and this representation stays relatively stable on the second execution. These results suggest that the RS effect does not reflect a trained sequence representation in M1, but rather a preparatory signal for movement initiation. More generally, our study demonstrates that across regions RS can reflect different representational changes in the neuronal population code, emphasizing the importance of combining pattern analysis and RS techniques.SIGNIFICANCE STATEMENT Previous studies using pattern analysis have suggested that primary motor cortex (M1) does not represent learnt sequential actions. However, a study using repetition suppression (RS) has reported M1 changes during motor sequence learning. Combining both techniques, we first replicate the discrepancy between them, with learning-related changes in M1 in RS, but not pattern dissimilarities. We further analyzed the representational changes with repetition, and found that the RS effects differ across regions. M1's activity represents the starting finger of the sequence, an effect that vanishes with repetition. In contrast, activity patterns in parietal areas exhibit sequence dependency, which persists with repetition. These results demonstrate the importance of combining RS and pattern analysis to understand the function of brain regions.

QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data

Diffusion-weighted magnetic resonance imaging (dMRI) is the primary method for noninvasively studying the organization of white matter in the human brain. Here we introduce QSIPrep, an integrative software platform for the processing of diffusion images that is compatible with nearly all dMRI sampling schemes. Drawing on a diverse set of software suites to capitalize on their complementary strengths, QSIPrep facilitates the implementation of best practices for processing of diffusion images.

Motor adaptation via distributional learning

Objective. Both artificial and biological controllers experience errors during learning that are probabilistically distributed. We develop a framework for modeling distributions of errors and relating deviations in these distributions to neural activity.Approach. The biological system we consider is a task where human subjects are required to learn to minimize the roll of an inverted T-shaped object with an unbalanced weight (i.e. one side of the object is heavier than the other side) during lift. We also collect BOLD activity during this process. For our experimental setup, we define the state of the system to be the maximum magnitude roll of the object after lift onset and give subjects the goal of achieving the zero state.Main Results. We derive a model for this problem from a variant of Temporal Difference Learning. We then combine this model with Distributional Reinforcement Learning (DRL), a framework that involves defining a value distribution by treating the reward as stochastic. This model transforms the goal of the controller from achieving a target state, to achieving a distribution over distances from the target state. We call it a Distributional Temporal Difference Model (DTDM). The DTDM allows us to model errors in unsuccessfully minimizing object roll using deviations in the value distribution when the center of mass of the unbalanced object is changed. We compute deviations in global neural activity and show that they vary continuously with deviations in the value distribution. Different aspects might contribute to this global shift or signal difference, including a difference in grasp and lift force at lift onset, as well as sensory feedback of error/roll after lift onset. We predict that there exists a coordinated, global response to errors that incorporates all of this information, which is encoding the DTDM objective and used on subsequent trials enabling success. We validate the utility of the DTDM as a model for biological adaptation by using it to engineer a robotic controller to solve a similar problem.Significance. We develop a novel theoretical framework and show that it can be used to model a non-trivial motor learning task. Because this theoretical framework is consistent with state-of-the-art reinforcement learning, we can also use it to program a robot to perform a similar task. These results suggest a way to model the multiple subsystems composing global neural activity in a way that transfers well to engineering artificial intelligence.

Ventromedial Prefrontal Cortex Activity and Sympathetic Allostasis During Value-Based Ambivalence

Anxiety is characterized by low confidence in daily decisions, coupled with high levels of phenomenological stress. Ventromedial prefrontal cortex (vmPFC) plays an integral role in maladaptive anxious behaviors via decreased sensitivity to threatening vs. non-threatening stimuli (fear generalization). vmPFC is also a key node in approach-avoidance decision making requiring two-dimensional integration of rewards and costs. More recently, vmPFC has been implicated as a key cortical input to the sympathetic branch of the autonomic nervous system. However, little is known about the role of this brain region in mediating rapid stress responses elicited by changes in confidence during decision making. We used an approach-avoidance task to examine the relationship between sympathetically mediated cardiac stress responses, vmPFC activity and choice behavior over long and short time-scales. To do this, we collected concurrent fMRI, EKG and impedance cardiography recordings of sympathetic drive while participants made approach-avoidance decisions about monetary rewards paired with painful electric shock stimuli. We observe first that increased sympathetic drive (shorter pre-ejection period) in states lasting minutes are associated with choices involving reduced decision ambivalence. Thus, on this slow time scale, sympathetic drive serves as a proxy for "mobilization" whereby participants are more likely to show consistent value-action mapping. In parallel, imaging analyses reveal that on shorter time scales (estimated with a trial-to-trial GLM), increased vmPFC activity, particularly during low-ambivalence decisions, is associated with decreased sympathetic state. Our findings support a role of sympathetic drive in resolving decision ambivalence across long time horizons and suggest a potential role of vmPFC in modulating this response on a moment-to-moment basis.

