Informatics and data mining tools and strategies for the human connectome project

Frontiers in Neuroinformatics

Volumn 5, Issue , 2011, Pages

  Marcus, Daniel S ^a   Harwell, John ^a   Olsen, Timothy ^a   Hodge, Michael ^a   Glasser, Matthew F ^a   Prior, Fred ^a   Jenkinson, Mark ^b   Laumann, Timothy ^a   Curtiss, Sandra W ^a   Van Essen, David C ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Brain parcellation; Caret; Connectomics; Diffusion imaging; Human Connectome Project; Network analysis; Resting state fMRI; XNAT

Indexed keywords

BRAIN; CONNECTOME; DATA ANALYSIS; DATA BASE; DATA MINING; DIFFUSION; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; INFORMATION SCIENCE; LICENCE; MAJOR CLINICAL STUDY; PIPELINE; REST; VISION;

EID: 84994018827     PISSN: None     EISSN: 16625196     Source Type: Journal    
DOI: 10.3389/fninf.2011.00004     Document Type: Article

References (28)

1. Beckmann, M., Johansen-Berg, H., and Rushworth, M. F. (2009). Connectivity-based parcellation of human cingulate cortex and its relation to functional specialization. J. Neurosci. 29, 1175-1190.
2. Briggman, K. L., and Denk, W. (2006). Towards neural circuit reconstruction with volume electron microscopy techniques. Curr. Opin. Neurobiol. 16, 562-570.
3. de Pasquale, F., Della Penna, S., Snyder, A. Z., Lewis, C., Mantini, D., Marzetti, L., Belardinelli, P., Ciancetta, L., Pizzella, V., Romani, G. L., and Corbetta, M. (2010). Temporal dynamics of spontaneous MEG activity in brain networks. Proc. Natl. Acad. Sci. U.S.A. 107, 6040-6045.
4. Feinberg, D. A., Moeller, S., Smith, S. M., Auerbach, E., Ramanna, S., Glasser, M. F., Miller, K. L., Ugurbil, K., and Yacoub, E. (2010). Multiplexed echo planar imaging for sub-second whole brain FMRI and fast diffusion imaging. PLoS ONE 5, e15710. doi: 10.1371/journal.pone.0015710
5. Fielding, R. T. (2000). Architectural Styles and The Design of Network-Based Software Architectures. Doctoral dissertation, University of California, Irvine. Available at: http://www.ics.uci.edu/∼fielding/pubs/dissertation/top.htm
6. Fox, M. D., and Raichle, M. E. (2007). Spontaneous fluctuations in brain activity observed with functional magnetic resonance imaging. Nat. Rev. Neurosci. 8, 700-711.
7. Gadde, S., Aucoin, N., Grethe, J. S., Keator, D. B., Marcus, D. S., and Pieper, S. (2011). XCEDE: an extensible schema for biomedical data. Neuroinformatics 1-14.
8. Gershon, R. C., Cella, D., Fox, N. A., Havlik, R. J., Hendrie, H. C., and Wagster, M. V. (2010). Assessment of neurological and behavioural function: the NIH Toolbox. Lancet Neurol. 9, 138-139.
9. Jack, C. R. Jr., Bernstein, M. A., Fox, N. C., Thompson, P., Alexander, G., Harvey, D., Borowski, B., Britson, P. J., Whitwell, J. L., Ward, C., Dale, A. M., Felmlee, J. P., Gunter, J. L., Hill, D. L., Killiany, R., Schuff, N., Fox-Bosetti, S., Lin, C., Studholme, C., DeCarli, C. S., Krueger, G., Ward, H. A., Metzger, G. J., Scott, K. T., Mallozzi, R., Blezek, D., Levy, J., Debbins, J. P., Fleisher, A. S., Albert, M., Green, R., Bartzokis, G., Glover, G., Mugler, J., and Weiner, M. W. (2008). The Alzheimer’s Disease Neuroimaging Initiative (ADNI): MRI methods. J. Magn. Reson. Imaging 27, 685-691.
