BrainNet Viewer: A Network Visualization Tool for Human Brain Connectomics

PLoS ONE - Tập 8 Số 7 - Trang e68910
Mingrui Xia1, Jinhui Wang1, Yong He1
1State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

O Sporns, 2005, The human connectome: A structural description of the human brain, PLoS Comput Biol, 1, e42, 10.1371/journal.pcbi.0010042

BB Biswal, 2010, Toward discovery science of human brain function, Proc Natl Acad Sci U S A, 107, 4734, 10.1073/pnas.0911855107

E Bullmore, 2009, Complex brain networks: graph theoretical analysis of structural and functional systems, Nat Rev Neurosci, 10, 186, 10.1038/nrn2575

E Bullmore, 2012, The economy of brain network organization, Nat Rev Neurosci, 13, 336, 10.1038/nrn3214

Y He, 2010, Graph theoretical modeling of brain connectivity, Curr Opin Neurol, 23, 341, 10.1097/WCO.0b013e32833aa567

Y He, 2007, Small-world anatomical networks in the human brain revealed by cortical thickness from MRI, Cereb Cortex, 17, 2407, 10.1093/cercor/bhl149

ZJ Chen, 2008, Revealing modular architecture of human brain structural networks by using cortical thickness from MRI, Cereb Cortex, 18, 2374, 10.1093/cercor/bhn003

P Hagmann, 2008, Mapping the structural core of human cerebral cortex, PLoS Biol, 6, e159, 10.1371/journal.pbio.0060159

G Gong, 2009, Mapping anatomical connectivity patterns of human cerebral cortex using in vivo diffusion tensor imaging tractography, Cereb Cortex, 19, 524, 10.1093/cercor/bhn102

Y He, 2009, Uncovering intrinsic modular organization of spontaneous brain activity in humans, PLoS One, 4, e5226, 10.1371/journal.pone.0005226

R Salvador, 2005, Neurophysiological architecture of functional magnetic resonance images of human brain, Cereb Cortex, 15, 1332, 10.1093/cercor/bhi016

S Achard, 2006, A resilient, low-frequency, small-world human brain functional network with highly connected association cortical hubs, J Neurosci, 26, 63, 10.1523/JNEUROSCI.3874-05.2006

DJ Watts, 1998, Collective dynamics of ‘small-world’ networks, Nature, 393, 440, 10.1038/30918

ME Newman, 2006, Modularity and community structure in networks, Proc Natl Acad Sci U S A, 103, 8577, 10.1073/pnas.0601602103

D Meunier, 2010, Modular and hierarchically modular organization of brain networks, Front Neurosci, 4, 200, 10.3389/fnins.2010.00200

RL Buckner, 2009, Cortical hubs revealed by intrinsic functional connectivity: mapping, assessment of stability, and relation to Alzheimer’s disease, J Neurosci, 29, 1860, 10.1523/JNEUROSCI.5062-08.2009

MP van den Heuvel, 2011, Rich-club organization of the human connectome, J Neurosci, 31, 15775, 10.1523/JNEUROSCI.3539-11.2011

MP van den Heuvel, 2012, High-cost, high-capacity backbone for global brain communication, Proc Natl Acad Sci U S A, 109, 11372, 10.1073/pnas.1203593109

G Gong, 2009, Age- and gender-related differences in the cortical anatomical network, J Neurosci, 29, 15684, 10.1523/JNEUROSCI.2308-09.2009

D Meunier, 2009, Age-related changes in modular organization of human brain functional networks, Neuroimage, 44, 715, 10.1016/j.neuroimage.2008.09.062

Tomasi D, Volkow ND (2012) Aging and functional brain networks. Mol Psychiatry 17: 471, 549–458.