Dynamic community detection reveals transient reorganization of functional brain networks across a female menstrual cycle

Sex steroid hormones have been shown to alter regional brain activity, but the extent to which they modulate connectivity within and between large-scale functional brain networks over time has yet to be characterized. Here, we applied dynamic community detection techniques to data from a highly sampled female with 30 consecutive days of brain imaging and venipuncture measurements to characterize changes in resting-state community structure across the menstrual cycle. Four stable functional communities were identified, consisting of nodes from visual, default mode, frontal control, and somatomotor networks. Limbic, subcortical, and attention networks exhibited higher than expected levels of nodal flexibility, a hallmark of between-network integration and transient functional reorganization. The most striking reorganization occurred in a default mode subnetwork localized to regions of the prefrontal cortex, coincident with peaks in serum levels of estradiol, luteinizing hormone, and follicle stimulating hormone. Nodes from these regions exhibited strong intranetwork increases in functional connectivity, leading to a split in the stable default mode core community and the transient formation of a new functional community. Probing the spatiotemporal basis of human brain–hormone interactions with dynamic community detection suggests that hormonal changes during the menstrual cycle result in temporary, localized patterns of brain network reorganization.

Sex steroid hormones influence the central nervous system across multiple spatiotemporal scales. Estrogen and progesterone concentrations rise and fall throughout the menstrual cycle, but it remains poorly understood whether day-to-day fluctuations in hormones shape human brain dynamics. Here, we assessed the structure and stability of resting-state brain network connectivity in concordance with serum hormone levels from a female who underwent fMRI and venipuncture for 30 consecutive days. Our results reveal that while network structure is largely stable over the course of a menstrual cycle, temporary reorganization of several large-scale functional brain networks occurs during the ovulatory window. In particular, a default mode subnetwork exhibits increased connectivity with itself and with nodes belonging to the temporoparietal and limbic networks, providing novel perspective into brain-hormone interactions.

Cerebellar network organization across the human menstrual cycle

The cerebellum contains the vast majority of neurons in the brain and houses distinct functional networks that constitute at least two homotopic maps of cerebral networks. It is also a major site of sex steroid hormone action. While the functional organization of the human cerebellum has been characterized, the influence of sex steroid hormones on intrinsic cerebellar network dynamics has yet to be established. Here we investigated the extent to which endogenous fluctuations in estradiol and progesterone alter functional cerebellar networks at rest in a woman densely sampled over a complete menstrual cycle (30 consecutive days). Edgewise regression analysis revealed robust negative associations between progesterone and cerebellar coherence. Graph theory metrics probed sex hormones' influence on topological brain states, revealing relationships between sex hormones and within-network integration in Ventral Attention, Dorsal Attention, and SomatoMotor Networks. Together these results suggest that the intrinsic dynamics of the cerebellum are intimately tied to day-by-day changes in sex hormones.

Overt and Covert Object Features Mediate Timing of Patterned Brain Activity during Motor Planning

Humans are seamless in their ability to efficiently and reliably generate fingertip forces to gracefully interact with objects. Such interactions rarely end in awkward outcomes like spilling, crushing, or tilting given advanced motor planning. Here we combine multiband imaging with deconvolution- and Bayesian pattern component modeling of functional magnetic resonance imaging data and in-scanner kinematics, revealing compelling evidence that the human brain differentially represents preparatory information for skillful object interactions depending on the saliency of visual cues. Earlier patterned activity was particularly evident in ventral visual processing stream-, but also selectively in dorsal visual processing stream and cerebellum in conditions of heightened uncertainty when an object’s superficial shape was incompatible rather than compatible with a key underlying object feature.

Structural Disconnection of the Tool Use Network after Left Hemisphere Stroke Predicts Limb Apraxia Severity

Producing a tool use gesture is a complex process drawing upon the integration of stored knowledge of tools and their associated actions with sensory-motor mechanisms supporting the planning and control of hand and arm actions. Understanding how sensory-motor systems in parietal cortex interface with semantic representations of actions and objects in the temporal lobe remains a critical issue and is hypothesized to be a key determinant of the severity of limb apraxia, a deficit in producing skilled action after left hemisphere stroke. We used voxel-based and connectome-based lesion-symptom mapping with data from 57 left hemisphere stroke participants to assess the lesion sites and structural disconnection patterns associated with poor tool use gesturing. We found that structural disconnection among the left inferior parietal lobule, lateral and ventral temporal cortices, and middle and superior frontal gyri predicted the severity of tool use gesturing performance. Control analyses demonstrated that reductions in right-hand grip strength were associated with motor system disconnection, largely bypassing regions supporting tool use gesturing. Our findings provide evidence that limb apraxia may arise, in part, from a disconnection between conceptual representations in the temporal lobe and mechanisms enabling skilled action production in the inferior parietal lobule.

Functional reorganization of brain networks across the human menstrual cycle

The brain is an endocrine organ, sensitive to the rhythmic changes in sex hormone production that occurs in most mammalian species. In rodents and nonhuman primates, estrogen and progesterone's impact on the brain is evident across a range of spatiotemporal scales. Yet, the influence of sex hormones on the functional architecture of the human brain is largely unknown. In this dense-sampling, deep phenotyping study, we examine the extent to which endogenous fluctuations in sex hormones alter intrinsic brain networks at rest in a woman who underwent brain imaging and venipuncture for 30 consecutive days. Standardized regression analyses illustrate estrogen and progesterone's widespread associations with functional connectivity. Time-lagged analyses examined the temporal directionality of these relationships and suggest that cortical network dynamics (particularly in the Default Mode and Dorsal Attention Networks, whose hubs are densely populated with estrogen receptors) are preceded-and perhaps driven-by hormonal fluctuations. A similar pattern of associations was observed in a follow-up study one year later. Together, these results reveal the rhythmic nature in which brain networks reorganize across the human menstrual cycle. Neuroimaging studies that densely sample the individual connectome have begun to transform our understanding of the brain's functional organization. As these results indicate, taking endocrine factors into account is critical for fully understanding the intrinsic dynamics of the human brain.

