Development and validation of consensus clustering-based framework for brain segmentation using resting fMRI

Journal of Neuroscience Methods

Volumn 240, Issue , 2015, Pages 128-140

  Ryali, Srikanth ^a   Chen, Tianwen ^a   Padmanabhan, Aarthi ^a   Cai, Weidong ^a   Menon, Vinod ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Consensus clustering; Data clustering; Parcellation; Resting state fMRI; Segmentation

Indexed keywords

ALGORITHM; ANGULAR GYRUS; ARTICLE; ASSESSMENT OF HUMANS; BRAIN REGION; CLUSTER ANALYSIS; COMPUTER SIMULATION; CONSENSUS CLUSTERING EVIDENCE ACCUMULATION FRAMEWORK; CORPUS STRIATUM; FUNCTIONAL MAGNETIC RESONANCE IMAGING; FUNCTIONAL NEUROIMAGING; HUMAN; INSULA; INTRAPARIETAL SULCUS; MODIFIED SILHOUETTE; PROBABILISTIC RAND INDEX; RAND INDEX; SUPPLEMENTARY MOTOR AREA; VALIDITY; BIOLOGICAL MODEL; BRAIN; BRAIN MAPPING; IMAGE PROCESSING; INFORMATION SCIENCE; NUCLEAR MAGNETIC RESONANCE IMAGING; PHYSIOLOGY; PROBABILITY; PROCEDURES; REST; VALIDATION STUDY;

ALGORITHMS; BRAIN; BRAIN MAPPING; CLUSTER ANALYSIS; COMPUTER SIMULATION; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; INFORMATION THEORY; MAGNETIC RESONANCE IMAGING; MODELS, NEUROLOGICAL; PROBABILITY; REST;

EID: 84919490920     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2014.11.014     Document Type: Article

References (77)

