Examining similarity structure: Multidimensional scaling and related approaches in neuroimaging

Computational and Mathematical Methods in Medicine

Volumn 2013, Issue , 2013, Pages

  Shinkareva, Svetlana V ^a   Wang, Jing ^a   Wedell, Douglas H ^a  

^a UNIVERSITY OF SOUTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN; DATA ACQUISITION; MAGNETIC RESONANCE IMAGING; NEUROIMAGING;

FUNCTIONAL MAGNETIC RESONANCE IMAGING; INDIVIDUAL DIFFERENCES; MULTI-DIMENSIONAL SCALING; MULTIVARIATE PATTERN ANALYSIS; MULTIVARIATE PATTERNS; SIMILARITY ANALYSIS; SIMILARITY SPACES; SPATIAL REPRESENTATIONS;

MULTIVARIANT ANALYSIS;

ASPERGER SYNDROME; BIOMETRY; BRAIN; BRAIN FUNCTION; BRAIN REGION; CLINICAL ASSESSMENT; CLUSTER ANALYSIS; CORRELATION COEFFICIENT; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; FUNCTIONAL MAGNETIC RESONANCE IMAGING; FUNCTIONAL NEUROIMAGING; HUMAN; IMAGE QUALITY; INFORMATION PROCESSING; MULTIDIMENSIONAL SCALING; MULTIVARIATE ANALYSIS; MULTIVARIATE PATTERN ANALYSIS; MULTIVOXEL PATTERN; NEUROLOGIC EXAMINATION; REVIEW; SCHIZOPHRENIA; SIGNAL NOISE RATIO; STATISTICAL ANALYSIS; STIMULUS; TASK PERFORMANCE; VISUAL FEEDBACK; VOXEL BASED MORPHOMETRY; AUTOMATED PATTERN RECOGNITION; BIOLOGY; BRAIN MAPPING; HISTOLOGY; NEUROIMAGING; NUCLEAR MAGNETIC RESONANCE IMAGING; PHYSIOLOGY; STATISTICS; ANATOMY AND HISTOLOGY; STATISTICS AND NUMERICAL DATA;

BRAIN; BRAIN MAPPING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; HUMANS; MAGNETIC RESONANCE IMAGING; MULTIVARIATE ANALYSIS; NEUROIMAGING; PATTERN RECOGNITION, AUTOMATED;

EID: 84877276107     PISSN: 1748670X     EISSN: 17486718     Source Type: Journal    
DOI: 10.1155/2013/796183     Document Type: Review

References (84)

