Visual analytics of brain networks

NeuroImage

Volumn 61, Issue 1, 2012, Pages 82-97

  Li, Kaiming ^a,b   Guo, Lei ^a   Faraco, Carlos ^c   Zhu, Dajiang ^b   Chen, Hanbo ^b   Yuan, Yixuan ^a   Lv, Jinglei ^a   Deng, Fan ^b   Jiang, Xi ^b   Zhang, Tuo ^a   Hu, Xintao ^a   Zhang, Degang ^a   Miller, L Stephen ^c,d   Liu, Tianming ^b  

^a NORTHWESTERN POLYTECHNICAL UNIVERSITY   (China)

^b The University of Georgia ^*  (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d University of Georgia   (United States)

Author keywords

Brain networks; Joint modeling; Multimodal neuroimaging; Visual analytics; Visualization and interaction

Indexed keywords

ACCURACY; ADULT; AGED; ARTICLE; BRAIN NETWORK; CLINICAL ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; FEMALE; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; IMAGE ANALYSIS; KNOWLEDGE; MALE; MILD COGNITIVE IMPAIRMENT; NEUROIMAGING; NEUROSCIENCE; PREDICTION; PRIORITY JOURNAL; RELIABILITY; SCHIZOPHRENIA; VISUAL ANALYTICS; WORKING MEMORY;

AGED; BRAIN MAPPING; DIFFUSION TENSOR IMAGING; FEMALE; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; KNOWLEDGE; MAGNETIC RESONANCE IMAGING; MALE; MEMORY, SHORT-TERM; MILD COGNITIVE IMPAIRMENT; NERVE NET; NEUROPSYCHOLOGICAL TESTS; NEUROSCIENCES; REPRODUCIBILITY OF RESULTS; SCHIZOPHRENIA; SCHIZOPHRENIC PSYCHOLOGY; SOFTWARE; USER-COMPUTER INTERFACE; YOUNG ADULT;

EID: 84859044604     PISSN: 10538119     EISSN: 10959572     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2012.02.075     Document Type: Article

References (70)

