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Hoffing RAC, Thurman SM, Lauharatanahirun N, Forster DE, Garcia JO, Wasylyshyn N, Gies-brecht B, Grafton ST, Vettel JM. Distinct pupil features correlate with between-participant and across-session performance variability in a 16-week, longitudinal data set. J Vis 2019. [DOI: 10.1167/19.10.126c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Bullock TW, MacLean MH, Boone AP, Santander T, Raymer J, Stuber A, Jimmons L, Okafor GN, Grafton ST, Miller MB, Giesbrecht B. Physical, mental and social stress selectively modulate inhibitory control during search of natural scenes. J Vis 2019. [DOI: 10.1167/19.10.283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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MacLean MH, Boone AP, Bullock T, Santander T, Raymer J, Jimmons L, Stuber A, Okafor GN, Grafton ST, Miller MB, Giesbrecht B. Acute stress, either social or physical, alters the priority of salient feared distracters but not neutral salient distracters. J Vis 2019. [DOI: 10.1167/19.10.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Thurman SM, Hoffing RAC, Lauharatanahirum N, Forster DE, Bansal K, Grafton ST, Giesbrecht B, Vettel JM. Applying linear additive models to isolate component processes in task-evoked pupil responses. J Vis 2019. [DOI: 10.1167/19.10.305c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Greene C, Cieslak M, Volz LJ, Hensel L, Grefkes C, Rose K, Grafton ST. Finding maximally disconnected subnetworks with shortest path tractography. NEUROIMAGE-CLINICAL 2019; 23:101903. [PMID: 31491834 PMCID: PMC6627647 DOI: 10.1016/j.nicl.2019.101903] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/16/2019] [Accepted: 06/16/2019] [Indexed: 11/25/2022]
Abstract
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. Significantly accelerated shortest path tractography approach for constructing connectomes and disconnectomes. New algorithm extracts the subnetwork containing cortical connections and regions with maximal shared connectivity loss. The size of the maximally disconnected subnetwork quantifies the extent of disconnection and correlates with stroke measures. Fast and accurate approach for visualizing and analyzing the disconnected portion of a patient's structural connectome.
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Grafton ST, Ralston AB, Ralston JD. Monitoring of postural sway with a head-mounted wearable device: effects of gender, participant state, and concussion. MEDICAL DEVICES-EVIDENCE AND RESEARCH 2019; 12:151-164. [PMID: 31118838 PMCID: PMC6503189 DOI: 10.2147/mder.s205357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
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.
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Greene C, Cieslak M, Grafton ST. Effect of different spatial normalization approaches on tractography and structural brain networks. Netw Neurosci 2018; 2:362-380. [PMID: 30294704 PMCID: PMC6145854 DOI: 10.1162/netn_a_00035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/30/2017] [Indexed: 11/29/2022] Open
Abstract
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.
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Mattar MG, Wymbs NF, Bock AS, Aguirre GK, Grafton ST, Bassett DS. Predicting future learning from baseline network architecture. Neuroimage 2018; 172:107-117. [PMID: 29366697 PMCID: PMC5910215 DOI: 10.1016/j.neuroimage.2018.01.037] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/09/2018] [Accepted: 01/15/2018] [Indexed: 12/24/2022] Open
Abstract
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.
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Hallgrímsson HT, Cieslak M, Foschini L, Grafton ST, Singh AK. Spatial coherence of oriented white matter microstructure: Applications to white matter regions associated with genetic similarity. Neuroimage 2018; 172:390-403. [PMID: 29410205 DOI: 10.1016/j.neuroimage.2018.01.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/31/2017] [Accepted: 01/19/2018] [Indexed: 11/26/2022] Open
Abstract
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.
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Vettel JM, Thurman SM, Wasylyshyn N, Roy H, Lieberman G, Asturias A, Okafor G, Elliot J, Giesbrecht B, Grafton ST, Garcia JO. 0191 Individual Differences In Sleep Log Compliance And Agreement With Wrist Actigraphy: A Longitudinal Study Of Naturalistic Sleep In Healthy Adults. Sleep 2018. [DOI: 10.1093/sleep/zsy061.190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Thurman SM, Wasylyshyn N, Garcia JO, Okafor G, Elliott JC, Giesbrecht B, Grafton ST, Flynn-Evans E, Vettel JM. 0207 Longitudinal Study of Psychomotor Vigilance Performance, Pupil Diameter, and Naturalistic Sleep History Across 16 Weeks. Sleep 2018. [DOI: 10.1093/sleep/zsy061.206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gu S, Cieslak M, Baird B, Muldoon SF, Grafton ST, Pasqualetti F, Bassett DS. The Energy Landscape of Neurophysiological Activity Implicit in Brain Network Structure. Sci Rep 2018; 8:2507. [PMID: 29410486 PMCID: PMC5802783 DOI: 10.1038/s41598-018-20123-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 01/08/2018] [Indexed: 01/03/2023] Open
Abstract
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.