1. O'Toole A. J., Jiang F., Abdi H., Pénard N., Dunlop J. P., Parent M. A., Theoretical, statistical, and practical perspectives on pattern-based classification approaches to the analysis of functional neuroimaging data. Journal of Cognitive Neuroscience 2007 19 11 1735 1752 2-s2.0-35748950120 10.1162/jocn.2007.19.11.1735 (Pubitemid 350043418)
2. Haynes J. D., Rees G., Decoding mental states from brain activity in humans. Nature Reviews Neuroscience 2006 7 7 523 534 2-s2.0-33745587777 10.1038/nrn1931 (Pubitemid 43989773)
3. Norman K. A., Polyn S. M., Detre G. J., Haxby J. V., Beyond mind-reading: multi-voxel pattern analysis of fMRI data. Trends in Cognitive Sciences 2006 10 9 424 430 2-s2.0-33748178966 10.1016/j.tics.2006.07.005 (Pubitemid 44308461)
4. Tong F., Pratte M. S., Decoding patterns of human brain activity. Annual Review of Psychology 2012 63 483 509
5. Edelman S., Grill-Spector K., Kushnir T., Malach R., Toward direct visualization of the internal shape representation space by fMRI. Psychobiology 1998 26 4 309 321 2-s2.0-0032428906 (Pubitemid 29068426)
6. Welchew D. E., Honey G. D., Sharma T., Robbins T. W., Bullmore E. T., Multidimensional scaling of integrated neurocognitive function and schizophrenia as a disconnexion disorder. NeuroImage 2002 17 3 1227 1239 2-s2.0-0036432037 10.1006/nimg.2002.1246 (Pubitemid 35333844)
7. Kriegeskorte N., Mur M., Bandettini P., Representational similarity analysis-connecting the branches of systems neuroscience. Frontiers in Systems Neuroscience 2008 2 1 28
8. Abdi H., Williams L. J., STATIS and DISTATIS: optimum multitable principal component analysis and three way metric multidimensional scaling. Wiley Interdisciplinary Reviews: Computational Statistics 2012 4 2 124 167
9. Raizada R. D. S., Connolly A. C., What makes different people's representations alike: neural similarity space solves the problem of across-subject fMRI decoding. Journal of Cognitive Neuroscience 2012 24 4 868 877
10. Shinkareva S. V., Malave V. L., Just M. A., Mitchell T. M., Exploring commonalities across participants in the neural representation of objects. Human Brain Mapping 2012 33 1375 1383 2-s2.0-79955802549 10.1002/hbm.21296
11. Connolly A. C., Gobbini M. I., Haxby J. V., Kriegeskorte N., Kreiman G., Three virtues of similarity-based multivariate pattern analysis: an example from the human object vision pathway. Understanding Visual Population Codes: Toward a Common multivariate framework for Cell Recording and functional imaging 2012 Cambridge, Massachusetts MIT Press
12. Nosofsky R. M., Similarity scaling and cognitive process models. Annual Review of Psychology 1992 43 1 25 53 2-s2.0-11944262572
13. Edelman S., Representation is representation of similarities. Behavioral and Brain Sciences 1998 21 4 449 498 2-s2.0-0031731695 10.1017/S0140525X98001253 (Pubitemid 28505637)
14. Edelman S., Shahbazi R., Renewing the respect for similarity. Frontiers in Computational Neuroscience 2012 6, article 45
15. Shoben E. J., Applications of multidimensional scaling in cognitive psychology. Applied Psychological Measurement 1983 7 473 490
16. Laakso A., Cottrell G., Content and cluster analysis: assessing representational similarity in neural systems. Philosophical Psychology 2000 13 1 46 76 2-s2.0-0034354275
17. Schurger A., Pereira F., Treisman A., Cohen J. D., Reproducibility distinguishes conscious from nonconscious neural representations. Science 2010 327 5961 97 99 2-s2.0-74549181616 10.1126/science.1180029
18. Abdi H., Williams L. J., Connolly A. C., Multiple Subject Barycentric Discriminant Analysis (MUSUBADA): how to assign scans to categories without using spatial normalization. Computational and Mathematical Methods in Medicine 2012 2012 15 634165 10.1155/2012/634165
19. Mur M., Bandettini P. A., Kriegeskorte N., Revealing representational content with pattern-information fMRI-an introductory guide. Social Cognitive and Affective Neuroscience 2009 4 1 101 109 2-s2.0-63349109274 10.1093/scan/nsn044
20. Pereira F., Mitchell T., Botvinick M., Machine learning classifiers and fMRI: a tutorial overview. NeuroImage 2009 45 1 S199 S209 2-s2.0-65549168742 10.1016/j.neuroimage.2008.11.007
21. Kriegeskorte N., Mur M., Ruff D. A., Kiani R., Bodurka J., Esteky H., Tanaka K., Bandettini P. A., Matching categorical object representations in inferior temporal cortex of man and monkey. Neuron 2008 60 6 1126 1141 2-s2.0-57649196582 10.1016/j.neuron.2008.10.043