L Wang, 2010, Age-related changes in topological patterns of large-scale brain functional networks during memory encoding and recognition, Neuroimage, 50, 862, 10.1016/j.neuroimage.2010.01.044

W Wen, 2011, Discrete neuroanatomical networks are associated with specific cognitive abilities in old age, J Neurosci, 31, 1204, 10.1523/JNEUROSCI.4085-10.2011

K Wu, 2012, Age-related changes in topological organization of structural brain networks in healthy individuals, Hum Brain Mapp, 33, 552, 10.1002/hbm.21232

DA Fair, 2007, Development of distinct control networks through segregation and integration, Proc Natl Acad Sci U S A, 104, 13507, 10.1073/pnas.0705843104

DA Fair, 2009, Functional brain networks develop from a “local to distributed” organization, PLoS Comput Biol, 5, e1000381, 10.1371/journal.pcbi.1000381

DA Fair, 2008, The maturing architecture of the brain’s default network, Proc Natl Acad Sci U S A, 105, 4028, 10.1073/pnas.0800376105

DA Fair, 2012, Distinct neuropsychological subgroups in typically developing youth inform heterogeneity in children with ADHD, Proc Natl Acad Sci U S A, 109, 6769, 10.1073/pnas.1115365109

D Batalle, 2012, Altered small-world topology of structural brain networks in infants with intrauterine growth restriction and its association with later neurodevelopmental outcome, Neuroimage, 60, 1352, 10.1016/j.neuroimage.2012.01.059

Hwang K, Hallquist MN, Luna B (2012) The Development of Hub Architecture in the Human Functional Brain Network. Cereb Cortex.

Khundrakpam BS, Reid A, Brauer J, Carbonell F, Lewis J, <etal>et al</etal>.. (2012) Developmental Changes in Organization of Structural Brain Networks. Cereb Cortex.

K Supekar, 2009, Development of large-scale functional brain networks in children, PLoS Biol, 7, e1000157, 10.1371/journal.pbio.1000157

PT Yap, 2011, Development trends of white matter connectivity in the first years of life, PLoS One, 6, e24678, 10.1371/journal.pone.0024678

K Wu, 2013, Topological organization of functional brain networks in healthy children: differences in relation to age, sex, and intelligence, PLoS One, 8, e55347, 10.1371/journal.pone.0055347

L Tian, 2011, Hemisphere- and gender-related differences in small-world brain networks: a resting-state functional MRI study, Neuroimage, 54, 191, 10.1016/j.neuroimage.2010.07.066

J Liu, 2011, Gender-related differences in the dysfunctional resting networks of migraine suffers, PLoS One, 6, e27049, 10.1371/journal.pone.0027049

C Yan, 2011, Sex- and brain size-related small-world structural cortical networks in young adults: a DTI tractography study, Cereb Cortex, 21, 449, 10.1093/cercor/bhq111

Y Li, 2009, Brain anatomical network and intelligence, PLoS Comput Biol, 5, e1000395, 10.1371/journal.pcbi.1000395

MP van den Heuvel, 2009, Efficiency of functional brain networks and intellectual performance, J Neurosci, 29, 7619, 10.1523/JNEUROSCI.1443-09.2009

JE Schmitt, 2008, Identification of genetically mediated cortical networks: a multivariate study of pediatric twins and siblings, Cereb Cortex, 18, 1737, 10.1093/cercor/bhm211

MP van den Heuvel, 2013, Genetic control of functional brain network efficiency in children, Eur Neuropsychopharmacol, 23, 19, 10.1016/j.euroneuro.2012.06.007

JA Brown, 2011, Brain network local interconnectivity loss in aging APOE-4 allele carriers, Proc Natl Acad Sci U S A, 108, 20760, 10.1073/pnas.1109038108

A Fornito, 2011, Genetic influences on cost-efficient organization of human cortical functional networks, J Neurosci, 31, 3261, 10.1523/JNEUROSCI.4858-10.2011

DS Bassett, 2009, Human brain networks in health and disease, Curr Opin Neurol, 22, 340, 10.1097/WCO.0b013e32832d93dd

M Guye, 2010, Graph theoretical analysis of structural and functional connectivity MRI in normal and pathological brain networks, MAGMA, 23, 409, 10.1007/s10334-010-0205-z

M Xia, 2011, Magnetic resonance imaging and graph theoretical analysis of complex brain networks in neuropsychiatric disorders, Brain Connect, 1, 349, 10.1089/brain.2011.0062

W Wen, 2011, Structural brain networks and neuropsychiatric disorders, Curr Opin Psychiatry, 24, 219, 10.1097/YCO.0b013e32834591f8

