Improving the analysis, storage and sharing of neuroimaging data using relational databases and distributed computing

NeuroImage

Volumn 39, Issue 2, 2008, Pages 693-706

  Hasson, Uri ^a   Skipper, Jeremy I ^a   Wilde, Michael J ^a,b   Nusbaum, Howard C ^a,c   Small, Steven L ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS; DATA BASE; FUNCTIONAL MAGNETIC RESONANCE IMAGING; INFORMATION PROCESSING; MEDICAL RESEARCH; NEUROIMAGING; PRIORITY JOURNAL; STATISTICAL DISTRIBUTION;

COMPUTER COMMUNICATION NETWORKS; DATABASE MANAGEMENT SYSTEMS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; INFORMATION STORAGE AND RETRIEVAL; MAGNETIC RESONANCE IMAGING; NERVOUS SYSTEM; POSITRON-EMISSION TOMOGRAPHY;

EID: 36148980900     PISSN: 10538119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuroimage.2007.09.021     Document Type: Article

References (44)

1. Argall B.D., Saad Z.S., and Beauchamp M.S. Simplified intersubject averaging on the cortical surface using SUMA. Hum. Brain Mapp. 27 (2005) 14-27
2. Ascoli G.A. Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat. Rev., Neurosci. 7 (2006) 318-324
3. Ashburner J., and Friston K.J. Voxel-based morphometry-The methods. NeuroImage 11 (2000) 805-821
4. Bowden D.M., and Martin R.F. NeuroNames brain hierarchy. NeuroImage 2 1 (1995) 63-83
5. Buchsbaum B.R., Olsen R.K., Koch P.F., Kohn P., Kippenhan J.S., and Berman K.F. Reading, hearing, and the planum temporale. NeuroImage 24 (2005) 444-454
6. Bullmore E.T., Suckling J., Overmeyer S., Rabe-Hesketh S., Taylor E., and Brammer M.J. Global, voxel, and cluster tests, by theory and permutation, for a difference between two groups of structural MR images of the brain. IEEE Trans. Med. Imag. 18 (1999) 32-42
7. Buyya R., Date S., Mizuno-Matsumoto Y., Venugopal S., and Abramson D. Neuroscience instrumentation and distributed analysis of brain activity data: a case for eScience on global Grids. Concurr. Comput.: Pract. Exper. 17 (2005) 1783-1798
8. Dale A.M., Fischl B., and Sereno M.I. Cortical surface-based analysis: I. Segmentation and surface reconstruction. NeuroImage 9 (1999) 179-194
9. Davidson S.B., Crabtree J., Brunk B.P., Schug J., Tannen V., Overton G.C., et al. K2/Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Syst. J. 40 2 (2001) 512-531
10. Desikan R.S., Segonne F., Fischl B., Quinn B.T., Dickerson B.C., Blacker D., et al. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. NeuroImage. 31 (2006) 968-980
11. Eisenberg A., Kulkarni K., Melton J., Michels J.-E., and Zemke F. SQL:2003 has been published. SIGMOD Rec. 33 (2004)
12. Fischl B., Sereno M.I., and Dale A.M. Cortical surface-based analysis: II. Inflation, flattening, and a surface-based coordinate system. NeuroImage 9 (1999) 195-207
13. Fischl B., Kouwe A.v.d., Destrieux C., Halgren E., Ségonne F., Salat D.H., et al. Automatically parcellating the human cerebral cortex. Cereb. Cortex 14 (2004) 11-22
14. Forman S.D., Cohen J.D., Fitzgerald M., Eddy W.F., Mintun M.A., and Noll D.C. Improved assessment of significant activation in functional magnetic resonance imaging (fMRI): use of a cluster-size threshold. Magn. Reson. Med. 33 (1995) 636-647
15. Foster I. Service-oriented science. Science 308 5723 (2005) 814-817
16. Foster I., Kesselman C., and Tuecke S. The anatomy of the Grid: enabling scalable virtual organizations. Int. J. High Perform. Comput. Appl. 15 (2001) 200-222
17. Fox P.T., and Lancaster J.L. Mapping context and content: the BrainMap model. Nat. Rev., Neurosci. 3 4 (2002) 319-321
18. Gardner D., et al. Towards effective and rewarding data sharing. Neuroinform. J. 1 (2003) 289-295
19. Genovese C.R., Lazar N.A., and Nichols T. Thresholding of statistical maps in functional neuroimaging using the false discovery rate. NeuroImage 15 4 (2002) 870-878
20. Gray J., Liu D.T., Nieto-Santisteban M., Szalay A., Heber G., and DeWitt D.J. Scientific data management in the coming decade. ACM SIGMOD Rec. 34 4 (2005) 34-41
21. Keator D.B., Gadde S., Grethe J.S., Taylor D.V., Potkin S.G., and FIRST BIRN. General XML schema and associated SPM toolbox for storage and retrieval of neuro-imaging results and anatomical labels. Neuroinformatics. 4 (2006) 199-212