22. Shinkareva S. V., Mason R. A., Malave V. L., Wang W., Mitchell T. M., Just M. A., Using fMRI brain activation to identify cognitive states associated with perception of tools and dwellings. PLoS ONE 2008 3 1 2-s2.0-38949165373 10.1371/journal.pone.0001394 e1394 (Pubitemid 351223130)
23. Shinkareva S. V., Malave V. L., Mason R. A., Mitchell T. M., Just M. A., Commonality of neural representations of words and pictures. NeuroImage 2011 54 3 2418 2425 2-s2.0-78650215949 10.1016/j.neuroimage.2010.10.042
24. Wang J., Baucom L. B., Shinkareva S. V., Decoding abstract and concrete concept representations based on single-trial fMRI data. Human Brain Mapping 2013 34 5 1133 1147
25. Baucom L. B., Wedell D. H., Wang J., Blitzer D. N., Shinkareva S. V., Decoding the neural representation of affective states. NeuroImage 2012 59 1 718 727
26. Polyn S. M., Natu V. S., Cohen J. D., Norman K. A., Neuroscience: category-specific cortical activity precedes retrieval during memory search. Science 2005 310 5756 1963 1966 2-s2.0-29344464279 10.1126/science.1117645 (Pubitemid 43005991)
27. Just M. A., Cherkassky V. L., Aryal S., Mitchell T. M., A neurosemantic theory of concrete noun representation based on the underlying brain codes. PLoS ONE 2010 5 1 e8622 2-s2.0-77952485144 10.1371/journal.pone.0008622
28. Mitchell T. M., Shinkareva S. V., Carlson A., Chang K. M., Malave V. L., Mason R. A., Just M. A., Predicting human brain activity associated with the meanings of nouns. Science 2008 320 5880 1191 1195 2-s2.0-45749091592 10.1126/science.1152876 (Pubitemid 351929502)
29. Hiramatsu C., Goda N., Komatsu H., Transformation from image-based to perceptual representation of materials along the human ventral visual pathway. NeuroImage 2011 57 2 482 494 2-s2.0-79958761969 10.1016/j.neuroimage.2011.04.056
30. Connolly A. C., Guntupalli J. S., Gors J., The representation of biological classes in the human brain. The Journal of Neuroscience 2012 32 8 2608 2618 10.1523/JNEUROSCI.5547-11.2012
31. Salvador R., Suckling J., Coleman M. R., Pickard J. D., Menon D., Bullmore E., Neurophysiological architecture of functional magnetic resonance images of human brain. Cerebral Cortex 2005 15 9 1332 2342 2-s2.0-18144431880 10.1093/cercor/bhi016 (Pubitemid 41191541)
32. Drucker D. M., Aguirre G. K., Different spatial scales of shape similarity representation in lateral and ventral LOC. Cerebral Cortex 2009 19 10 2269 2280 2-s2.0-66349137050 10.1093/cercor/bhn244
33. Op De Beeck H. P., Torfs K., Wagemans J., Perceived shape similarity among unfamiliar objects and the organization of the human object vision pathway. Journal of Neuroscience 2008 28 40 10111 10123 2-s2.0-54049158930 10.1523/JNEUROSCI.2511-08.2008
34. Op de Beeck H. P., Brants M., Baeck A., Wagemans J., Distributed subordinate specificity for bodies, faces, and buildings in human ventral visual cortex. NeuroImage 2010 49 4 3414 3425 2-s2.0-73749083587 10.1016/j.neuroimage. 2009.11.022
35. Tzagarakis C., Jerde T. A., Lewis S. M., Uurbil K., Georgopoulos A. P., Cerebral cortical mechanisms of copying geometrical shapes: a multidimensional scaling analysis of fMRI patterns of activation. Experimental Brain Research 2009 194 3 369 380 2-s2.0-63949085018 10.1007/s00221-009-1709-5
36. Weber M., Thompson-Schill S. L., Osherson D., Haxby J., Parsons L., Predicting judged similarity of natural categories from their neural representations. Neuropsychologia 2009 47 3 859 868 2-s2.0-59749096854 10.1016/j.neuropsychologia.2008.12.029
37. O'Toole A. J., Jiang F., Abdi H., Haxby J. V., Partially distributed representations of objects and faces in ventral temporal cortex. Journal of Cognitive Neuroscience 2005 17 4 580 590 2-s2.0-16444364709 10.1162/ 0898929053467550 (Pubitemid 40478281)
38. Cichy R. M., Sterzer P., Heinzle J., Probing principles of large-scale object representation: category preference and location encoding. Human Brain Mapping 2012
39. Greenstein D., Malley J. D., Weisinger B., Clasen L., Gogtay N., Using multivariate machine learning methods and structural MRI to classify childhood onset schizophrenia and healthy controls. Frontiers in Psychiatry 2012 3, article 53
40. Steiger J. H., Tests for comparing elements of a correlation matrix. Psychological Bulletin 1980 87 2 245 251 2-s2.0-0000957052 10.1037/0033-2909.87. 2.245