Neural substrates of anticipatory motor adaptation for object lifting

Anticipatory force control is a fundamental means by which humans stave off slipping, spilling, and tilting disasters while manipulating objects. This control must often be adapted due to changes in an object’s dynamics (e.g. a lighter than expected mug of coffee) or its relation with involved effectors or digits (e.g. lift a mug with three vs. five digits). The neural processes guiding such anticipatory and adaptive control is understudied but presumably operates along multiple time scales, analogous to what has been identified with adaptation in other motor tasks, such as perturbations during reaching. Learning of anticipatory forces must be ultrafast to minimize tilting a visually symmetric object towards its concealed asymmetric center of mass (CoM), but slower when the CoM is explicitly and systematically switched from side to side. Studying the neural substrates of this latter slower learning process with rapid multiband brain imaging, in-scanner kinematics and Bayesian pattern component modelling, we show that CoM-specific pattern distances increase with repeated CoM switching exposures and improved learning. The cerebellum showed the most prominent effects, fitting with the idea that it forms a stored internal model that is used to build and update anticipatory control. CoM-specific pattern distances were present 24 h later, in line with the presence of consolidation effects.

Representational Neural Mapping of Dexterous Grasping Before Lifting in Humans

The ability of humans to reach and grasp objects in their environment has been the mainstay paradigm for characterizing the neural circuitry driving object-centric actions. Although much is known about hand shaping, a persistent question is how the brain orchestrates and integrates the grasp with lift forces of the fingers in a coordinated manner. The objective of the current study was to investigate how the brain represents grasp configuration and lift force during a dexterous object-centric action in a large sample of male and female human subjects. BOLD activity was measured as subjects used a precision-grasp to lift an object with a center of mass (CoM) on the left or right with the goal of minimizing tilting the object. The extent to which grasp configuration and lift force varied between left and right CoM conditions was manipulated by grasping the object collinearly (requiring a non-collinear force distribution) or non-collinearly (requiring more symmetrical forces). Bayesian variational representational similarity analyses on fMRI data assessed the evidence that a set of cortical and cerebellar regions were sensitive to grasp configuration or lift force differences between CoM conditions at differing time points during a grasp to lift action. In doing so, we reveal strong evidence that grasping and lift force are not represented by spatially separate functionally specialized regions, but by the same regions at differing time points. The coordinated grasp to lift effort is shown to be under dorsolateral (PMv and AIP) more than dorsomedial control, and under SPL7, somatosensory PSC, ventral LOC and cerebellar control.SIGNIFICANCE STATEMENT Clumsy disasters such as spilling, dropping, and crushing during our daily interactions with objects are a rarity rather than the norm. These disasters are avoided in part as a result of our orchestrated anticipatory efforts to integrate and coordinate grasping and lifting of object interactions, all before the lift of an object even commences. How the brain orchestrates this integration process has been largely neglected by historical approaches independently and solely focusing on reaching and grasping and the neural principles that guide them. Here, we test the extent to which grasping and lifting are represented in a spatially or temporally distinct manner and identified strong evidence for the consecutive emergence of sensitivity to grasping, then lifting within the same region.

Subjective value then confidence in human ventromedial prefrontal cortex

Two fundamental goals of decision making are to select actions that maximize rewards while minimizing costs and to have strong confidence in the accuracy of a judgment. Neural signatures of these two forms of value: the subjective value (SV) of choice alternatives and the value of the judgment (confidence), have both been observed in ventromedial prefrontal cortex (vmPFC). However, the relationship between these dual value signals and their relative time courses are unknown. Twenty-eight men and women underwent fMRI while performing a two-phase approach-avoidance (Ap-Av) task with mixed-outcomes of monetary rewards paired with painful shock stimuli. Neural responses were measured during offer valuation (offer phase) and choice valuation (commit phase) and analyzed with respect to observed decision outcomes, model-estimated SV and confidence. During the offer phase, vmPFC tracked SV and the decision but not confidence. During the commit phase, vmPFC tracked confidence, computed as the quadratic extension of SV, but not the offer valuation nor the decision. In fact, vmPFC responses from the commit phase were selective for confidence even for reject decisions wherein confidence and SV are inversely related. Conversely, activation of the cognitive control network, including within lateral prefrontal cortex (lPFC) and dorsal anterior cingulate cortex (dACC) was associated with ambivalence, during both the offer and commit phases. Taken together, our results reveal complementary representations in vmPFC during value-based decision making that temporally dissociate such that offer valuation (SV) emerges before decision valuation (confidence).