CJ Stam, 2007, Small-world networks and functional connectivity in Alzheimer’s disease, Cereb Cortex, 17, 92, 10.1093/cercor/bhj127

Y He, 2008, Structural insights into aberrant topological patterns of large-scale cortical networks in Alzheimer’s disease, J Neurosci, 28, 4756, 10.1523/JNEUROSCI.0141-08.2008

CY Lo, 2010, Diffusion tensor tractography reveals abnormal topological organization in structural cortical networks in Alzheimer’s disease, J Neurosci, 30, 16876, 10.1523/JNEUROSCI.4136-10.2010

J Wang, 2013, Disrupted functional brain connectome in individuals at risk for Alzheimer’s disease, Biol Psychiatry, 73, 472, 10.1016/j.biopsych.2012.03.026

Z Yao, 2010, Abnormal cortical networks in mild cognitive impairment and Alzheimer’s disease, PLoS Comput Biol, 6, e1001006, 10.1371/journal.pcbi.1001006

EH Seo, 2013, Whole-brain functional networks in cognitively normal, mild cognitive impairment, and Alzheimer’s disease, PLoS One, 8, e53922, 10.1371/journal.pone.0053922

DS Bassett, 2008, Hierarchical organization of human cortical networks in health and schizophrenia, J Neurosci, 28, 9239, 10.1523/JNEUROSCI.1929-08.2008

Y Liu, 2008, Disrupted small-world networks in schizophrenia, Brain, 131, 945, 10.1093/brain/awn018

A Zalesky, 2011, Disrupted axonal fiber connectivity in schizophrenia, Biol Psychiatry, 69, 80, 10.1016/j.biopsych.2010.08.022

W Liao, 2010, Altered functional connectivity and small-world in mesial temporal lobe epilepsy, PLoS One, 5, e8525, 10.1371/journal.pone.0008525

Z Zhang, 2011, Altered functional-structural coupling of large-scale brain networks in idiopathic generalized epilepsy, Brain, 134, 2912, 10.1093/brain/awr223

M Rubinov, 2010, Complex network measures of brain connectivity: uses and interpretations, Neuroimage, 52, 1059, 10.1016/j.neuroimage.2009.10.003

B He, 2011, eConnectome: A MATLAB toolbox for mapping and imaging of brain functional connectivity, J Neurosci Methods, 195, 261, 10.1016/j.jneumeth.2010.11.015

SM Hosseini, 2012, GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks, PLoS One, 7, e40709, 10.1371/journal.pone.0040709

Z Cui, 2013, PANDA: a pipeline toolbox for analyzing brain diffusion images, Front Hum Neurosci, 7, 42

AM Dale, 1999, Cortical surface-based analysis. I. Segmentation and surface reconstruction, Neuroimage, 9, 179, 10.1006/nimg.1998.0395

JF Mangin, 2004, A framework to study the cortical folding patterns, Neuroimage, 23, S129, 10.1016/j.neuroimage.2004.07.019

N Tzourio-Mazoyer, 2002, Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain, Neuroimage, 15, 273, 10.1006/nimg.2001.0978

Brodmann K (1909) Vergleichende lokalisationslehre der grobhirnrinde. Barth: Leipzig.

SM Smith, 2004, Advances in functional and structural MR image analysis and implementation as FSL, Neuroimage, 23, S208, 10.1016/j.neuroimage.2004.07.051

NU Dosenbach, 2010, Prediction of individual brain maturity using fMRI, Science, 329, 1358, 10.1126/science.1194144

DW Shattuck, 2008, Construction of a 3D probabilistic atlas of human cortical structures, Neuroimage, 39, 1064, 10.1016/j.neuroimage.2007.09.031

C Yan, 2010, DPARSF: A MATLAB Toolbox for “Pipeline” Data Analysis of Resting-State fMRI, Front Syst Neurosci, 4, 13

C Chang, 2010, Time-frequency dynamics of resting-state brain connectivity measured with fMRI, Neuroimage, 50, 81, 10.1016/j.neuroimage.2009.12.011

J Kang, 2011, Characterizing dynamic functional connectivity in the resting brain using variable parameter regression and Kalman filtering approaches, Neuroimage, 56, 1222, 10.1016/j.neuroimage.2011.03.033

Allen EA, Damaraju E, Plis SM, Erhardt EB, Eichele T, <etal>et al</etal>.. (2012) Tracking Whole-Brain Connectivity Dynamics in the Resting State. Cereb Cortex.

