Skip to main content

Challenges in the Analysis of Neuroscience Data

  • Conference paper
  • First Online:
Studies in Neural Data Science (START UP RESEARCH 2017)

Part of the book series: Springer Proceedings in Mathematics & Statistics ((PROMS,volume 257))

Included in the following conference series:

Abstract

In the last two decades, our understanding of the mechanisms underlying the functioning and disruption of the human brain has advanced considerably. The previous chapters of the book have provided a compelling argument for demonstrating the advantages of thoughtful, non-naive, statistical approaches for analyzing brain imaging data. Here, we provide a review of the main themes highlighted in those chapters, and we further discuss some of the challenges that statistical imaging is currently confronted with. In particular, we emphasize the importance of developing analytical frameworks that allow to characterize the heterogeneity typically observed in brain imaging both within- and between- subjects, by capturing the main sources of variability in the data. More specifically, we focus on clustering methods that identify groups of subjects characterized by similar patterns of brain responses to a task; on dynamic temporal models that characterize the heterogeneity in individual functional connectivity networks; and on multimodal imaging analysis and imaging genetics that combine information from multiple data sources in order to achieve a better understanding of brain processes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Friston, K.J., Ashburnet, J.T., Kiebe, Nichols, T.E., Penny, W.D.: Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press (2007)

    Google Scholar 

  2. Prados, F., Boada, I., Prats-Galino, A., Martin-Fernandez, J.A., Feixas, M., Blasco, G., Puig, J., Pedraza, S.: Analysis of new diffusion tensor imaging anisotropy measures in the three-phase plot. J. Magn. Reson. Imaging 31(6), 1435–1444 (2010)

    Article  Google Scholar 

  3. Weber, B., Fliessbach, K., Elger, C.: Magnetic resonance imaging in epilepsy research: recent and upcoming developments. In: Schwartzkroin, P.A. (ed.) Encyclopedia of Basic Epilepsy Research, pp. 1549–1554. Academic Press, Oxford (2009)

    Chapter  Google Scholar 

  4. Oguz, I., Farzinfar, M., Matsui, J., Budin, F., Liu, Z., Gerig, G., Johnson, H., Styner, M.: Dtiprep: quality control of diffusion-weighted images. Front. Neuroinformatics 8, 4 (2014)

    Article  Google Scholar 

  5. Durante, D., Dunson, D.B.: Bayesian inference and testing of group differences in brain networks. Bayesian Anal. 13(1), 29–58 (2018)

    Article  MathSciNet  MATH  Google Scholar 

  6. Poldrack, R., Mumford, J., Nichols, T.: Handbook of fMRI Data Analysis. Cambridge University Press (2011)

    Google Scholar 

  7. Handwerker, D.A., Gonzalez-Castillo, J., D’Esposito, M., Bandettini, P.A.: The continuing challenge of understanding and modeling hemodynamic variation in fMRI. NeuroImage 62(2), 1017–1023 (2012)

    Article  Google Scholar 

  8. Handwerker, D.A., Ollinger, J.M., D’Esposito, M.: Variation of BOLD hemodynamic responses across subjects and brain regions and their effects on statistical analyses. NeuroImage 21(4), 1639–1651 (2004)

    Article  Google Scholar 

  9. Rangaprakash, D., Wu, G.R., Marinazzo, D., Hu, X., Deshpande, G.: Hemodynamic response function (HRF) variability confounds resting-state fMRI functional connectivity. Magn. Reson. Med. (2018)

    Google Scholar 

  10. Wu, G.R., Liao, W., Stramaglia, S., Ding, J.R., Chen, H., Marinazzo, D.: A blind deconvolution approach to recover effective connectivity brain networks from resting state fMRI data. Med. Image Anal. 17(3), 365–374 (2013)

    Article  Google Scholar 

  11. Friston, K.: Functional and effective connectivity in neuroimaging: a synthesis. Hum. Brain Mapp. 2, 56–78 (1994)

    Article  Google Scholar 

  12. Andersen, A., Gash, D., Avison, M.: Principal component analysis of the dynamic response measured by fMRI: a generalized linear systems framework. Magn. Reson. Imaging 17(6), 795–815 (1999)

    Article  Google Scholar 

  13. Calhoun, V., Adali, T., Pearlson, G., Pekar, J.: A method for making group inferences from functional MRI data using independent component analysis. Hum. Brain Mapp. 14(3), 140–151 (2001)

    Article  Google Scholar 

  14. Varoquaux, G., Gramfort, A., Poline, J., Thirion, B., Zemel, R., Shawe-Taylor, J.: Brain covariance selection: better individual functional connectivity models using population prior. Adv. Neural Inf. Process. Syst. (2010)