Finding maximally disconnected subnetworks with shortest path tractography

Connectome-based lesion symptom mapping (CLSM) can be used to relate disruptions of brain network connectivity with clinical measures. We present a novel method that extends current CLSM approaches by introducing a fast reliable and accurate way for computing disconnectomes, i.e. identifying damaged or lesioned connections. We introduce a new algorithm that finds the maximally disconnected subgraph containing regions and region pairs with the greatest shared connectivity loss. After normalizing a stroke patient's segmented MRI lesion into template space, probability weighted structural connectivity matrices are constructed from shortest paths found in white matter voxel graphs of 210 subjects from the Human Connectome Project. Percent connectivity loss matrices are constructed by measuring the proportion of shortest-path probability weighted connections that are lost because of an intersection with the patient's lesion. Maximally disconnected subgraphs of the overall connectivity loss matrix are then derived using a computationally fast greedy algorithm that closely approximates the exact solution. We illustrate the approach in eleven stroke patients with hemiparesis by identifying expected disconnections of the corticospinal tract (CST) with cortical sensorimotor regions. Major disconnections are found in the thalamus, basal ganglia, and inferior parietal cortex. Moreover, the size of the maximally disconnected subgraph quantifies the extent of cortical disconnection and strongly correlates with multiple clinical measures. The methods provide a fast, reliable approach for both visualizing and quantifying the disconnected portion of a patient's structural connectome based on their routine clinical MRI, without reliance on concomitant diffusion weighted imaging. The method can be extended to large databases of stroke patients, multiple sclerosis or other diseases causing focal white matter injuries helping to better characterize clinically relevant white matter lesions and to identify biomarkers for the recovery potential of individual patients.

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Significantly accelerated shortest path tractography approach for constructing connectomes and disconnectomes.

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New algorithm extracts the subnetwork containing cortical connections and regions with maximal shared connectivity loss.

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The size of the maximally disconnected subnetwork quantifies the extent of disconnection and correlates with stroke measures.

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Fast and accurate approach for visualizing and analyzing the disconnected portion of a patient's structural connectome.

Monitoring of postural sway with a head-mounted wearable device: effects of gender, participant state, and concussion

Objective: To assess the utility of a head-mounted wearable inertial motion unit (IMU)-based sensor and 3 proposed measures of postural sway to detect outliers in athletic populations at risk of balance impairments.

Methods: Descriptive statistics are used to define a normative reference range of postural sway (eyes open and eyes closed) in a cross-sectional sample of 347 college students using a wireless head-mounted IMU-based sensor. Three measures of postural sway were derived: linear sway power, eyes closed vs eyes open sway power ratio (Ec/Eo ratio), and weight-bearing asymmetry (L-R ratio), and confidence intervals for these measures were calculated. Questionnaires were used to identify potentially confounding state variables. A prospective study of postural sway changes in 47 professional, college, and high school athletes was then carried out in on-field settings to provide estimates of session-to-session variability and the influence of routine physical activity on sway measures. Finally, pre-post-injury changes in sway are measured for a participant who was diagnosed with a concussion.

Results: Despite the heterogenous population and sampling environments, well-defined confidence intervals were established for all 3 sway measures. Men demonstrated significantly greater sway than women. Two state variables significantly increased sway: the use of nicotine and prescription medications. In the athletes, session-to-session variability and changes due to routine physical activity remained well within 95% confidence intervals defined by the cross-sectional sample for all 3 sway measures. The increase in sway power following a diagnosed concussion was more than an order of magnitude greater than the increases due to session-to-session variability, physical activity, or other participant state variables.

Conclusion: The proposed postural sway measures and head-mounted wearable sensor demonstrate analytic utility for on-field detection of abnormal sway that could be potentially useful when making remove-from-activity and return-to-activity decisions for athletes at risk of impact-induced balance impairments.

Effect of different spatial normalization approaches on tractography and structural brain networks

To facilitate the comparison of white matter morphologic connectivity across target populations, it is invaluable to map the data to a standardized neuroanatomical space. Here, we evaluated direct streamline normalization (DSN), where the warping was applied directly to the streamlines, with two publically available approaches that spatially normalize the diffusion data and then reconstruct the streamlines. Prior work has shown that streamlines generated after normalization from reoriented diffusion data do not reliably match the streamlines generated in native space. To test the impact of these different normalization methods on quantitative tractography measures, we compared the reproducibility of the resulting normalized connectivity matrices and network metrics with those originally obtained in native space. The two methods that reconstruct streamlines after normalization led to significant differences in network metrics with large to huge standardized effect sizes, reflecting a dramatic alteration of the same subject’s native connectivity. In contrast, after normalizing with DSN we found no significant difference in network metrics compared with native space with only very small-to-small standardized effect sizes. DSN readily outperformed the other methods at preserving native space connectivity and introduced novel opportunities to define connectome networks without relying on gray matter parcellations.

Direct streamline normalization (DSN) directly warps the streamlines into any template space by using the transformations output from Advanced Normalization Tools (ANTs). DSN overcomes the limitations of diffusion weighted images (DWI) spatial normalization. It allows DWIs to be acquired with any desired sampling scheme. Fiber orientation distributions (FODs) or orientation distribution functions (ODFs) can also be reconstructed using any desired method and streamlines generated using any algorithm. Most importantly, it avoids the problem of generating tracts from FODs or ODFs that have become distorted because of spatial normalization. Our results show that DSN has minimal influence on tractography measures such as tract count and structure and does not significantly alter structural networks with only very small to small effect sizes. We have developed a framework in Python that works with most diffusion software platforms. It is available at http://github.com/clintg6/DSN.