10. Johansen-Berg, H., and Behrens, T. E. (2009). From Quantitative Measurement in-vivo Neuroanatomy Boston, MA: Elsevier.
11. Johansen-Berg, H., and Rushworth, M. F. (2009). Using diffusion imaging to study human connectional anatomy. Annu. Rev. Neurosci. 32, 75-94.
12. Langille, M. G. I., and Eisen, J. A. (2010). BioTorrents: a file sharing service for scientific data. PLoS ONE 5(4)::e10071. doi:10.1371/journal.pone.0010071
13. Lichtman, J. W., Livet, J., and Sanes, J. R. (2008). A technicolour approach to the connectome. Nat. Rev. Neurosci. 9, 417-422.
14. Marcus, D. S., Olsen, T. R., Ramaratnam, M., and Buckner, R. L. (2007). The Extensible Neuroimaging Archive Toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 5, 11-34.
15. Nelson, S. M., Cohen, A. L., Power, J. D., Wig, G. S., Miezin, F. M., Wheeler, M. E., Velanova, K., Donaldson, D. I., Phillips, J. S., Schlaggar, B. L., and Petersen, S. E. (2010). A parcellation scheme for human left lateral parietal cortex. Neuron 67, 156-170.
16. Newman, M. E. (2006). Modularity and community structure in networks. Proc. Natl. Acad. Sci. USA 103, 8577-8582.
17. Ou, W., Nummenmaa, A., Ahveninen, J., Belliveau, J. W., H�m�l�inen, M. S., and Golland, P. (2010). Multimodal functional imaging using fMRI-informed regional EEG/MEG source estimation. NeuroImage 52, 97-108.
18. Patel, V., Dinov, I. D., Van Horn, J. D., Thompson, P. M., and Toga, A. W. (2010). LONI MiND: metadata in NIfTI for DWI. Neuroimage 51, 665-676.
19. Petrovic, V. S., Cootes, T. F., Mills, A. M., Twining, C. J., and Taylor, C. J. (2007). Automated analysis of deformable structure in groups of images. Proc. British Machine Vision Conference 2, 1060-1069.
20. Rubinov, M., and Sporns, O. (2010). Complex network measures of brain connectivity: uses and interpretations. Neuroimage. 52, 1059-1069.
21. Sabuncu, M. R., Singer, B. D., Conroy, B., Bryan, R. E., Ramadge, P. J., and Haxby, J. V. (2010). Function-based intersubject alignment of human cortical anatomy. Cereb. Cortex 20, 130-140.
22. Scheeringa, R., Fries, P., Petersson, K.-M., Oostenveld, R., Grothe, I., Norris, D. G., Hagoort, P., and Bastiaansen, M. C. M. (2011). Neuronal dynamics underlying high-and low-frequency EEG oscillations contribute independently to the human BOLD signal. Neuron 69, 572-583.
23. Sporns, O., Tononi, G., and K�tter, R. (2005). The human connectome: a structural description of the human brain. PLoS Comput. Biol. 1:e42. doi:10.1371/journal.pcbi.0010042
24. Sporns, O. (2010). Networks of the Brain. Cambridge, MA: MIT Press, 375 pp.
25. Van Essen, D. C., Drury, H. A., Dickson, J., Harwell, J., Hanlon, D., and Anderson, C. H. (2001). An integrated software suite for surface-based analyses of cerebral cortex. J. Am. Med. Inform. Assoc. 8, 443-459.
26. Vincent, J. L., Patel, G. H., Fox, M. D., Snyder, A. Z., Baker, J. T., Van Essen, D. C., Zempel, J. M., Snyder, L. H., Corbetta, M., and Raichle, M. E. (2007). Intrinsic functional architecture in the anaesthetized monkey brain. Nature 447, 83-86.
27. Visscher, P. M., and Montgomery, G. W. (2009). Genome-wide association studies and human disease: from trickle to flood. JAMA 302, 2028-2029.
28. Wipf, D., and Nagarajan, S. A. (2009). Unified Bayesian framework for MEG/EEG source imaging. NeuroImage 44, 947-966.