1. Amunts K., Malikovic A., Mohlberg H., Schormann T., Zilles K. Brodmann's areas 17 and 18 brought into stereotaxic space-where and how variable?. NeuroImage 2000, 11(1):66-84. Jan.
2. Anderson E.J., Jones D.K., O'Gorman R.L., Leemans A., Catani M., Husain M. Cortical network for gaze control in humans revealed using multimodal MRI. Cereb. Cortex 2011, Jun 21.
3. Andersson J., Smith S., Jenkinson M. FNIRT - FMRIB's non-linear image registration tool. Organization for Human Brain Mapping. Melbourne, Australia, 15th to 19th June 2008. 2008.
4. Ashburner J., Friston K.J., Penny W. Human Brain Function 2004, Academic Press.
5. Atri A., O'Brien J.L., Sreenivasan A., Rastegar S., Salisbury S., DeLuca A.N., O'Keefe K.M., LaViolette P.S., Rentz D.M., Locascio J.J., Sperling R.A. Test-retest reliability of memory task functional magnetic resonance imaging in Alzheimer disease clinical trials. Arch. Neurol. 2011, 68(5):599-606.
6. Avants B.B., Epstein C.L., Grossman M., Gee J.C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med. Image Anal. 2008, 12(1):26-41. Feb.
7. Azar Fred S., ElBawab Mazen, Khamene Ali, Lee Kijoon, Choe Regine, Corlu Alper, Konecky Soren D., Yodh Arjun G., Sauer Frank Multimodal information integration and visualization: optical imaging and MRI. Proc. SPIE 2005, 6009:60090E.
8. Bai F., Zhang Z., Yu H., Shi Y., Yuan Y., Zhu W., Zhang X., Qian Y. Default-mode network activity distinguishes amnestic type mild cognitive impairment from healthy aging: a combined structural and resting-state functional MRI study. Neurosci. Lett. 2008, 438:111-115.
9. Baum K.G., Helguera M., Krol A. Fusion viewer: a new tool for fusion and visualization of multimodal medical data sets. J. Digit Imaging 2008, 21(Suppl. 1):S59-S68. Oct.
10. Beckmann C.F., DeLuca M., Devlin J.T., Smith S.M. Investigations into resting-state connectivity using independent component analysis. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2005, 360:1001-1013. 29 May.
11. Biswal B.B., Mennes M., Zuo X.N., et al. Toward discovery science of human brain function. PNAS 2010, 107(10):4734-4739.
12. Bluhm R.L., Williamson P.C., Osuch E.A., Frewen P.A., Stevens T.K., Boksman K., Neufeld R.W.J., Théberge J., Lanius R.A. Alterations in default network connectivity in posttraumatic stress disorder related to early-life trauma. J. Psychiatry Neurosci. 2009, 34(3):187-194.
13. Brun A., Knutsson H., Park H.J., Shenton M.E., Westin C.F. Clustering fiber tracts using normalized cuts, MICCAI 2004, LINCS 3216 2004, 368-375.
14. Bullmore Ed, Sporns Olaf Complex brain networks: graph theoretical analysis of structural and functional systems. Nat. Neurosci. Rev. 2009, 186(10). March.
15. Calhoun V.D., Adali T., Pearlson G.D., Pekar J.J. A Method for Making Group Inferences from Functional MRI Data Using Independent Component Analysis, HBM, vol. 14 2001, 140-151.
16. Chen Hanbo, Guo Lei, Li Kaiming, Hu Xintao, Liu Tianming Assessment of Regularity and Variability of Cortical Folding Patterns of Working Memory ROIs, MICCAI 2011.
17. Cherubini A., Spoletini I., Peran P., Luccichenti G., Di Paola M., Sancesario G., Gianni W., Giubilei F., Bossu P., Sabatini U., Caltagirone C., Spalletta G. A multimodal MRI investigation of the subventricular zone in mild cognitive impairment and Alzheimer's disease patients. Neurosci. Lett. 2010, 469:214-218.
18. Faraco C.C., Unsworth N., Lagnely J., Terry D., Li K., Zhang D., Liu T., Miller L.S. Complex span tasks and hippocampal recruitment during working memory. NeuroImage 2011, 55(2):773-787. 15 March.
19. Fillard P., Gerig G. Analysis tool for diffusion tensor MR. Proc. of MICCAI'03, Part II, volume 2879 of LNCS 2003, 979-980. Springer, November.
20. Fischl B., Rajendran N., Busa E., Augustinack J., Hinds O., Yeo B.T.T., Mohlberg H., Amunts K., Zilles K. Cortical folding patterns and predicting cytoarchitecture. Cereb. Cortex 2008, 18:1973-1980.
21. Fox M.D., Raichle M.E. Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat. Rev. Neurosci. 2007, 8:700-711.
22. Fox M.D., Corbetta M., Snyder A.Z., Vincent J.L., Raichle M.E. Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems. PNAS 2006, 103.
23. Fransson P., Aden U., Blennow M., Lagercrantz H. The functional architecture of the infant brain as revealed by resting-state fMRI. Cereb. Cortex 2010, Apr.