41. Roberts J. S., Wedell D. H., Context effects on similarity judgments of multidimensional stimuli: inferring the structure of the emotion space. Journal of Experimental Social Psychology 1994 30 1 1 38 2-s2.0-38149145147 10.1006/jesp.1994.1001 (Pubitemid 24761966)
42. Hasselmo M. E., Rolls E. T., Baylis G. C., The role of expression and identity in the face-selective responses of neurons in the temporal visual cortex of the monkey. Behavioural Brain Research 1989 32 3 203 218 2-s2.0-0024596573 (Pubitemid 19078311)
43. Op De Beeck H., Wagemans J., Vogels R., Inferotemporal neurons represent low-dimensional configurations of parameterized shapes. Nature Neuroscience 2001 4 12 1244 1252 2-s2.0-0035195699 10.1038/nn767 (Pubitemid 33135631)
44. Kiani R., Esteky H., Mirpour K., Tanaka K., Object category structure in response patterns of neuronal population in monkey inferior temporal cortex. Journal of Neurophysiology 2007 97 6 4296 4309 2-s2.0-34447500578 10.1152/jn.00024.2007 (Pubitemid 47080657)
45. Sereno A. B., Lehky S. R., Population coding of visual space: comparison of spatial representations in dorsal and ventral pathways. Frontiers in Computational Neuroscience 2011 4, article 159
46. Lehky S. R., Sereno A. B., Comparison of shape encoding in primate dorsal and ventral visual pathways. Journal of Neurophysiology 2007 97 1 307 319 2-s2.0-33846433202 10.1152/jn.00168.2006 (Pubitemid 46143359)
47. Young M. P., Yamane S., Sparse population coding of faces in the inferotemporal cortex. Science 1992 256 5061 1327 1331 2-s2.0-0026724565
48. Borg I., Groenen P., Modern Multidimensional Scaling: Theory and Applications 1997 New York, NY, USA Springer
49. Zhang Z., Takane Y., Baker E., McGaw B., Peterson P. P., Statistics: multidimensional scaling. International Encyclopedia of Education 2010 Oxford, UK Elsevier 304 311
50. Takane Y., Jung S., Oshima-Takane Y., Millsap R. E., Maydeu-Olivares A., Multidimensional scaling. Handbook of Quantitative Methods in Psychology 2009 London, UK Sage 219 242
51. Shepard R. N., Attention and the metric structure of the stimulus space. Journal of Mathematical Psychology 1964 1 1 54 87 2-s2.0-0002994064
52. Groenen P. J. F., Heiser W. J., The tunneling method for global optimization in multidimensional scaling. Psychometrika 1996 61 3 529 550 2-s2.0-0030490277
53. Hubert L., Arabie P., Hesson-Mcinnis M., Multidimensional scaling in the city-block metric: a combinatorial approach. Journal of Classification 1992 19929 2 211 236
54. Shepard R. N., The analysis of proximities: multidimensional scaling with an unknown distance function-I. Psychometrika 1962 27 2 125 140 2-s2.0-34250926052 10.1007/BF02289630
55. Shepard R. N., The analysis of proximities: multidimensional scaling with an unknown distance function-II. Psychometrika 1962 27 3 219 246 2-s2.0-34250920725 10.1007/BF02289621
56. Schönemann P. H., Carroll R. M., Fitting one matrix to another under choice of a central dilation and a rigid motion. Psychometrika 1970 35 2 245 255 2-s2.0-0005718706 10.1007/BF02291266
57. Tucker L. R., Messick S., An individual differences model for multidimensional scaling. Psychometrika 1963 28 4 333 367 2-s2.0-0000830865 10.1007/BF02289557
58. Carroll J. D., Chang J. J., Analysis of individual differences in multidimensional scaling via an n-way generalization of «Eckart- Young» decomposition. Psychometrika 1970 35 3 283 319 2-s2.0-34250499792 10.1007/BF02310791
59. Welchew D. E., Ashwin C., Berkouk K., Salvador R., Suckling J., Baron-Cohen S., Bullmore E., Functional disconnectivity of the medial temporal lobe in Asperger's syndrome. Biological Psychiatry 2005 57 9 991 998 2-s2.0-18144423466 10.1016/j.biopsych.2005.01.028 (Pubitemid 40613034)
60. Tagaris G. A., Kim S. G., Strupp J. P., Andersen P., Uurbil K., Georgopoulos A. P., Quantitative relations between parietal activation and performance in mental rotation. NeuroReport 1996 7 3 773 776 2-s2.0-0029995203 (Pubitemid 26145339)
61. Abdi H., Dunlop J. P., Williams L. J., How to compute reliability estimates and display confidence and tolerance intervals for pattern classifiers using the Bootstrap and 3-way multidimensional scaling (DISTATIS). NeuroImage 2009 45 1 89 95 2-s2.0-60149110530 10.1016/j.neuroimage.2008.11.008