1. Afifi A.K. The basal ganglia: a neural network with more than motor function. Semin Pediatr Neurol 2003, 10:3-10.
2. Alexander G.E., DeLong M.R., Strick P.L. Parallel organization of functionally segregated circuits linking basal ganglia and cortex. Annu Rev Neurosci 1986, 9:357-381.
3. Aron A.R., Behrens T.E., Smith S., Frank M.J., Poldrack R.A. Triangulating a cognitive control network using diffusion-weighted magnetic resonance imaging (MRI) and functional MRI. J Neurosci 2007, 27:3743-3752.
4. Arsalidou M., Taylor M.J. Is 2+2=4? Meta-analyses of brain areas needed for numbers and calculations. Neuroimage 2011, 54:2382-2393.
5. Barnes K.A., Cohen A.L., Power J.D., Nelson S.M., Dosenbach Y.B., Miezin F.M., et al. Identifying basal ganglia divisions in individuals using resting-state functional connectivity MRI. Front Syst Neurosci 2010, 4:18.
6. Barnes K.A., Nelson S.M., Cohen A.L., Power J.D., Coalson R.S., Miezin F.M., et al. Parcellation in left lateral parietal cortex is similar in adults and children. Cereb Cortex 2012, 22:1148-1158.
7. Beckmann C., Smith S. Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans Med Imaging 2004, 23:137-152.
8. Behrens T.E., Jenkinson M., Robson M.D., Smith S.M., Johansen-Berg H. A consistent relationship between local white matter architecture and functional specialisation in medial frontal cortex. Neuroimage 2006, 30:220-227.
9. Belger A., Puce A., Krystal J.H., Gore J.C., Goldman-Rakic P., McCarthy G. Dissociation of mnemonic and perceptual processes during spatial and nonspatial working memory using fMRI. Hum Brain Mapp 1998, 6:14-32.
10. Bellec P., Rosa-Neto P., Lyttelton O.C., Benali H., Evans A.C. Multi-level bootstrap analysis of stable clusters in resting-state fMRI. Neuroimage 2010, 51:1126-1139.
11. Binder J.R., Desai R.H. The neurobiology of semantic memory. Trends Cogn Sci 2011, 15:527-536.
12. Brodmann K. Vergleichende Lokalisationslehre der Groszhirnrinde in ihren Prinzipien dargestellt auf Grund des Zellenbaues Brodmann's Localization in the Cerebral Cortex 1994, Nature Publishing Group.
13. 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. Hum Brain Mapp 2001, 14:140-151.
14. Carpineto C., Romano G. Consensus clustering based on a new probabilistic Rand index with application to subtopic retrieval. IEEE Trans Pattern Anal 2012, 34:2315-2326.
15. Caspers S., Eickhoff S.B., Geyer S., Scheperjans F., Mohlberg H., Zilles K., et al. The human inferior parietal lobule in stereotaxic space. Brain Struct Funct 2008, 212:481-495.
16. Caspers S., Geyer S., Schleicher A., Mohlberg H., Amunts K., Zilles K. The human inferior parietal cortex: cytoarchitectonic parcellation and interindividual variability. Neuroimage 2006, 33:430-448.
17. Cauda F., D'Agata F., Sacco K., Duca S., Geminiani G., Vercelli A. Functional connectivity of the insula in the resting brain. Neuroimage 2011, 55:8-23.
18. Cauda F., Vercelli A. How many clusters in the insular cortex?. Cereb Cortex 2012.
19. Chang L.J., Yarkoni T., Khaw M.W., Sanfey A.G. Decoding the role of the insula in human cognition: functional parcellation and large-scale reverse inference. Cereb Cortex 2013, 23(3):739-749.
20. Chen T., Ryali S., Qin S., Menon V. Estimation of resting-state functional connectivity using random subspace based partial correlation: a novel method for reducing global artifacts. Neuroimage 2013, 82:87-100.
21. Choi H.J., Zilles K., Mohlberg H., Schleicher A., Fink G.R., Armstrong E., et al. Cytoarchitectonic identification and probabilistic mapping of two distinct areas within the anterior ventral bank of the human intraparietal sulcus. J Comp Neurol 2006, 495:53-69.
22. Cohen A.L., Fair D.A., Dosenbach N.U., Miezin F.M., Dierker D., Van Essen D.C., et al. Defining functional areas in individual human brains using resting functional connectivity MRI. Neuroimage 2008, 41:45-57.
23. Corbetta M., Shulman G.L. Control of goal-directed and stimulus-driven attention in the brain. Nat Rev Neurosci 2002, 3:201-215.
24. De Martino F., Valente G., Staeren N., Ashburner J., Goebel R., Formisano E. Combining multivariate voxel selection and support vector machines for mapping and classification of fMRI spatial patterns. Neuroimage 2008, 43:44-58.
25. Deen B., Pitskel N.B., Pelphrey K.A. Three systems of insular functional connectivity identified with cluster analysis. Cereb Cortex 2011, 21:1498-1506.
26. Di Martino A., Scheres A., Margulies D.S., Kelly A.M., Uddin L.Q., Shehzad Z., et al. Functional connectivity of human striatum: a resting state FMRI study. Cereb Cortex 2008, 18:2735-2747.