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Thurman SM, Wasylyshyn N, Roy H, Lieberman G, Garcia JO, Asturias A, Okafor GN, Elliott JC, Giesbrecht B, Grafton ST, Mednick SC, Vettel JM. Individual differences in compliance and agreement for sleep logs and wrist actigraphy: A longitudinal study of naturalistic sleep in healthy adults. PLoS One 2018; 13:e0191883. [PMID: 29377925 PMCID: PMC5788380 DOI: 10.1371/journal.pone.0191883] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/12/2018] [Indexed: 12/20/2022] Open
Abstract
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.
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Becker CO, Pequito S, Pappas GJ, Miller MB, Grafton ST, Bassett DS, Preciado VM. Spectral mapping of brain functional connectivity from diffusion imaging. Sci Rep 2018; 8:1411. [PMID: 29362436 PMCID: PMC5780460 DOI: 10.1038/s41598-017-18769-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/15/2017] [Indexed: 01/22/2023] Open
Abstract
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.
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Reddy PG, Mattar MG, Murphy AC, Wymbs NF, Grafton ST, Satterthwaite TD, Bassett DS. Brain state flexibility accompanies motor-skill acquisition. Neuroimage 2018; 171:135-147. [PMID: 29309897 PMCID: PMC5857429 DOI: 10.1016/j.neuroimage.2017.12.093] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/09/2017] [Accepted: 12/29/2017] [Indexed: 11/23/2022] Open
Abstract
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.
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Cieslak M, Brennan T, Meiring W, Volz LJ, Greene C, Asturias A, Suri S, Grafton ST. Analytic tractography: A closed-form solution for estimating local white matter connectivity with diffusion MRI. Neuroimage 2017; 169:473-484. [PMID: 29274744 DOI: 10.1016/j.neuroimage.2017.12.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/22/2017] [Accepted: 12/13/2017] [Indexed: 11/29/2022] Open
Abstract
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.
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Schlesinger KJ, Turner BO, Grafton ST, Miller MB, Carlson JM. Improving resolution of dynamic communities in human brain networks through targeted node removal. PLoS One 2017; 12:e0187715. [PMID: 29261662 PMCID: PMC5737970 DOI: 10.1371/journal.pone.0187715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/24/2017] [Indexed: 01/01/2023] Open
Abstract
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.
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Wei K, Cieslak M, Greene C, Grafton ST, Carlson JM. Sensitivity analysis of human brain structural network construction. Netw Neurosci 2017; 1:446-467. [PMID: 30090874 PMCID: PMC6063716 DOI: 10.1162/netn_a_00025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 09/04/2017] [Indexed: 12/03/2022] Open
Abstract
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.
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Khambhati AN, Mattar MG, Wymbs NF, Grafton ST, Bassett DS. Beyond modularity: Fine-scale mechanisms and rules for brain network reconfiguration. Neuroimage 2017; 166:385-399. [PMID: 29138087 DOI: 10.1016/j.neuroimage.2017.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/18/2017] [Accepted: 11/07/2017] [Indexed: 11/15/2022] Open
Abstract
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.
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Cross ES, Hamilton AFDC, Cohen NR, Grafton ST. Learning to tie the knot: The acquisition of functional object representations by physical and observational experience. PLoS One 2017; 12:e0185044. [PMID: 29023463 PMCID: PMC5638238 DOI: 10.1371/journal.pone.0185044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 09/04/2017] [Indexed: 11/19/2022] Open
Abstract
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.
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Bogdanov P, Dereli N, Dang XH, Bassett DS, Wymbs NF, Grafton ST, Singh AK. Learning about learning: Mining human brain sub-network biomarkers from fMRI data. PLoS One 2017; 12:e0184344. [PMID: 29016686 PMCID: PMC5634545 DOI: 10.1371/journal.pone.0184344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/22/2017] [Indexed: 01/24/2023] Open
Abstract
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.
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Cieslak M, Ryan WS, Babenko V, Erro H, Rathbun ZM, Meiring W, Kelsey RM, Blascovich J, Grafton ST. Quantifying rapid changes in cardiovascular state with a moving ensemble average. Psychophysiology 2017; 55. [PMID: 28972674 DOI: 10.1111/psyp.13018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/08/2017] [Accepted: 09/05/2017] [Indexed: 12/27/2022]
Abstract
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.
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Telesford QK, Ashourvan A, Wymbs NF, Grafton ST, Vettel JM, Bassett DS. Cohesive network reconfiguration accompanies extended training. Hum Brain Mapp 2017. [PMID: 28646563 PMCID: PMC5554863 DOI: 10.1002/hbm.23699] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
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.
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Bassett DS, Khambhati AN, Grafton ST. Emerging Frontiers of Neuroengineering: A Network Science of Brain Connectivity. Annu Rev Biomed Eng 2017; 19:327-352. [PMID: 28375650 PMCID: PMC6005206 DOI: 10.1146/annurev-bioeng-071516-044511] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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.
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Bernier PM, Whittingstall K, Grafton ST. Differential Recruitment of Parietal Cortex during Spatial and Non-spatial Reach Planning. Front Hum Neurosci 2017; 11:249. [PMID: 28536517 PMCID: PMC5423362 DOI: 10.3389/fnhum.2017.00249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/26/2017] [Indexed: 12/04/2022] Open
Abstract
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.
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