22. Kotter R. Neuroscience databases: tools for exploring brain structure-function relationships. Philos. Trans. R. Soc. Lond., B Biol. Sci. 356 (2001) 1111-1120
23. Li N., and Rossini A. RPVM: cluster statistical computing in R [Electronic Version]. R. News 13 (2001) 4-7. http://CRAN.R-project.org/doc/Rnews/ (URL: http://CRAN.R-project.org/doc/Rnews/)
24. Marchini J. AnalyzeFMRI: an R package for the exploration and analysis of MRI and fMRI datasets. R. News 2 (2002) 17-24. http://CRAN.R-project.org/doc/Rnews/ (URL: http://CRAN.R-project.org/doc/Rnews/)
25. Nichols T.E., and Holmes A.P. Nonparametric permutation tests for functional neuroimaging: a primer with examples. Hum. Brain Mapp. 15 (2002) 1-25
26. Nieto-Santisteban M.A., Szalay A.S., Thakar A.R., O'Mullane W.J., Gray J., and Annis J. When database systems meet the grid. Paper Presented at the CIDR 2005 (2005)
27. Patterson R.D., Uppenkamp S., Johnsrude I.S., and Griffiths T.D. The processing of temporal pitch and melody information in auditory cortex. Neuron 36 (2002) 767-776
28. Pfister G.F. In Search of Clusters: Prentice-Hall, Inc. (1998), Upper Saddle River, NJ
29. Polzehl, J., Tabelow, K., in press. fMRI: a package for analyzing fmri data. R News.
30. R Development Core Team. R: A Language and Environment for Statistical Computing, Vienna, Austria (2005)
31. Rundell G. Peakfit. Non-linear Curve Fitting Software (1990), Jandel Scientific, San Rafael, USA
32. Saad Z.S., Reynolds R.C., Argall B., Japee S., and Cox R.W. SUMA: an interface for surface-based intra- and inter-subject analysis with AFNI. Paper Presented at the Proceedings of the 2004 IEEE International Symposium on Biomedical Imaging (2004)
33. Skipper J.I., Nusbaum H.C., Josse G., Goldin-Meadow S., and Small S.L. The cortical motor system simulates action descriptions conveyed by words and gestures. Paper Presented at The Annual Meeting of the Cognitive Neuroscience Society, San Francisco, CA (2006)
34. Skipper J.I., Goldin-Meadow S., Nusbaum H.C., and Small S.L. Speech associated gestures, Broca's area, and the human mirror system. Brain Lang. 101 (2007) 260-277
35. Skipper J.I., van Wassenhove V., Nusbaum H.C., and Small S.L. Hearing lips and seeing voices: how cortical areas supporting speech production mediate audiovisual speech perception. Cereb. Cortex (2007) 10.1093/cercor/bhl147 (Advance Access published on January 19, 2007)
36. Smith S.M. Preparing fMRI data for statistical analysis. In: Jezzard P., Matthews P.M., and Smith S.M. (Eds). Functional MRI: An Introduction to Methods (2002), Oxford University Press, New York
37. Smith K., Jajodia S., Swarup V., Hoyt J., Hamilton G., Faatz D., et al. Enabling the sharing of neuroimaging data through well-defined intermediate levels of visibility. NeuroImage 22 (2004) 1646-1656
38. Stef-Praun T., Foster I., Hasson U., Hategan M., Small S.L., and Wilde M. Accelerating medical research using the Swift Workflow System. Paper Presented at the HealthGrid 2007, Geneva (2007)
39. Stoeckert C.J. Functional genomics databases on the web. Cell. Microbiol. 7 (2005) 1053-1059
40. Szalay A., and Gray J. 2020 Computing: science in an exponential world. Nature 440 7083 (2006) 413-414
41. Temal L., Lando P., Gibaud B., Dojat M., Kassel G., and Lapujade A. OntoNeuroBase: a multi-layered application ontology in neuroimaging. Paper Presented at the Formal Ontology meets Industry (FOMI) (2006)
42. Van Horn J.D., Grethe J.S., Kostelec P., Woodward J.B., Aslam J.A., Rus D., et al. The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies. Philos. Trans. R. Soc. Lond., B Biol. Sci. 356 (2001) 1323-1339
43. Wagner A.D., Schacter D.L., Rotte M., Koutstaal W., Maril A., Dale A.M., et al. Building memories: remembering and forgetting of verbal experiences as predicted by brain activity. Science 281 (1998) 1188-1191
44. Worsley K.J., Marrett S., Neelin P., Vandal A.C., Friston K.J., and Evans A.C. A unified statistical approach for determining significant signals in images of cerebral activation. Hum. Brain Mapp. 4 1 (1996) 58-73