62. Kherif F., Poline J. B., Mériaux S., Benali H., Flandin G., Brett M., Group analysis in functional neuroimaging: selecting subjects using similarity measures. NeuroImage 2003 20 4 2197 2208 2-s2.0-0345734447 10.1016/j.neuroimage.2003.08.018 (Pubitemid 37543633)
63. Churchill N. W., Oder A., Abdi H., Tam F., Lee W., Thomas C., Ween J. E., Graham S. J., Strother S. C., Optimizing preprocessing and analysis pipelines for single-subject fMRI-I. Standard temporal motion and physiological noise correction methods. Human Brain Mapping 2012 33 609 627 2-s2.0-79953262489 10.1002/hbm.21238
64. Lavit C., Escoufier Y., Sabatier R., Traissac P., The ACT (STATIS method). Computational Statistics and Data Analysis 1994 18 1 97 119 2-s2.0-2142747356
65. Abdi H., Valentin D., Salkind N. J., STATIS. Encyclopedia of Measurement and Statistics 2007 Thousand Oaks, Calif, USA Sage 955 962
66. Johnson R. A., Wichern D. W., Applied Multivariate Statistical Analysis 2007 6th Prentice Hall
67. Arabie P., Hubert L. J., De Soete G., Clustering and Classification 1999 World Scientific Publishing
68. Landau S., Ster I. C., Cluster analysis: overview. International Encyclopedia of Education 2010 72 83
69. Popivanov I. D., Jastorff J., Vanduffela W., Stimulus representations in body-selective regions of the macaque cortex assessed with event-related fMRI. NeuroImage 2012 63 723 741 10.1016/j.neuroimage.2012.07.013
70. Haushofer J., Livingstone M. S., Kanwisher N., Multivariate patterns in object-selective cortex dissociate perceptual and physical shape similarity. PLoS Biology 2008 6 7, article e187 723 741 2-s2.0-58149192523 10.1371/journal.pbio.0060187
71. Haxby J. V., Gobbini M. I., Furey M. L., Ishai A., Schouten J. L., Pietrini P., Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science 2001 293 5539 2425 2430 2-s2.0-0035964792 10.1126/science.1063736 (Pubitemid 32917318)
72. Hanson S. J., Matsuka T., Haxby J. V., Combinatorial codes in ventral temporal lobe for object recognition: Haxby (2001) revisited: Is there a "face" area? NeuroImage 2004 23 1 156 166 2-s2.0-4344638967 10.1016/j.neuroimage.2004.05.020 (Pubitemid 39119445)
73. Onton J., Makeig S., High-frequency broadband modulations of electroencephalographic spectra. Frontiers in Human Neuroscience 2009 3, article 61
74. Braet W., Wagemans J., Op de Beeck H., The visual word form area is organized according to orthography. NeuroImage 2012 59 2751 2759
75. Soto F. A., Waldschmidt J. G., Helie S., Ashby F. G., Brain activity across the development of automatic categorization: a comparison of categorization tasks using multi-voxel pattern analysis. NeuroImage 2013 71 284 297 10.1016/j.neuroimage.2013.01.008
76. Aguirre G. K., Continuous carry-over designs for fMRI. NeuroImage 2007 35 4 1480 1494 2-s2.0-34147174404 10.1016/j.neuroimage.2007.02.005 (Pubitemid 46561360)
77. Yang Z., Zuo X. N., Wang P., Generalized RAICAR: discover homogeneous subject (sub)groups by reproducibility of their intrinsic connectivity networks. NeuroImage 2012 63 403 414 10.1016/j.neuroimage.2012.06.060
78. Janoos F., Machiraju R., Singh S., Morocz I. Á., Spatio-temporal models of mental processes from fMRI. NeuroImage 2011 57 2 362 377 2-s2.0-79958745825 10.1016/j.neuroimage.2011.03.047
79. Friston K. J., Frith C. D., Fletcher P., Liddle P. F., Frackowiak R. S. J., Functional topography: multidimensional scaling and functional connectivity in the brain. Cerebral Cortex 1996 6 2 156 164 2-s2.0-0029984565 10.1093/cercor/6.2.156 (Pubitemid 26117393)
80. Hervé P.-Y., Razafimandimby A., Vigneau M., Disentangling the brain networks supporting affective speech comprehension. NeuroImage 2012 61 1255 1267 10.1016/j.neuroimage.2012.03.073
81. Etkin A., Wager T. D., Functional neuroimaging of anxiety: a meta-ana lysis of emotional processing in PTSD, social anxiety disorder, and specific phobia. American Journal of Psychiatry 2007 164 10 1476 1488 2-s2.0-35748963237 10.1176/appi.ajp.2007.07030504 (Pubitemid 350069724)
82. de Leeuw J., Mair P., Multidimensional scaling using majorization: SMACOF in R. Journal of Statistical Software 2009 31 3 1 30 2-s2.0-70349291078
83. Dray S., Dufour A. B., Chessel D., The ade4 package-II: two-table and K-table methods. R News 2007 7 2 47 52
84. Hubert L., Koehn H.-F., Steinley D., Millsap R. E., Maydeu-Olivares A., Cluster analysis: a toolbox for MATLAB. Handbook of Quantitative Methods in Psychology 2009 London, UK Sage 444 512