Predicting future learning from baseline network architecture

Human behavior and cognition result from a complex pattern of interactions between brain regions. The flexible reconfiguration of these patterns enables behavioral adaptation, such as the acquisition of a new motor skill. Yet, the degree to which these reconfigurations depend on the brain's baseline sensorimotor integration is far from understood. Here, we asked whether spontaneous fluctuations in sensorimotor networks at baseline were predictive of individual differences in future learning. We analyzed functional MRI data from 19 participants prior to six weeks of training on a new motor skill. We found that visual-motor connectivity was inversely related to learning rate: sensorimotor autonomy at baseline corresponded to faster learning in the future. Using three additional scans, we found that visual-motor connectivity at baseline is a relatively stable individual trait. These results suggest that individual differences in motor skill learning can be predicted from sensorimotor autonomy at baseline prior to task execution.

Spatial coherence of oriented white matter microstructure: Applications to white matter regions associated with genetic similarity

We present a method to discover differences between populations with respect to the spatial coherence of their oriented white matter microstructure in arbitrarily shaped white matter regions. This method is applied to diffusion MRI scans of a subset of the Human Connectome Project dataset: 57 pairs of monozygotic and 52 pairs of dizygotic twins. After controlling for morphological similarity between twins, we identify 3.7% of all white matter as being associated with genetic similarity (35.1 k voxels, p<10^-4, false discovery rate 1.5%), 75% of which spatially clusters into twenty-two contiguous white matter regions. Furthermore, we show that the orientation similarity within these regions generalizes to a subset of 47 pairs of non-twin siblings, and show that these siblings are on average as similar as dizygotic twins. The regions are located in deep white matter including the superior longitudinal fasciculus, the optic radiations, the middle cerebellar peduncle, the corticospinal tract, and within the anterior temporal lobe, as well as the cerebellum, brain stem, and amygdalae. These results extend previous work using undirected fractional anisotrophy for measuring putative heritable influences in white matter. Our multidirectional extension better accounts for crossing fiber connections within voxels. This bottom up approach has at its basis a novel measurement of coherence within neighboring voxel dyads between subjects, and avoids some of the fundamental ambiguities encountered with tractographic approaches to white matter analysis that estimate global connectivity.

The Energy Landscape of Neurophysiological Activity Implicit in Brain Network Structure

A critical mystery in neuroscience lies in determining how anatomical structure impacts the complex functional dynamics of the brain. How does large-scale brain circuitry constrain states of neuronal activity and transitions between those states? We address these questions using a maximum entropy model of brain dynamics informed by white matter tractography. We demonstrate that the most probable brain states - characterized by minimal energy - display common activation profiles across brain areas: local spatially-contiguous sets of brain regions reminiscent of cognitive systems are co-activated frequently. The predicted activation rate of these systems is highly correlated with the observed activation rate measured in a separate resting state fMRI data set, validating the utility of the maximum entropy model in describing neurophysiological dynamics. This approach also offers a formal notion of the energy of activity within a system, and the energy of activity shared between systems. We observe that within- and between-system energies cleanly separate cognitive systems into distinct categories, optimized for differential contributions to integrated versus segregated function. These results support the notion that energetic and structural constraints circumscribe brain dynamics, offering insights into the roles that cognitive systems play in driving whole-brain activation patterns.

Individual differences in compliance and agreement for sleep logs and wrist actigraphy: A longitudinal study of naturalistic sleep in healthy adults

There is extensive laboratory research studying the effects of acute sleep deprivation on biological and cognitive functions, yet much less is known about naturalistic patterns of sleep loss and the potential impact on daily or weekly functioning of an individual. Longitudinal studies are needed to advance our understanding of relationships between naturalistic sleep and fluctuations in human health and performance, but it is first necessary to understand the efficacy of current tools for long-term sleep monitoring. The present study used wrist actigraphy and sleep log diaries to obtain daily measurements of sleep from 30 healthy adults for up to 16 consecutive weeks. We used non-parametric Bland-Altman analysis and correlation coefficients to calculate agreement between subjectively and objectively measured variables including sleep onset time, sleep offset time, sleep onset latency, number of awakenings, the amount of wake time after sleep onset, and total sleep time. We also examined compliance data on the submission of daily sleep logs according to the experimental protocol. Overall, we found strong agreement for sleep onset and sleep offset times, but relatively poor agreement for variables related to wakefulness including sleep onset latency, awakenings, and wake after sleep onset. Compliance tended to decrease significantly over time according to a linear function, but there were substantial individual differences in overall compliance rates. There were also individual differences in agreement that could be explained, in part, by differences in compliance. Individuals who were consistently more compliant over time also tended to show the best agreement and lower scores on behavioral avoidance scale (BIS). Our results provide evidence for convergent validity in measuring sleep onset and sleep offset with wrist actigraphy and sleep logs, and we conclude by proposing an analysis method to mitigate the impact of non-compliance and measurement errors when the two methods provide discrepant estimates.

