A correlation-matrix-based hierarchical clustering method for functional connectivity analysis

Journal of Neuroscience Methods

Volumn 211, Issue 1, 2012, Pages 94-102

  Liu, Xiao ^a,b   Zhu, Xiao Hong ^a   Qiu, Peihua ^b   Chen, Wei ^a  

^a UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Clustering method; Resting state functional connectivity; Spontaneous BOLD fluctuations; Thalamocortical connections

Indexed keywords

ANIMAL EXPERIMENT; ARTICLE; BOLD SIGNAL; CLUSTER ANALYSIS; CORRELATION ANALYSIS; CORRELATION MATRIX BASED HIERARCHICAL CLUSTERING METHOD; FUNCTIONAL MAGNETIC RESONANCE IMAGING; INDEPENDENT COMPONENT ANALYSIS; MALE; MULTIVARIATE ANALYSIS; NERVE CELL NETWORK; NONHUMAN; PRIORITY JOURNAL; RAT; RESTING STATE NETWORK; SENSITIVITY ANALYSIS; THALAMOCORTICAL TRACT;

ALGORITHMS; ANIMALS; CEREBRAL CORTEX; CLUSTER ANALYSIS; DATA INTERPRETATION, STATISTICAL; MAGNETIC RESONANCE IMAGING; MALE; MULTIVARIATE ANALYSIS; NERVE NET; PRINCIPAL COMPONENT ANALYSIS; RATS; RATS, SPRAGUE-DAWLEY; THALAMUS;

EID: 84865983960     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2012.08.016     Document Type: Article

References (37)

