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Source-Based Morphometry: Data-Driven Multivariate Analysis of Structural Brain Imaging Data

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Brain Morphometry

Part of the book series: Neuromethods ((NM,volume 136))

Abstract

This chapter discusses a now established linear multivariate technique called source-based morphometry (SBM), a data-driven multivariate approach for decomposing structural brain imaging data into commonly covarying components and subject-specific loading parameters. It has been used to study neuroanatomic differences between healthy controls and patients with neuropsychiatric diseases. We start by discussing the advantages of data-driven multivariate techniques over univariate analysis for imaging studies. We then discuss results from a range of recent imaging studies which have successfully applied this linear technique. We also present extensions of this framework such as nonlinear SBM, morphometric analysis using independent vector analysis (IVA), and related approaches such as parallel independent component analysis with reference (pICA-R). This chapter thus reviews a wide range of multivariate, data-driven approaches which have been successfully applied to brain imaging studies.

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References

  1. Xu L, Groth KM, Pearlson G, Schretlen DJ, Calhoun VD (2009) Source-based morphometry: the use of independent component analysis to identify gray matter differences with application to schizophrenia. Hum Brain Mapp 30(3):711–724

    Article  PubMed  PubMed Central  Google Scholar 

  2. Ashburner J, Friston KJ (2000) Voxel-based morphometry—the methods. NeuroImage 11(6):805–821

    Article  CAS  PubMed  Google Scholar 

  3. McKeown MJ, Sejnowski TJ (1998) Independent component analysis of fMRI data: examining the assumptions. Hum Brain Mapp 6(5–6):368–372

    Article  CAS  PubMed  Google Scholar 

  4. Sui J, Adali T, Yu Q, Chen J, Calhoun VD (2012) A review of multivariate methods for multimodal fusion of brain imaging data. J Neurosci Methods 204(1):68–81

    Article  PubMed  Google Scholar 

  5. Pearlson GD, Liu J, Calhoun VD (2015) An introductory review of parallel independent component analysis (p-ICA) and a guide to applying p-ICA to genetic data and imaging phenotypes to identify disease-associated biological pathways and systems in common complex disorders. Front Genet 6:276

    Article  PubMed  PubMed Central  Google Scholar 

  6. Hyvärinen A, Oja E (2000) Independent component analysis: algorithms and applications. Neural Netw 13(4):411–430

    Article  PubMed  Google Scholar 

  7. Lee T-W (1998) Independent component analysis: theory and applications. Springer, New York, London, pp 27–66

    Book  Google Scholar 

  8. Comon P, Jutten C (2010) Handbook of blind source separation: independent component analysis and applications. Academic press

    Google Scholar 

  9. Calhoun VD, Liu J, Adali T (2009) A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data. NeuroImage 45(1):S163–S172

    Article  PubMed  Google Scholar 

  10. Gupta CN, Calhoun VD, Rachakonda S et al (2015) Patterns of gray matter abnormalities in schizophrenia based on an international mega-analysis. Schizophr Bull 41(5):1133–1142

    Article  PubMed  Google Scholar 

  11. Turner JA, Calhoun VD, Michael A et al (2012) Heritability of multivariate gray matter measures in schizophrenia. Twin Res Hum Genet 15(03):324–335

    Article  PubMed  PubMed Central  Google Scholar 

  12. Sprooten E, Gupta CN, Knowles EE et al (2015) Genome-wide significant linkage of schizophrenia-related neuroanatomical trait to 12q24. Am J Med Genet B Neuropsychiatr Genet 168(8):678–686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kubera KM, Sambataro F, Vasic N et al (2014) Source-based morphometry of gray matter volume in patients with schizophrenia who have persistent auditory verbal hallucinations. Prog Neuro-Psychopharmacol Biol Psychiatry 50:102–109

    Article  Google Scholar 

  14. Palaniyappan L, Mahmood J, Balain V, Mougin O, Gowland PA, Liddle PF (2015) Structural correlates of formal thought disorder in schizophrenia: an ultra-high field multivariate morphometry study. Schizophr Res 168(1):305–312

    Article  PubMed  PubMed Central  Google Scholar 

  15. Chen J, Liu J, Calhoun VD et al (2014) Exploration of scanning effects in multi-site structural MRI studies. J Neurosci Methods 230:37–50

    Article  PubMed  PubMed Central  Google Scholar 

  16. Caprihan A, Abbott C, Yamamoto J et al (2011) Source-based morphometry analysis of group differences in fractional anisotropy in schizophrenia. Brain Connect 1(2):133–145

    Article  PubMed  PubMed Central  Google Scholar 

  17. Wolf RC, Huber M, Lepping P et al (2014) Source-based morphometry reveals distinct patterns of aberrant brain volume in delusional infestation. Prog Neuro-Psychopharmacol Biol Psychiatry 48:112–116

    Article  Google Scholar 

  18. Xu L, Adali T, Schretlen D, Pearlson G, Calhoun VD (2011) Structural angle and power images reveal interrelated gray and white matter abnormalities in schizophrenia. Neurol Res Int 2012:735249

    PubMed  PubMed Central  Google Scholar 

  19. Xu L, Pearlson G, Calhoun VD (2009) Joint source based morphometry identifies linked gray and white matter group differences. NeuroImage 44(3):777–789

    Article  PubMed  Google Scholar 

  20. Segall J, Allen EA, Jung RE, Erhardt E, Arja S, Kiehl KA, Calhoun VD (2012) Correspondence between structure and function in the human brain at rest. Front Neuroinform 6:10

    Article  PubMed  PubMed Central  Google Scholar 

  21. Arbabshirani MR, Plis S, Sui J, Calhoun VD (2016) Single subject prediction of brain disorders in neuroimaging: promises and pitfalls. NeuroImage 145(Pt B):137–165