Spectral mapping of brain functional connectivity from diffusion imaging

Understanding the relationship between the dynamics of neural processes and the anatomical substrate of the brain is a central question in neuroscience. On the one hand, modern neuroimaging technologies, such as diffusion tensor imaging, can be used to construct structural graphs representing the architecture of white matter streamlines linking cortical and subcortical structures. On the other hand, temporal patterns of neural activity can be used to construct functional graphs representing temporal correlations between brain regions. Although some studies provide evidence that whole-brain functional connectivity is shaped by the underlying anatomy, the observed relationship between function and structure is weak, and the rules by which anatomy constrains brain dynamics remain elusive. In this article, we introduce a methodology to map the functional connectivity of a subject at rest from his or her structural graph. Using our methodology, we are able to systematically account for the role of structural walks in the formation of functional correlations. Furthermore, in our empirical evaluations, we observe that the eigenmodes of the mapped functional connectivity are associated with activity patterns associated with different cognitive systems.

Brain state flexibility accompanies motor-skill acquisition

Learning requires the traversal of inherently distinct cognitive states to produce behavioral adaptation. Yet, tools to explicitly measure these states with non-invasive imaging – and to assess their dynamics during learning – remain limited. Here, we describe an approach based on a distinct application of graph theory in which points in time are represented by network nodes, and similarities in brain states between two different time points are represented as network edges. We use a graph-based clustering technique to identify clusters of time points representing canonical brain states, and to assess the manner in which the brain moves from one state to another as learning progresses. We observe the presence of two primary states characterized by either high activation in sensorimotor cortex or high activation in a frontal-subcortical system. Flexible switching among these primary states and other less common states becomes more frequent as learning progresses, and is inversely correlated with individual differences in learning rate. These results are consistent with the notion that the development of automaticity is associated with a greater freedom to use cognitive resources for other processes. Taken together, our work offers new insights into the constrained, low dimensional nature of brain dynamics characteristic of early learning, which give way to less constrained, high-dimensional dynamics in later learning.

Analytic tractography: A closed-form solution for estimating local white matter connectivity with diffusion MRI

White matter structures composed of myelinated axons in the living human brain are primarily studied by diffusion-weighted MRI (dMRI). These long-range projections are typically characterized in a two-step process: dMRI signal is used to estimate the orientation of axon segments within each voxel, then these local orientations are linked together to estimate the spatial extent of putative white matter bundles. Tractography, the process of tracing bundles across voxels, either requires computationally expensive (probabilistic) simulations to model uncertainty in fiber orientation or ignores it completely (deterministic). Furthermore, simulation necessarily generates a finite number of trajectories, introducing "simulation error" to trajectory estimates. Here we introduce a method to analytically (via a closed-form solution) take an orientation distribution function (ODF) from each voxel and calculate the probabilities that a trajectory projects from a voxel into each directly adjacent voxels. We validate our method by demonstrating experimentally that probabilistic simulations converge to our analytically computed transition probabilities at the voxel level as the number of simulated seeds increases. We then show that our method accurately calculates the ground-truth transition probabilities from a publicly available phantom dataset. As a demonstration, we incorporate our analytic method for voxel transition probabilities into the Voxel Graph framework, creating a quantitative framework for assessing white matter structure, which we call "analytic tractography". The long-range connectivity problem is reduced to finding paths in a graph whose adjacency structure reflects voxel-to-voxel analytic transition probabilities. We demonstrate that this approach performs comparably to the current most widely-used probabilistic and deterministic approaches at a fraction of the computational cost. We also demonstrate that analytic tractography works on multiple diffusion sampling schemes, reconstruction method or parameters used to define paths. Open source software compatible with popular dMRI reconstruction software is provided.

Improving resolution of dynamic communities in human brain networks through targeted node removal

Current approaches to dynamic community detection in complex networks can fail to identify multi-scale community structure, or to resolve key features of community dynamics. We propose a targeted node removal technique to improve the resolution of community detection. Using synthetic oscillator networks with well-defined “ground truth” communities, we quantify the community detection performance of a common modularity maximization algorithm. We show that the performance of the algorithm on communities of a given size deteriorates when these communities are embedded in multi-scale networks with communities of different sizes, compared to the performance in a single-scale network. We demonstrate that targeted node removal during community detection improves performance on multi-scale networks, particularly when removing the most functionally cohesive nodes. Applying this approach to network neuroscience, we compare dynamic functional brain networks derived from fMRI data taken during both repetitive single-task and varied multi-task experiments. After the removal of regions in visual cortex, the most coherent functional brain area during the tasks, community detection is better able to resolve known functional brain systems into communities. In addition, node removal enables the algorithm to distinguish clear differences in brain network dynamics between these experiments, revealing task-switching behavior that was not identified with the visual regions present in the network. These results indicate that targeted node removal can improve spatial and temporal resolution in community detection, and they demonstrate a promising approach for comparison of network dynamics between neuroscientific data sets with different resolution parameters.