27. Duda R.O., Hart P.E., Stork D.G. Pattern classification 2001, John Wiley and Sons.
28. Egner T., Monti J.M., Trittschuh E.H., Wieneke C.A., Hirsch J., Mesulam M.M. Neural integration of top-down spatial and feature-based information in visual search. J Neurosci 2008, 28:6141-6151.
29. Eickhoff S.B., Stephan K.E., Mohlberg H., Grefkes C., Fink G.R., Amunts K., et al. A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. Neuroimage 2005, 25:1325-1335.
30. Fred A.L.N., Jain A.K. Combining multiple clusterings using evidence accumulation. IEEE Trans Pattern Anal 2005, 27:835-850.
31. Freund Y., Schapire R.E. A decision-theoretic generalization of on-line learning and an application to boosting. J Comput Syst Sci 1997, 55:119-139.
32. Frey S.H., Vinton D., Norlund R., Grafton S.T. Cortical topography of human anterior intraparietal cortex active during visually guided grasping. Brain research. Cogn Brain Res 2005, 23:397-405.
33. Glover G.H., Law C.S. Spiral-in/out BOLD fMRI for increased SNR and reduced susceptibility artifacts. Magn Reson Med 2001, 46:515-522.
34. Hastie T., Tibshirani R., Friedman J. The elements of statistical learning: data mining, inference and prediction 2001, Springer.
35. Jain A.K., Murty M.N., Flynn P.J. Data clustering: a review. ACM Comput Surv 1999, 31:264-323.
36. Johansen-Berg H., Behrens T.E., Robson M.D., Drobnjak I., Rushworth M.F., Brady J.M., et al. Changes in connectivity profiles define functionally distinct regions in human medial frontal cortex. Proc Natl Acad Sci U S A 2004, 101:13335-13340.
37. Kelly C., Toro R., Di Martino A., Cox C.L., Bellec P., Castellanos F.X., et al. A convergent functional architecture of the insula emerges across imaging modalities. Neuroimage 2012, 61(4):1129-1142.
38. Kelly C., Uddin L.Q., Shehzad Z., Margulies D.S., Castellanos F.X., Milham M.P., et al. Broca's region: linking human brain functional connectivity data and non-human primate tracing anatomy studies. Eur J Neurosci 2010, 32:383-398.
39. Kim J.H., Lee J.M., Jo H.J., Kim S.H., Lee J.H., Kim S.T., et al. Defining functional SMA and pre-SMA subregions in human MFC using resting state fMRI: functional connectivity-based parcellation method. Neuroimage 2010, 49:2375-2386.
40. Kittler J., Hatef M., Duin R.P.W., Matas J. On combining classifiers. IEEE Trans Pattern Anal 1998, 20:226-239.
41. Meila M. Comparing clusterings - an information based distance. J Multivar Anal 2007, 98:873-895.
42. Menon V., Uddin L.Q. Saliency, switching, attention and control: a network model of insula function. Brain Struct Funct 2010, 214:655-667.
43. Mesulam M.M., Mufson E.J. Insula of the old world monkey. I. Architectonics in the insulo-orbito-temporal component of the paralimbic brain. J Comp Neurol 1982, 212:1-22.
44. Monti S., Tamayo P., Mesirov J., Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn 2003, 52:91-118.
45. Nanetti L., Cerliani L., Gazzola V., Renken R., Keysers C. Group analyses of connectivity-based cortical parcellation using repeated k-means clustering. Neuroimage 2009, 47:1666-1677.
46. Nelson S.M., Cohen A.L., Power J.D., Wig G.S., Miezin F.M., Wheeler M.E., et al. A parcellation scheme for human left lateral parietal cortex. Neuron 2010, 67:156-170.
47. Ng A.Y., Jordan M.I., Weiss Y. On spectral clustering: analysis and an algorithm. Adv Neural Inform Process Syst 2002, 14:849-856.
48. Picard N., Strick P.L. Imaging the premotor areas. Curr Opin Neurobiol 2001, 11:663-672.
49. Polderman T.J., Gosso M.F., Posthuma D., Van Beijsterveldt T.C., Heutink P., Verhulst F.C., et al. A longitudinal twin study on IQ, executive functioning, and attention problems during childhood and early adolescence. Acta Neurol Belg 2006, 106:191-207.
50. Postuma R.B., Dagher A. Basal ganglia functional connectivity based on a meta-analysis of 126 positron emission tomography and functional magnetic resonance imaging publications. Cereb Cortex 2006, 16:1508-1521.
51. Prichard D., Theiler J. Generating surrogate data for time series with several simultaneously measured variables. Phys Rev Lett 1994, 73:951-954.
52. Quinlan J.R. Bagging, boosting, and C4.5. Proceedings of the thirteenth national conference on artificial intelligence and the eighth innovative applications of artificial intelligence conference, vols. 1 and 2 1996, 725-730.
53. Rosenberg-Lee M., Chang T.T., Young C.B., Wu S., Menon V. Functional dissociations between four basic arithmetic operations in the human posterior parietal cortex: a cytoarchitectonic mapping study. Neuropsychologia 2011, 49:2592-2608.