24. Friston K.J. Modalities, modes, and models in functional neuroimaging. Science 2009, 326(5951):399-403.
25. Friston K.J., Harrison L., Penny W. Dynamic causal modeling. NeuroImage 2003, 19:1273-1302.
26. Garrity A.G., Pearlson G.D., McKiernan K., Lloyd D., Kiehl K.A., Calhoun V.D. Aberrant "default mode" functional connectivity in schizophrenia. Am. J. Psychiatry 2007, 164(7):1123.
27. Garyfallidis E., Brett M., Nimmo-Smith I. 16th Annual Meeting of the Organization for Human Brain Mapping 2010.
28. Geissler A., Lanzenberger R., Barth M., Tahamtan A.R., Milakara D., Gartus A., Beisteiner R. Influence of fMRI smoothing procedures on replicability of fine scale motor localization. NeuroImage 2005, 24:323-331.
29. Granger C.W.J. Investigating causal relations by econometric models and cross-spectral methods. Econometrica 1969, (3):37.
30. Greicius M.D., Srivastava G., Reiss A.L., Menon V. Default-mode network activity distinguishes Alzheimer's disease from healthy aging: evidence from functional MRI. Proc. Natl. Acad. Sci. U. S. A. 2004, 101(13):4637-4642.
31. Hagmann P., Cammoun L., Gigandet X., Gerhard S., Grant P.E., Wedeen V., Meuli R., Thiran J.P., Honey C.J., Sporns O. MR connectomics: principles and challenges. J. Neurosci. Methods 2010, 194(1):34-45. (Dec 15).
32. Harrison L., Penny W., Friston K.J. Multivariate autoregressive modeling of fMRI time series. NeuroImage 2003, 19:1477-1491.
33. Ho A., Hua X., Lee S., Leow A.D., Yanovsky I., Gutman B., Dinov I.D., Lepore N., Stein J., Toga A.W., Jack C.R., Bernstein M.A., Reiman E.M., Harvey D.J., Kornak J., Schuff N., Alexander G.E., Weiner M.W., Thompson P.M. Comparing 3Tesla and 1.5Tesla MRI for tracking Alzheimer's disease progression with tensor-based morphometry. Hum. Brain Mapp. 2010, 31:499-514.
34. Jack C.R., Bernstein M.A., Borowski B.J., et al. Update on the magnetic resonance imaging core of the Alzheimer's disease neuroimaging initiative. Alzheimers Dement. 2010, 6(3):212-220.
35. Jenkinson M., Smith S.M. A global optimisation method for robust affine registration of brain images. Med. Image Anal. 2001, 5(2):143-156.
36. Jo H.J., Lee J.M., Kim J.H., Choi C.H., Gu B.M., Kang D.H., Ku J., Kwon J.S., Kim S.I. Artificial shifting of fMRI activation localized by volume- and surface-based analyses. NeuroImage 2008, 40(3):1077-1089. Apr 15.
37. Li Kaiming, Guo Lei, Nie Jingxin, Li Gang, Liu Tianming Review of methods for functional brain connectivity detection using fMRI. Comput. Med. Imaging Graph. 2009, 33(2):131-139. March.
38. Li Kaiming, Guo Lei, Faraco Carlos, Zhu Dajiang, Deng Fan, Zhang Tuo, Jiang Xi, Zhang Degang, Chen Hanbo, Hu Xintao, Miller L.Stephen, Liu Tianming Individualized ROI optimization via maximization of group-wise consistency of structural and functional profiles, accepted, neural information processing systems (NIPS) 2010.
39. Li Kaiming, Guo Lei, Li Gang, Nie Jingxin, Faraco Carlos, Zhao Qun, Miller Stephen, Liu Tianming Cortical surface based identification of brain networks using high spatial resolution resting state fMRI data, International Symposium Of Biomedical Imaging (ISBI) 2010.
40. Liu Tianming A few thoughts on brain ROIs. Brain Imaging Behav 2011, 5(3):189-202. (Sep).
41. Liu Tianming, Li Hai, Wong Kelvin, Tarokh Ashley, Guo Lei, Wong Stephen Brain tissue segmentation based on DTI data. NeuroImage 2007, 38(1):114-123.
42. Liu Tianming, Nie Jingxin, Tarokh Ashley, Guo Lei, Wong Stephen TC Reconstruction of central cortical surface from MRI brain images: method and application. NeuroImage 2008, 40(3):991-1002.
43. Lorensen W.E., Cline H. Marching cubes: a high resolution 3D surface construction algorithm. Comput. Graph. 1987, 21(4).
44. Lynall M.E., Bassett D.S., Kerwin R., McKenna P.J., Kitzbichler M., Muller U., Bullmore E. Functional connectivity and brain networks in schizophrenia. J. Neurosci. 2010, 30(28):9477-9487. Jul 14.
45. Maddah M., Mewes A.U., Haker S., Grimson W.E., Warfield S.K. Automated atlas-based clustering of white matter fiber tracts from DTMRI. MICCAI 2005, 8:188-195.
46. Manssour I.H., Furuie S.S., Nedel L.P., Freitas C.M.D.S. A framework to interact and visualize with multimodal medical images (ST). Proceedings of volume graphics 2001.
47. Meyer-Lindenberg A., Poline J.B., Kohn P.D., Holt J.L., Egan M.F., Weinberger D.R., Berman K.F. Evidence for abnormal cortical functional connectivity during working memory in schizophrenia. Am. J. Psychiatry 2001, 158:1809-1817.