Sensitivity analysis of human brain structural network construction

Network neuroscience leverages diffusion-weighted magnetic resonance imaging and tractography to quantify structural connectivity of the human brain. However, scientists and practitioners lack a clear understanding of the effects of varying tractography parameters on the constructed structural networks. With diffusion images from the Human Connectome Project (HCP), we characterize how structural networks are impacted by the spatial resolution of brain atlases, total number of tractography streamlines, and grey matter dilation with various graph metrics. We demonstrate how injudicious combinations of highly refined brain parcellations and low numbers of streamlines may inadvertently lead to disconnected network models with isolated nodes. Furthermore, we provide solutions to significantly reduce the likelihood of generating disconnected networks. In addition, for different tractography parameters, we investigate the distributions of values taken by various graph metrics across the population of HCP subjects. Analyzing the ranks of individual subjects within the graph metric distributions, we find that the ranks of individuals are affected differently by atlas scale changes. Our work serves as a guideline for researchers to optimize the selection of tractography parameters and illustrates how biological characteristics of the brain derived in network neuroscience studies can be affected by the choice of atlas parcellation schemes.

Diffusion tractography has been proven to be a promising noninvasive technique to study the network properties of the human brain. However, how various tractography and network construction parameters affect network properties has not been studied using a large cohort of high-quality data. We utilize data provided by the Human Connectome Project to characterize the changes to network properties induced by varying the brain parcellation atlas scales, the number of reconstructed tractography tracks, and the degree of grey matter dilation with graph metrics. We illustrate the importance of increasing the reconstructed track sampling rate when higher atlas scales are used. In addition to changing the raw values of graph metrics, we find that the ranks of individuals relative to the population metric distributions are altered. We further discuss how the dependency of graph metric ranks can affect the brain characteristics derived in group comparison studies using network neuroscience techniques.

Beyond modularity: Fine-scale mechanisms and rules for brain network reconfiguration

The human brain is in constant flux, as distinct areas engage in transient communication to support basic behaviors as well as complex cognition. The collection of interactions between cortical and subcortical areas forms a functional brain network whose topology evolves with time. Despite the nontrivial dynamics that are germane to this networked system, experimental evidence demonstrates that functional interactions organize into putative brain systems that facilitate different facets of cognitive computation. We hypothesize that such dynamic functional networks are organized around a set of rules that constrain their spatial architecture - which brain regions may functionally interact - and their temporal architecture - how these interactions fluctuate over time. To objectively uncover these organizing principles, we apply an unsupervised machine learning approach called non-negative matrix factorization to time-evolving, resting state functional networks in 20 healthy subjects. This machine learning approach automatically groups temporally co-varying functional interactions into subgraphs that represent putative topological modes of dynamic functional architecture. We find that subgraphs are stratified based on both the underlying modular organization and the topographical distance of their strongest interactions: while many subgraphs are largely contained within modules, others span between modules and are expressed differently over time. The relationship between dynamic subgraphs and modular architecture is further highlighted by the ability of time-varying subgraph expression to explain inter-individual differences in module reorganization. Collectively, these results point to the critical role that subgraphs play in constraining the topography and topology of functional brain networks. More broadly, this machine learning approach opens a new door for understanding the architecture of dynamic functional networks during both task and rest states, and for probing alterations of that architecture in disease.

Learning to tie the knot: The acquisition of functional object representations by physical and observational experience

Here we examined neural substrates for physically and observationally learning to construct novel objects, and characterized brain regions associated with each kind of learning using fMRI. Each participant was assigned a training partner, and for five consecutive days practiced tying one group of knots (“tied” condition) or watched their partner tie different knots (“watched” condition) while a third set of knots remained untrained. Functional MRI was obtained prior to and immediately following the week of training while participants performed a visual knot-matching task. After training, a portion of left superior parietal lobule demonstrated a training by scan session interaction. This means this parietal region responded selectively to knots that participants had physically learned to tie in the post-training scan session but not the pre-training scan session. A conjunction analysis on the post-training scan data showed right intraparietal sulcus and right dorsal premotor cortex to respond when viewing images of knots from the tied and watched conditions compared to knots that were untrained during the post-training scan session. This suggests that these brain areas track both physical and observational learning. Together, the data provide preliminary evidence of engagement of brain regions associated with hand-object interactions when viewing objects associated with physical experience, and with observational experience without concurrent physical practice.

Learning about learning: Mining human brain sub-network biomarkers from fMRI data

Modeling the brain as a functional network can reveal the relationship between distributed neurophysiological processes and functional interactions between brain structures. Existing literature on functional brain networks focuses mainly on a battery of network properties in "resting state" employing, for example, modularity, clustering, or path length among regions. In contrast, we seek to uncover functionally connected subnetworks that predict or correlate with cohort differences and are conserved within the subjects within a cohort. We focus on differences in both the rate of learning as well as overall performance in a sensorimotor task across subjects and develop a principled approach for the discovery of discriminative subgraphs of functional connectivity based on imaging acquired during practice. We discover two statistically significant subgraph regions: one involving multiple regions in the visual cortex and another involving the parietal operculum and planum temporale. High functional coherence in the former characterizes sessions in which subjects take longer to perform the task, while high coherence in the latter is associated with high learning rate (performance improvement across trials). Our proposed methodology is general, in that it can be applied to other cognitive tasks, to study learning or to differentiate between healthy patients and patients with neurological disorders, by revealing the salient interactions among brain regions associated with the observed global state. The discovery of such significant discriminative subgraphs promises a better data-driven understanding of the dynamic brain processes associated with high-level cognitive functions.