    Google Scholar 

  15. Bowman, F., Caffo, B., Bassett, S., Kilts, C.: A Bayesian hierarchical framework for spatial modeling of fMRI data. NeuroImage 39(1), 146–156 (2008)

    Article  Google Scholar 

  16. Zhang, L., Guindani, M., Versace, F., Vannucci, M.: A spatio-temporal nonparametric Bayesian variable selection model of fMRI data for clustering correlated time courses. NeuroImage 95, 162–175 (2014)

    Article  Google Scholar 

  17. Ferguson, T.S.: A Bayesian analysis of some nonparametric problems. Ann. Stat., 209–230 (1973)

    Article  MathSciNet  MATH  Google Scholar 

  18. Bullmore, E., Sporns, O.: Complex brain networks: graph theoretical analysis of structural and functional systems. Nat. Rev. Neurosci. 10(3), 186–198 (2009)

    Article  Google Scholar 

  19. van den Heuvel, M.P., Sporns, O.: Network hubs in the human brain. Trends Cogn. Sci. 17(12), 683–696 (2013)

    Article  Google Scholar 

  20. Stam, C.J., Reijneveld, J.C.: Graph theoretical analysis of complex networks in the brain. Nonlinear Biomed. Phys. 1, 3–3 (2007)

    Article  Google Scholar 

  21. Ginestet, C.E., Li, J., Balachandran, P., Rosenberg, S., Kolaczyk, E.D.: Hypothesis testing for network data in functional neuroimaging. Ann. Appl. Stat. 11(2), 725–750 (2017)

    Article  MathSciNet  MATH  Google Scholar 

  22. Friston, K.J., Frith, C.D., Frackowiak, R.S.J.: Time-dependent changes in effective connectivity measured with pet. Hum. Brain Mapp. 1(1), 69–79 (1993). https://doi.org/10.1002/hbm.460010108

    Article  Google Scholar 

  23. Büchel, C., Friston, K.: Modulation of connectivity in visual pathways by attention: cortical interactions evaluated with structural equation modelling and fMRI. Cereb. Cortex 7(8), 768–778 (1997)

    Article  Google Scholar 

  24. Mclntosh, A., Gonzalez-Lima, F.: Structural equation modeling and its application to network analysis in functional brain imaging. Hum. Brain Mapp. 2(1), 2–22 (1994)

    Article  Google Scholar 

  25. Friston, K., Harrison, L., Penny, W.: Dynamic causal modelling. NeuroImage 19(4), 1273–1302 (2003)

    Article  Google Scholar 

  26. Harrison, L., Penny, W., Friston, K.: Multivariate autoregressive modeling of fMRI time series. NeuroImage 19(4), 1477–1491 (2003)

    Article  Google Scholar 

  27. Goebel, R., Roebroeck, A., Kim, D., Formisano, E.: Investigating directed cortical interactions in time-resolved fMRI data using vector autoregressive modeling and Granger causality mapping. Magn. Reson. Imaging 21(10), 1251–1261 (2003)

    Article  Google Scholar 

  28. Zheng, X., Rajapakse, J.: Learning functional structure from fMR images. NeuroImage 31(4), 1601–1613 (2006)

    Article  Google Scholar 

  29. Yu, Z., Pluta, D., Shen, T., Chen, C., Xue, G., Ombao, H.: Statistical challenges in modeling big brain signals. ArXiv e-prints (2018)

    Google Scholar 

  30. Gorrostieta, C., Fiecas, M., Ombao, H., Burke, E., Cramer, S.: Hierarchical vector auto-regressive models and their applications to multi-subject effective connectivity. Front. Comput. Neurosci. 7 (2013)

    Google Scholar 

  31. Yu, Z., Prado, R., Quinlan, E.B., Cramer, S.C., Ombao, H.: Understanding the impact of stroke on brain motor function: a hierarchical Bayesian approach. J. Am. Stat. Assoc. 111(514), 549–563 (2016)

    Article  MathSciNet  Google Scholar 

  32. Friston, K.: Functional and effective connectivity: a review. Brain Connect. 1(1), 13–36 (2011)

    Article  MathSciNet  Google Scholar 

  33. Bowman, F.: Brain imaging analysis. Annu. Rev. Stat. Its Appl. 1, 61–85 (2014)

    Article  Google Scholar 

  34. Enno, S.K., J., F.K.: Analyzing effective connectivity with functional magnetic resonance imaging. Wiley Interdiscip. Rev. Cogn. Sci. 1(3), 446–459 (2010)