    PubMed  PubMed Central  Google Scholar 

  22. Castro E, Gupta CN, Martínez-Ramón M, Calhoun VD, Arbabshirani MR, Turner J (2014) Identification of patterns of gray matter abnormalities in schizophrenia using source-based morphometry and bagging. Paper presented at: 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

    Google Scholar 

  23. Koutsouleris N, Meisenzahl EM, Davatzikos C et al (2009) Use of neuroanatomical pattern classification to identify subjects in at-risk mental states of psychosis and predict disease transition. Arch Gen Psychiatry 66(7):700–712

    Article  PubMed  PubMed Central  Google Scholar 

  24. Castro E, Hjelm RD, Plis SM, Dinh L, Turner JA, Calhoun VD (2016) Deep independence network analysis of structural brain imaging: application to schizophrenia. IEEE Trans Med Imaging 35:1729–1740

    Article  PubMed  PubMed Central  Google Scholar 

  25. Plis SM, Hjelm DR, Salakhutdinov R, Allen EA, Bockholt HJ, Long JD, Johnson HJ, Paulsen JS, Turner JA, Calhoun VD (2014) Deep learning for neuroimaging: a validation study. Front Neurosci 8:229

    Article  PubMed  PubMed Central  Google Scholar 

  26. Castro E, Ulloa A, Plis SM, Turner JA, Calhoun VD (2015) Generation of synthetic structural magnetic resonance images for deep learning pre-training. Paper presented at: 2015 I.E. 12th International Symposium on Biomedical Imaging (ISBI)

    Google Scholar 

  27. Gupta CN, Arias-Vasquez A, Liu J, Andreassen O, Agartz I, Calhoun VD (2016) Canonicality of structural patterns compared using source based morphometry and independent vector analysis. Organization for Human Brain Mapping Conference, June 2016

    Google Scholar 

  28. Kim T, Lee I, Lee T-W (2006) Independent vector analysis: definition and algorithms. Paper presented at: 2006 Fortieth Asilomar Conference on Signals, Systems and Computers

    Google Scholar 

  29. Sullivan PF, Kendler KS, Neale MC (2003) Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry 60(12):1187–1192

    Article  PubMed  Google Scholar 

  30. Gottesman II, Gould TD (2003) The endophenotype concept in psychiatry: etymology and strategic intentions. Am J Psychiatr 160(4):636–645

    Article  PubMed  Google Scholar 

  31. Stein JL, Medland SE, Vasquez AA et al (2012) Identification of common variants associated with human hippocampal and intracranial volumes. Nat Genet 44(5):552–561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Thompson PM, Stein JL, Medland SE et al (2014) The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data. Brain Imaging Behav 8(2):153–182

    PubMed  PubMed Central  Google Scholar 

  33. Liu J, Calhoun VD (2014) A review of multivariate analyses in imaging genetics. Front Neuroinform 8:29

    PubMed  PubMed Central  Google Scholar 

  34. Wright C, Gupta C, Chen J et al (2016) Polymorphisms in MIR137HG and microRNA-137-regulated genes influence gray matter structure in schizophrenia. Transl Psychiatry 6(2):e724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Calhoun VD, Sui J (2016) Multimodal fusion of brain imaging data: a key to finding the missing link(s) in complex mental illness. Biol Psychiatry Cogn Neurosci Neuroimaging 1(3):230–244

    Article  PubMed  PubMed Central  Google Scholar 

  36. Liu J, Pearlson G, Windemuth A, Ruano G, Perrone-Bizzozero NI, Calhoun V (2009) Combining fMRI and SNP data to investigate connections between brain function and genetics using parallel ICA. Hum Brain Mapp 30(1):241–255

    Article  PubMed  PubMed Central  Google Scholar 

  37. Gupta CN, Chen J, Liu J et al (2014) Genetic markers of white matter integrity in schizophrenia revealed by parallel ICA. Front Hum Neurosci 9:100–100

    Google Scholar 

  38. Yarosh HL, Meda SA, De Wit H, Hart AB, Pearlson GD (2015) Multivariate analysis of subjective responses to d-amphetamine in healthy volunteers finds novel genetic pathway associations. Psychopharmacology 232(15):2781–2794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Narayanan B, Soh P, Calhoun V et al (2015) Multivariate genetic determinants of EEG oscillations in schizophrenia and psychotic bipolar disorder from the BSNIP study. Transl Psychiatry 5(6):e588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Meier T, Wildenberg J, Liu J et al (2012) Parallel ICA identifies sub-components of resting state networks that covary with behavioral indices. Front Hum Neurosci 6:281

    Article  PubMed  PubMed Central  Google Scholar 

  41. Chen J, Calhoun VD, Pearlson GD et al (2013) Guided exploration of genomic risk for gray matter abnormalities in schizophrenia using parallel independent component analysis with reference. NeuroImage 83:384–396

    Article  PubMed  Google Scholar 

  42. Chen J, Calhoun VD, Ulloa AE, Liu J (2014) Parallel ICA with multiple references: A semi-blind multivariate approach. Paper presented at: 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

    Google Scholar 

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Acknowledgments

This work was supported by NIH 1R01MH094524 (to JT and VDC) as well as P20GM103472, 1R01EB006841, and R01EB005846 (to VDC).

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Correspondence to Vince D. Calhoun .

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Gupta, C.N., Turner, J.A., Calhoun, V.D. (2018). Source-Based Morphometry: Data-Driven Multivariate Analysis of Structural Brain Imaging Data. In: Spalletta, G., Piras, F., Gili, T. (eds) Brain Morphometry. Neuromethods, vol 136. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7647-8_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7647-8_7

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7645-4

  • Online ISBN: 978-1-4939-7647-8

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