DT Jones, 2012, Non-Stationarity in the “Resting Brain’s” Modular Architecture, PLoS One, 7, e39731, 10.1371/journal.pone.0039731

Margulies DS, Böttger J, Watanabe A, Gorgolewski KJ (2013) Visualizing the Human Connectome. NeuroImage.

S Gerhard, 2011, The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes, Front Neuroinform, 5, 3, 10.3389/fninf.2011.00003

P Gleeson, 2007, neuroConstruct: a tool for modeling networks of neurons in 3D space, Neuron, 54, 219, 10.1016/j.neuron.2007.03.025

AP Davison, 2008, PyNN: A Common Interface for Neuronal Network Simulators, Front Neuroinform, 2, 11, 10.3389/neuro.11.011.2008

E Nordlie, 2010, Visualizing neuronal network connectivity with connectivity pattern tables, Front Neuroinform, 3, 39

X Liang, 2012, Effects of different correlation metrics and preprocessing factors on small-world brain functional networks: a resting-state functional MRI study, PLoS One, 7, e32766, 10.1371/journal.pone.0032766

X Liang, 2013, Coupling of functional connectivity and regional cerebral blood flow reveals a physiological basis for network hubs of the human brain, Proc Natl Acad Sci U S A, 110, 1929, 10.1073/pnas.1214900110

Liu M, Zhang D, Shen D, the Alzheimer’s Disease Neuroimaging I (2013) Hierarchical fusion of features and classifier decisions for Alzheimer’s disease diagnosis. Hum Brain Mapp.

Z Dai, 2012, Discriminative analysis of early Alzheimer’s disease using multi-modal imaging and multi-level characterization with multi-classifier (M3), Neuroimage, 59, 2187, 10.1016/j.neuroimage.2011.10.003

F Bai, 2012, Topologically convergent and divergent structural connectivity patterns between patients with remitted geriatric depression and amnestic mild cognitive impairment, J Neurosci, 32, 4307, 10.1523/JNEUROSCI.5061-11.2012

L Yi, 2012, Structural and functional changes in subcortical vascular mild cognitive impairment: a combined voxel-based morphometry and resting-state fMRI study, PLoS One, 7, e44758, 10.1371/journal.pone.0044758

P Fang, 2012, Increased cortical-limbic anatomical network connectivity in major depression revealed by diffusion tensor imaging, PLoS One, 7, e45972, 10.1371/journal.pone.0045972

J Zhang, 2011, Disrupted brain connectivity networks in drug-naive, first-episode major depressive disorder, Biol Psychiatry, 70, 334, 10.1016/j.biopsych.2011.05.018

Wang L, Dai Z, Peng H, Tan L, Ding Y, <etal>et al</etal>.. (2013) Overlapping and segregated resting-state functional connectivity in patients with major depressive disorder with and without childhood neglect. Hum Brain Mapp.

PN Taylor, 2013, Towards a large-scale model of patient-specific epileptic spike-wave discharges, Biol Cybern, 107, 83, 10.1007/s00422-012-0534-2

KM Sequeira, 2013, Perfusion network shift during seizures in medial temporal lobe epilepsy, PLoS One, 8, e53204, 10.1371/journal.pone.0053204

SB Hong, 2013, Decreased functional brain connectivity in adolescents with internet addiction, PLoS One, 8, e57831, 10.1371/journal.pone.0057831

N Shu, 2011, Diffusion tensor tractography reveals disrupted topological efficiency in white matter structural networks in multiple sclerosis, Cereb Cortex, 21, 2565, 10.1093/cercor/bhr039

Z Wang, 2011, Spatial patterns of intrinsic brain activity in mild cognitive impairment and Alzheimer’s disease: a resting-state functional MRI study, Hum Brain Mapp, 32, 1720, 10.1002/hbm.21140