    Google Scholar 

  35. Savitz, J.B., Rauch, S.L., Drevets, W.C.: Clinical application of brain imaging for the diagnosis of mood disorders: the current state of play. Mol. Psychiatry 18, 528 EP (2013)

    Article  Google Scholar 

  36. Insel, T., Cuthbert, B.: Brain disorders? Precisely. Science 348(6234) (2015)

    Article  Google Scholar 

  37. Paulus, M.P., Stein, M.B.: Role of functional magnetic resonance imaging in drug discovery. Neuropsychol. Rev. 17(2), 179–188 (2007)

    Article  Google Scholar 

  38. Kaufman, J., Gelernter, J., Hudziak, J.J., Tyrka, A.R., Coplan, J.D.: The Research Domain Criteria (RDoC) project and studies of risk and resilience in maltreated children. J. Am. Acad. Child Adolesc. Psychiatry 54(8), 617–625 (2015)

    Article  Google Scholar 

  39. Kose, S., M., C.: The research domain criteria framework: transitioning from dimensional systems to integrating neuroscience and psychopathology. Psychiatry Clin. Psychopharmacol. 27(1), 1–5 (2017)

    Article  Google Scholar 

  40. Johnson, T., Liu, Z., Bartsch, A., Nichols, T.: A Bayesian non-parametric Potts model with application to pre-surgical fMRI data. Stat. Methods Med. Res. 22(4), 364–381 (2013)

    Article  MathSciNet  Google Scholar 

  41. Kim, S., Smyth, P., Stern, H.: A nonparametric Bayesian approach to detecting spatial activation patterns in fMRI data. Med. Image Comput. Comput. Assist. Interv., 217–224 (2006)

    Google Scholar 

  42. Jbabdi, S., Woolrich, M., Behrens, T.: Multiple-subjects connectivity-based parcellation using hierarchical Dirichlet process mixture models. NeuroImage 44(2), 373–384 (2009)

    Article  Google Scholar 

  43. Xu, L., Johnson, T., Nichols, T., Nee, D.: Modeling inter-subject variability in fMRI activation location: a Bayesian hierarchical spatial model. Biometrics 65(4), 1041–1051 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  44. Zhang, L., Guindani, M., Versace, F., Engelmann, J.M., Vannucci, M.: A spatiotemporal nonparametric Bayesian model of multi-subject fMRI data. Ann. Appl. Stat. 10(2), 638–666 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  45. Teh, Y.W., Jordan, M.I., Beal, M.J., Blei, D.M.: Hierarchical dirichlet processes. J. Am. Stat. Assoc. 101(476), 1566–1581 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  46. Flandin, G., Penny, W.: Bayesian fMRI data analysis with sparse spatial basis function priors. NeuroImage 34(3), 1108–1125 (2007)

    Article  Google Scholar 

  47. Harrison, L., Green, G.: A Bayesian spatiotemporal model for very large data sets. NeuroImage 50(3), 1126–1141 (2010)

    Article  Google Scholar 

  48. Penny, W., Kiebel, S., Friston, K.: Variational Bayesian inference for fMRI time series. NeuroImage 19(3), 727–741 (2003)

    Article  Google Scholar 

  49. Penny, W., Trujillo-Barreto, N., Friston, K.: Bayesian fMRI time series analysis with spatial priors. NeuroImage 24(2), 350–362 (2005)

    Article  Google Scholar 

  50. Woolrich, M., Behrens, T., Smith, S.: Constrained linear basis sets for HRF modelling using variational Bayes. NeuroImage 21(4), 1748–1761 (2004b)

    Article  Google Scholar 

  51. Kook, J.H., Guindani, M., Zhang, L., Vannucci, M.: NPBayes-fMRI: Non-parametric Bayesian General Linear Models for Single- and Multi-Subject fMRI Data (2017, in press)

    Google Scholar 

  52. Muschelli, J., Gherman, A., Fortin, J.P., Avants, B., Whitcher, B., Clayden, J.D., Caffo, B.S., Crainiceanu, C.M.: Neuroconductor: an R platform for medical imaging analysis (2018, in press)

    Google Scholar 

  53. Fornito, A., Zalesky, A., Pantelis, C., Bullmore, E.T.: Schizophrenia, neuroimaging and connectomics. NeuroImage 62(4), 2296–2314 (2012)

    Article  Google Scholar 

  54. Li, J., Wang, Z., Palmer, S., McKeown, M.: Dynamic Bayesian network modeling of fMRI: a comparison of group-analysis methods. NeuroImage 41(2), 398–407 (2008)