1. Bandettini P.A., Wong E.C., Hinks R.S., Tikofsky R.S., Hyde J.S. Time course EPI of human brain function during task activation. Magn Reson Med 1992, 25:390-397.
2. 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.
3. Beckmann C.F., Smith S.M. Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans Med Imaging 2004, 23:137-152.
4. Beckmann C.F., Smith S.M. Tensorial extensions of independent component analysis for multisubject FMRI analysis. Neuroimage 2005, 25:294-311.
5. Biswal B., Yetkin F.Z., Haughton V.M., Hyde J.S. Functional connectivity in the motor cortex of resting human brain using echo-planar MRI. Magn Reson Med 1995, 34:537-541.
6. Boly M., Tshibanda L., Vanhaudenhuyse A., Noirhomme Q., Schnakers C., Ledoux D., et al. Functional connectivity in the default network during resting state is preserved in a vegetative but not in a brain dead patient. Hum Brain Mapp 2009, 30:2393-2400.
7. Comon P. Independent Component Analysis, a new concept. Signal Process 1994, 36:287-314.
8. Cordes D., Haughton V., Carew J.D., Arfanakis K., Maravilla K. Hierarchical clustering to measure connectivity in fMRI resting-state data. Magn Reson Imaging 2002, 20:305-317.
9. Cordes D., Haughton V.M., Arfanakis K., Wendt G.J., Turski P.A., Moritz C.H., et al. Mapping functionally related regions of brain with functional connectivity MR imaging. AJNR Am J Neuroradiol 2000, 21:1636-1644.
10. Fox M.D., Corbetta M., Snyder A.Z., Vincent J.L., Raichle M.E. Spontaneous neuronal activity distinguishes human dorsal and ventral attention systems. Proc Natl Acad Sci USA 2006, 103:10046-10051.
11. Fox M.D., Snyder A.Z., Vincent J.L., Corbetta M., Van Essen D.C., Raichle M.E. The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proc Natl Acad Sci USA 2005, 102:9673-9678.
12. Greicius M.D., Kiviniemi V., Tervonen O., Vainionpaa V., Alahuhta S., Reiss A.L., et al. Persistent default-mode network connectivity during light sedation. Hum Brain Mapp 2008, 29:839-847.
13. Greicius M.D., Krasnow B., Reiss A.L., Menon V. Functional connectivity in the resting brain: a network analysis of the default mode hypothesis. Proc Natl Acad Sci USA 2003, 100:253-258.
14. Hampson M., Peterson B.S., Skudlarski P., Gatenby J.C., Gore J.C. Detection of functional connectivity using temporal correlations in MR images. Hum Brain Mapp 2002, 15:247-262.
15. He H.S., DeZonia B.E., Mladenoff D.J. An aggregation index (AI) to quantify spatial patterns of landscapes. Landscape Ecol 2000, 15:591-601.
16. Horovitz S.G., Fukunaga M., de Zwart J.A., van Gelderen P., Fulton S.C., Balkin T.J., et al. Low frequency BOLD fluctuations during resting wakefulness and light sleep: a simultaneous EEG-fMRI study. Hum Brain Mapp 2008, 29:671-682.
17. Jenkinson M., Bannister P., Brady M., Smith S. Improved optimization for the robust and accurate linear registration and motion correction of brain images. Neuroimage 2002, 17:825-841.
18. Kiviniemi V., Kantola J.H., Jauhiainen J., Hyvarinen A., Tervonen O. Independent component analysis of nondeterministic fMRI signal sources. Neuroimage 2003, 19:253-260.
19. Liu X., Zhu X.H., Zhang Y., Chen W. Neural origin of spontaneous hemodynamic fluctuations in rats under burst-suppression anesthesia condition. Cereb Cortex 2011, 21:374-384.
20. Lowe M.J., Mock B.J., Sorenson J.A. Functional connectivity in single and multislice echoplanar imaging using resting-state fluctuations. Neuroimage 1998, 7:119-132.
21. Lu H., Zuo Y., Gu H., Waltz J.A., Zhan W., Scholl C.A., et al. Synchronized delta oscillations correlate with the resting-state functional MRI signal. Proc Natl Acad Sci USA 2007, 104:18265-18269.
22. Ma L., Wang B., Chen X., Xiong J. Detecting functional connectivity in the resting brain: a comparison between ICA and CCA. Magn Reson Imaging 2007, 25:47-56.
23. Mansfield P. Multi-planar image formation using NMR spin-echos. J Phys C Solid State Phys 1977, 10:L55-L58.
24. Mantini D., Perrucci M.G., Del Gratta C., Romani G.L., Corbetta M. Electrophysiological signatures of resting state networks in the human brain. Proc Natl Acad Sci USA 2007, 104:13170-13175.
25. Mezer A., Yovel Y., Pasternak O., Gorfine T., Assaf Y. Cluster analysis of resting-state fMRI time series. Neuroimage 2009, 45:1117-1125.
26. Ogawa S., Lee T.-M., Kay A.R., Tank D.W. Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Proc Natl Acad Sci USA 1990, 87:9868-9872.
27. Ogawa S., Tank D.W., Menon R., Ellermann J.M., Kim S.G., Merkle H., et al. Intrinsic signal changes accompanying sensory stimulation: functional brain mapping with magnetic resonance imaging. Proc Natl Acad Sci USA 1992, 89:5951-5955.
28. Paxinos G., Watson C. The rat brain in stereotaxic coordinates 1998, Academic Press, San Diego, CA.
29. Pearson K. On lines and planes of closest fit to systems of points in space. Philos Mag 1901, 559-572.
30. Raichle M.E. Neuroscience. The brain's dark energy. Science 2006, 314:1249-1250.
31. Scholvinck M.L., Maier A., Ye F.Q., Duyn J.H., Leopold D.A. Neural basis of global resting-state fMRI activity. Proc Natl Acad Sci USA 2010, 107:10238-10243.
32. Shmuel A., Leopold D.A. Neuronal correlates of spontaneous fluctuations in fMRI signals in monkey visual cortex: implications for functional connectivity at rest. Hum Brain Mapp 2008, 29:751-761.
33. 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.
34. van de Ven V.G., Formisano E., Prvulovic D., Roeder C.H., Linden D.E. Functional connectivity as revealed by spatial independent component analysis of fMRI measurements during rest. Hum Brain Mapp 2004, 22:165-178.
35. van den Heuvel M.P., Hulshoff Pol H.E. Specific somatotopic organization of functional connections of the primary motor network during resting state. Hum Brain Mapp 2009, 31:631-644.
36. Vincent J.L., Patel G.H., Fox M.D., Snyder A.Z., Baker J.T., Van Essen D.C., et al. Intrinsic functional architecture in the anaesthetized monkey brain. Nature 2007, 447:83-86.
37. Zahn C.T. Graph-theoretical methods for detecting and describing Gestalt clusters. IEEE Trans Comput 1971, C-20:68-86.