54. Ryali S., Chen T., Supekar K., Menon V. A parcellation scheme based on von Mises-Fisher distributions and Markov random fields for segmenting brain regions using resting-state fMRI. Neuroimage 2013, 65:83-96.
55. Salvador R., Suckling J., Coleman M.R., Pickard J.D., Menon D., Bullmore E. Neurophysiological architecture of functional magnetic resonance images of human brain. Cereb Cortex 2005, 15:1332-1342.
56. Scheperjans F., Eickhoff S.B., Homke L., Mohlberg H., Hermann K., Amunts K., et al. Probabilistic maps, morphometry, and variability of cytoarchitectonic areas in the human superior parietal cortex. Cereb Cortex 2008, 18:2141-2157.
57. Seghier M.L. The angular gyrus: multiple functions and multiple subdivisions. Neuroscientist 2013, 19:43-61.
58. Shen X., Papademetris X., Constable R.T. Graph-theory based parcellation of functional subunits in the brain from resting-state fMRI data. Neuroimage 2010, 50:1027-1035.
59. Shen X., Tokoglu F., Papademetris X., Constable R.T. Groupwise whole-brain parcellation from resting-state fMRI data for network node identification. Neuroimage 2013, 82:403-415.
60. Shikata E., Hamzei F., Glauche V., Koch M., Weiller C., Binkofski F., et al. Functional properties and interaction of the anterior and posterior intraparietal areas in humans. Eur J Neurosci 2003, 17:1105-1110.
61. Strehl A., Ghosh J. Cluster ensembles - a knowledge reuse framework for combining partitionings. Proceedings of the eighteenth national conference on artificial intelligence (AAAI-02)/fourteenth innovative applications of artificial intelligence conference (IAAI-02) 2002, 93-98.
62. Supekar K., Menon V. Developmental maturation of dynamic causal control signals in higher-order cognition: a neurocognitive network model. PLoS Comput Biol 2012, 8:e1002374.
63. Topchy A., Jain A.K., Punch W. Clustering ensembles: models of consensus and weak partitions. IEEE Trans Pattern Anal 2005, 27:1866-1881.
64. Topchy A., Jain A.K., Punch W. Combining multiple weak clusterings. Proceedings of the third IEEE international conference on data mining 2003, 331-338.
65. Tzourio-Mazoyer N., Landeau B., Papathanassiou D., Crivello F., Etard O., Delcroix N., et al. Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage 2002, 15:273-289.
66. Uddin L.Q., Supekar K., Amin H., Rykhlevskaia E., Nguyen D.A., Greicius M.D., et al. Dissociable connectivity within human angular gyrus and intraparietal sulcus: evidence from functional and structural connectivity. Cereb Cortex 2010, 20:2636-2646.
67. Uddin L.Q., Supekar K., Menon V. Typical and atypical development of functional human brain networks: insights from resting-state FMRI. Front Syst Neurosci 2010, 4:21.
68. Uddin L.Q., Supekar K.S., Ryali S., Menon V. Dynamic reconfiguration of structural and functional connectivity across core neurocognitive brain networks with development. J Neurosci 2011, 31:18578-18589.
69. Wig G.S., Laumann T.O., Cohen A.L., Power J.D., Nelson S.M., Glasser M.F., et al. Parcellating an individual subject's cortical and subcortical brain structures using snowball sampling of resting-state correlations. Cereb Cortex 2014, 24(8):2036-2054.
70. Wig G.S., Laumann T.O., Petersen S.E. An approach for parcellating human cortical areas using resting-state correlations. Neuroimage 2014, 93:276-291.
71. Wu S.S., Chang T.T., Majid A., Caspers S., Eickhoff S.B., Menon V. Functional heterogeneity of inferior parietal cortex during mathematical cognition assessed with cytoarchitectonic probability maps. Cereb Cortex 2009, 19:2930-2945.
72. Yelnik J. Modeling the organization of the basal ganglia. Rev Neurol 2008, 164:969-976.
73. Yeo B.T.T., Krienen F.M., Sepulcre J., Sabuncu M.R., Lashkari D., Hollinshead M., et al. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol 2011, 106:1125-1165.
74. Zarei M., Beckmann C.F., Binnewijzend M.A., Schoonheim M.M., Oghabian M.A., Sanz-Arigita E.J., et al. Functional segmentation of the hippocampus in the healthy human brain and in Alzheimer's disease. Neuroimage 2012, 66C:28-35.
75. Zhang D., Snyder A.Z., Shimony J.S., Fox M.D., Raichle M.E. Noninvasive functional and structural connectivity mapping of the human thalamocortical system. Cereb Cortex 2010, 20:1187-1194.
76. Zilles K., Amunts K. Centenary of Brodmann's map - conception and fate. Nat Rev Neurosci 2010, 11:139-145.
77. Zilles K., Schlaug G., Geyer S., Luppino G., Matelli M., Qu M., et al. Anatomy and transmitter receptors of the supplementary motor areas in the human and nonhuman primate brain. Adv Neurol 1996, 70:29-43.