    Article  Google Scholar 

  55. Hutchison, R.M., Womelsdorf, T., Allen, E.A., Bandettini, P.A., Calhoun, V.D., Corbetta, M., Penna, S.D., Duyn, J.H., Glover, G.H., Gonzalez-Castillo, J., Handwerker, D.A., Keilholz, S., Kiviniemi, V., Leopold, D.A., de Pasquale, F., Sporns, O., Walter, M., Chang, C.: Dynamic functional connectivity: promise, issues, and interpretations. NeuroImage 80(0), 360–378 (2013). Mapping the Connectome

    Article  Google Scholar 

  56. Allen, E.A., Damaraju, E., Plis, S.M., Erhardt, E.B., Eichele, T., Calhoun, V.D.: Tracking whole-brain connectivity dynamics in the resting state. Cereb. Cortex (2012)

    Google Scholar 

  57. Lindquist, M.A., Xu, Y., Nebel, M.B., Caffo, B.S.: Evaluating dynamic bivariate correlations in resting-state fMRI: a comparison study and a new approach. NeuroImage (2014)

    Google Scholar 

  58. Cribben, I., Haraldsdottir, R., Atlas, L., Wager, T., Lindquist, M.: Dynamic connectivity regression: determining state-related changes in brain connectivity. NeuroImage 61, 907–920 (2012)

    Article  Google Scholar 

  59. Xu, Y., Lindquist, M.A.: Dynamic connectivity detection: an algorithm for determining functional connectivity change points in fMRI data. Front. Neurosci. 9(285) (2015)

    Google Scholar 

  60. Chiang, S., Cassese, A., Guindani, M., Vannucci, M., Yeh, H.J., Haneef, Z., Stern, J.M.: Time-dependence of graph theory metrics in functional connectivity analysis. NeuroImage 125, 601–615 (2015)

    Article  Google Scholar 

  61. Warnick, R., Guindani, M., Erhardt, E., Allen, E., Calhoun, V., Vannucci, M.: A Bayesian approach for estimating dynamic functional network connectivity in fMRI data. J. Am. Stat. Assoc. 113(521), 134–151 (2018)

    Article  MathSciNet  MATH  Google Scholar 

  62. Dobra, A., Lenkoski, A., Rodriguez, A.: Bayesian inference for general gaussian graphical models with application to multivariate lattice data. J. Am. Stat. Assoc. 106(496), 1418–1433 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  63. Roverato, A.: Hyper inverse Wishart distribution for non-decomposable graphs and its application to Bayesian inference for Gaussian graphical models. Scand. J. Stat. 29(3), 391–411 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  64. Baker, A., Brookes, M., Rezek, A., Smith, S., Behrens, T., Penny, J., Smith, R., Woolrich, M.: Fast transient networks in spontaneous human brain activity. eLife 3(3), 1–18 (2014)

    Google Scholar 

  65. Balqis-Samdin, S., Ting, C.M., Ombao, H., Salleh, S.H.: A unified estimation framework for state-related changes in effective brain connectivity. IEEE Trans. Biomed. Eng. 64(4), 844–858 (2017)

    Article  Google Scholar 

  66. Peterson, C., Stingo, F.C., Vannucci, M.: Bayesian inference of multiple gaussian graphical models. J. Am. Stat. Assoc. 110(509), 159–174 (2015)

    Article  MathSciNet  MATH  Google Scholar 

  67. Chiang, S., Guindani, M., Yeh, H.J., Dewar, S., Haneef, Z., Stern, J.M., Vannucci, M.: A hierarchical Bayesian model for the identification of pet markers associated to the prediction of surgical outcome after anterior temporal lobe resection. Front. Neurosci. 11, 669 (2017)

    Article  Google Scholar 

  68. Haynes, J.D., Rees, G.: Predicting the stream of consciousness from activity in human visual cortex. Curr. Biol. 15(14), 1301–1307 (2005)

    Article  Google Scholar 

  69. LaConte, S., Strother, S., Cherkassky, V., Anderson, J., Hu, X.: Support vector machines for temporal classification of block design fMRI data. NeuroImage 26(2), 317–329 (2005)

    Article  Google Scholar 

  70. Mitchell, T., Hutchinson, R., Niculescu, R., Pereira, F., Wang, X., Just, M., Newman, S.: Learning to decode cognitive states from brain images. Mach. Learn. 57(1–2), 145–175 (2004)

    Article  MATH  Google Scholar 

  71. Arribas, J., Calhoun, V.D., Adali, T.: Automatic Bayesian classification of healthy controls, bipolar disorder, and schizophrenia using intrinsic connectivity maps from fMRI data. IEEE Trans. Biomed. Eng. 57(12) (2010)