Quantifying rapid changes in cardiovascular state with a moving ensemble average

MEAP, the moving ensemble analysis pipeline, is a new open-source tool designed to perform multisubject preprocessing and analysis of cardiovascular data, including electrocardiogram (ECG), impedance cardiogram (ICG), and continuous blood pressure (BP). In addition to traditional ensemble averaging, MEAP implements a moving ensemble averaging method that allows for the continuous estimation of indices related to cardiovascular state, including cardiac output, preejection period, heart rate variability, and total peripheral resistance, among others. Here, we define the moving ensemble technique mathematically, highlighting its differences from fixed-window ensemble averaging. We describe MEAP's interface and features for signal processing, artifact correction, and cardiovascular-based fMRI analysis. We demonstrate the accuracy of MEAP's novel B point detection algorithm on a large collection of hand-labeled ICG waveforms. As a proof of concept, two subjects completed a series of four physical and cognitive tasks (cold pressor, Valsalva maneuver, video game, random dot kinetogram) on 3 separate days while ECG, ICG, and BP were recorded. Critically, the moving ensemble method reliably captures the rapid cyclical cardiovascular changes related to the baroreflex during the Valsalva maneuver and the classic cold pressor response. Cardiovascular measures were seen to vary considerably within repetitions of the same cognitive task for each individual, suggesting that a carefully designed paradigm could be used to capture fast-acting event-related changes in cardiovascular state.

Cohesive network reconfiguration accompanies extended training

Human behavior is supported by flexible neurophysiological processes that enable the fine‐scale manipulation of information across distributed neural circuits. Yet, approaches for understanding the dynamics of these circuit interactions have been limited. One promising avenue for quantifying and describing these dynamics lies in multilayer network models. Here, networks are composed of nodes (which represent brain regions) and time‐dependent edges (which represent statistical similarities in activity time series). We use this approach to examine functional connectivity measured by non‐invasive neuroimaging techniques. These multilayer network models facilitate the examination of changes in the pattern of statistical interactions between large‐scale brain regions that might facilitate behavior. In this study, we define and exercise two novel measures of network reconfiguration, and demonstrate their utility in neuroimaging data acquired as healthy adult human subjects learn a new motor skill. In particular, we identify putative functional modules in multilayer networks and characterize the degree to which nodes switch between modules. Next, we define cohesive switches, in which a set of nodes moves between modules together as a group, and we define disjoint switches, in which a single node moves between modules independently from other nodes. Together, these two concepts offer complementary yet distinct insights into the changes in functional connectivity that accompany motor learning. More generally, our work offers statistical tools that other researchers can use to better understand the reconfiguration patterns of functional connectivity over time. Hum Brain Mapp 38:4744–4759, 2017. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity

Neuroengineering is faced with unique challenges in repairing or replacing complex neural systems that are composed of many interacting parts. These interactions form intricate patterns over large spatiotemporal scales and produce emergent behaviors that are difficult to predict from individual elements. Network science provides a particularly appropriate framework in which to study and intervene in such systems by treating neural elements (cells, volumes) as nodes in a graph and neural interactions (synapses, white matter tracts) as edges in that graph. Here, we review the emerging discipline of network neuroscience, which uses and develops tools from graph theory to better understand and manipulate neural systems from micro- to macroscales. We present examples of how human brain imaging data are being modeled with network analysis and underscore potential pitfalls. We then highlight current computational and theoretical frontiers and emphasize their utility in informing diagnosis and monitoring, brain-machine interfaces, and brain stimulation. A flexible and rapidly evolving enterprise, network neuroscience provides a set of powerful approaches and fundamental insights that are critical for the neuroengineer's tool kit.

Differential Recruitment of Parietal Cortex during Spatial and Non-spatial Reach Planning

The planning of goal-directed arm reaching movements is associated with activity in the dorsal parieto-frontal cortex, within which multiple regions subserve the integration of arm- and target-related sensory signals to encode a motor goal. Surprisingly, many of these regions show sustained activity during reach preparation even when target location is not specified, i.e., when a motor goal cannot be unambiguously formed. The functional role of these non-spatial preparatory signals remains unresolved. Here this process was investigated in humans by comparing reach preparatory activity in the presence or absence of information regarding upcoming target location. In order to isolate the processes specific to reaching and to control for visuospatial attentional factors, the reaching task was contrasted to a finger movement task. Functional MRI and electroencephalography (EEG) were used to characterize the spatio-temporal pattern of reach-related activity in the parieto-frontal cortex. Reach planning with advance knowledge of target location induced robust blood oxygenated level dependent and EEG responses across parietal and premotor regions contralateral to the reaching arm. In contrast, reach preparation without knowledge of target location was associated with a significant BOLD response bilaterally in the parietal cortex. Furthermore, EEG alpha- and beta-band activity was restricted to parietal scalp sites, the magnitude of the latter being correlated with reach reaction times. These results suggest an intermediate stage of sensorimotor transformations in bilateral parietal cortex when target location is not specified.