48. Minzenberg M.J., Laird A.R., Thelen S., Carter C.S., Glahn D.C. Meta-analysis of 41 functional neuroimaging studies of executive function in schizophrenia. Arch. Gen. Psychiatry 2009, 66:811-822.
49. O'Donnell L.J., Kubicki M., Shenton M.E., Dreusicke M.H., Grimson W.E., Westin C.F. A method for clustering white matter fiber tracts. AJNR Am. J. Neuroradiol. 2006, 27:1032-1036.
50. Ou W., Wells W.M., Golland P. Combining spatial priors and anatomical information for fMRI detection. Med. Image Anal. 2010, 14(3):318-331.
51. Passingham R.E., Stephan K.E., Kötter R. The anatomical basis of functional localization in the cortex. Nat. Rev. Neurosci. 2002, 3(8):606-616.
52. Roebroeck A., Formisano E., Goebel R. Mapping directed influence over the brain using Granger causality and fMRI. NeuroImage 2005, 25(1):230-242. Mar.
53. Sepulcre J., Liu H., Talukdar T., Martincorena I., Yeo B.T., Buckner R.L. The organization of local and distant functional connectivity in the human brain. PLoS Comput. Biol. 2010, 6(6). Jun 10.
54. Shen Dinggang, Davatzikos Christos HAMMER: hierarchical attribute matching mechanism for elastic registration. IEEE Trans. Med. Imaging 2002, 21(11):1421-1439.
55. Smith S.M. Fast robust automated brain extraction. Hum. Brain Mapp. 2002, 17:143-155.
56. Smith S.M., Jenkinson M., Woolrich M.W., Beckmann C.F., Behrens T.E., Johansen-Berg H., et al. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage 2004, 23(Suppl. 1):S208-S219.
57. Sorg C., Riedl V., Mühlau M., Calhoun V.D., Eichele T., Läer L., Drzezga A., Förstl H., Kurz A., Zimmer C., Wohlschläger A.M. Selective changes of resting-state networks in individuals at risk for Alzheimer's disease. Proc. Natl. Acad. Sci. U. S. A. 2007, 104(47):18760-18765.
58. Sui J., Pearlson G., Caprihan A., Adali T., Kiehl K.A., Liu J., Yamamoto J., Calhoun V.D. Discriminating schizophrenia and bipolar disorder by fusing fMRI and DTI in a multimodal CCA+ joint ICA model. NeuroImage 2011, 57(3):839-855. Aug 1.
59. Supekar K., Menon V., Rubin D., Musen M., Greicius M.D. Network analysis of intrinsic functional brain connectivity in Alzheimer's disease. PLoS Comput. Biol. 2008, 4(6):e1000100.
60. Toro R., Burnod Y. A morphogenetic model of the development of cortical convolutions. Cereb. Cortex 2005, 15:1900-1913.
61. Van Dijk K.R., Hedden T., Venkataraman A., Evans K.C., Lazar S.W., Buckner R.L. Intrinsic functional connectivity as a tool for human connectomics: theory, properties, and optimization. J. Neurophysiol. 2010, 103(1):297-321. Jan.
62. Venkataraman A., Rathi Y., Kubicki M., Westin C.-F., Golland P. Joint generative model for fMRI/DWI and its application to population studies. Int. Conf. Med. Image Comput. Comput. Assist. Interv. 2010, 13(Pt 1):191-199.
63. Viergever M.A., Maintz J.B., Niessen W.J., Noordmans H.J., Pluim J.P., Stokking R., Vincken K.L. Registration, segmentation, and visualization of multimodal brain images. Comput. Med. Imaging Graph. 2001, 25(2):147-151.
64. White T.O., Leary D., Magnotta V., Arndt S., Flaum M., Andreasen N.C. Anatomic and functional variability: the effects of filter size in group fMRI data analysis. NeuroImage 2001, 13:577-588.
65. Zang Y., Jiang T., Lu Y., He Y., Tian L. Regional homogeneity approach to fMRI data analysis. NeuroImage 2004, 22(1):394-400.
66. Zhang Tuo, Guo Lei, Li Kaiming, Jing Changfeng, Yin Yan, Zhu Dajing, Cui Guangbin, Li Lingjiang, Liu Tianming Predicting Functional Cortical ROIs via DTI-derived Fiber Shape Models. Cerebral Cortex 2012, 22(4):854-864.
67. Zhang Y., Brady M., Smith S. Segmentation of brain MR images through a hidden Markov random field model and the expectation maximization algorithm. IEEE Trans. Med. Imaging 2001, 20(1):45-57.
68. Zhang Tuo, Guo Lei, Hu Xintao, Li Kaiming, Liu Tianming Predicting functional cortical ROIs based on fiber shape models, MICCAI 2011.
69. Zhu Dajiang, Li Kaiming, Faraco Carlos, Deng Fan, Zhang Degang, Jiang Xi, Chen Hanbo, Guo Lei, Miller Stephen, Liu Tianming Discovering dense and consistent landmarks in the brain, IPMI 2011.
70. Zylberberg A., Fernández Slezak D., Roelfsema P.R., Dehaene S., Sigman M. The brain's router: a cortical network model of serial processing in the primate brain. PLoS Comput. Biol. 2010, 6(4). Apr. 29.