    Article  Google Scholar 

  72. Burge, J., Lane, T., Link, H., Qiu, S., Clark, V.P.: Discrete dynamic Bayesian network analysis of fMRI data. Hum. Brain Mapp. 30, 122–137 (2009)

    Article  Google Scholar 

  73. Zhang, L., Guindani, M., Vannucci, M.: Bayesian models for functional magnetic resonance imaging data analysis. Wiley Interdiscip. Rev. Comput. Stat. 7(1), 21–41 (2015)

    Article  MathSciNet  Google Scholar 

  74. Uludag, K., Roebroeck, A.: General overview on the merits of multimodal neuroimaging data fusion. NeuroImage 102, 3–10 (2014)

    Article  Google Scholar 

  75. Valdes-Sosa, P.A., Kotter, R., Friston, K.J.: Introduction: multimodal neuroimaging of brain connectivity. Philos. Trans. R. Soc. B Biol. Sci. 360(1457), 865–867 (2005)

    Article  Google Scholar 

  76. Biessmann, F., Plis, S., Meinecke, F.C., Eichele, T., Muller, K.R.: Analysis of multimodal neuroimaging data. IEEE Rev. Biomed. Eng. 4, 26–58 (2011)

    Article  Google Scholar 

  77. Jorge, J., van der Zwaag, W., Figueiredo, P.: EEG-fMRI integration for the study of human brain function. NeuroImage 102, 24–34 (2014)

    Article  Google Scholar 

  78. Kalus, S., Sämann, P., Czisch, M., Fahrmeir, L.: fMRI activation detection with EEG priors. Technical report, University of Munich (2013)

    Google Scholar 

  79. Chiang, S., Guindani, M., Yeh, H.J., Haneef, Z., Stern, J.M., Vannucci, M.: Bayesian vector autoregressive model for multi-subject effective connectivity inference using multi-modal neuroimaging data. Hum. Brain Mapp. 38(3), 1311–1332 (2016)

    Article  Google Scholar 

  80. Nathoo, F., Kong, L., Zhu, H.: A review of statistical methods in imaging genetics. Technical report, ArXiv (2018)

    Google Scholar 

  81. Stingo, F.C., Guindani, M., Vannucci, M., Calhoun, V.D.: An integrative Bayesian modeling approach to imaging genetics. J. Am. Stat. Assoc. 108(503), 876–891 (2013)

    Article  MathSciNet  MATH  Google Scholar 

  82. Greenlaw, K., Szefer, E., Graham, J., Lesperance, M., Nathoo, F.S., The Alzheimer’s Disease Neuroimaging Initiative: A Bayesian group sparse multi-task regression model for imaging genetics. Bioinformatics 33(16), 2513–2522 (2017)

    Article  Google Scholar 

  83. Wang, H., Nie, F., Huang, H., Risacher, S.L., Saykin, A.J., Shen, L., The Alzheimer’s Disease Neuroimaging Initiative: Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning. Bioinformatics 28(12), i127–i136 (2012)

    Article  Google Scholar 

  84. Chekouo, T., Stingo, F.C., Guindani, M., Do, K.A.: A Bayesian predictive model for imaging genetics with application to schizophrenia. Ann. Appl. Stat. 10(3), 1547–1571 (2016)

    Article  MathSciNet  MATH  Google Scholar 

  85. Yu, C.H., Prado, R., Ombao, H., Rowe, D.: A Bayesian variable selection approach yields improved detection of brain activation from complex-valued fMRI. J. Am. Stat. Assoc., 1–61 (2018)

    Google Scholar 

  86. Rockova, V., George, E.I.: EMVS: the EM approach to Bayesian variable selection. J. Am. Stat. Assoc. 109(506), 828–846 (2014)

    Article  MathSciNet  MATH  Google Scholar 

  87. Boto, E., Holmes, N., Leggett, J., Roberts, G., Shah, V., Meyer, S.S., Muñoz, L.D., Mullinger, K.J., Tierney, T.M., Bestmann, S., Barnes, G.R., Bowtell, R., Brookes, M.J.: Moving magnetoencephalography towards real-world applications with a wearable system. Nature 555, 657 EP (2018)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Michele Guindani .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Guindani, M., Vannucci, M. (2018). Challenges in the Analysis of Neuroscience Data. In: Canale, A., Durante, D., Paci, L., Scarpa, B. (eds) Studies in Neural Data Science. START UP RESEARCH 2017. Springer Proceedings in Mathematics & Statistics, vol 257. Springer, Cham. https://doi.org/10.1007/978-3-030-00039-4_8

Download citation

Publish with us

Policies and ethics