Towards open sharing of task-based fMRI data: The OpenfMRI project

Frontiers in Neuroinformatics

Volumn 7, Issue JUNE, 2013, Pages

  Poldrack, Russell A ^a   Barch, Deanna M ^b   Mitchell, Jason P ^c   Wager, Tor D ^d   Wagner, Anthony D ^e   Devlin, Joseph T ^f   Cumba, Chad ^a   Koyejo, Oluwasanmi ^a   Milham, Michael P ^g  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b WASHINGTON UNIVERSITY   (United States)

^c HARVARD UNIVERSITY   (United States)

^d UNIVERSITY OF COLORADO   (United States)

^e STANFORD UNIVERSITY   (United States)

^f UNIVERSITY COLLEGE LONDON   (United Kingdom)

^g CHILD MIND INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOANALYSIS; BEHAVIOR; BRAIN FUNCTION; BRAIN MAPPING; CLASSIFICATION; CLINICAL DATA REPOSITORY; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONFIDENTIALITY; DATA ANALYSIS; DATA BASE; DATA PROCESSING; FEEDBACK SYSTEM; FUNCTIONAL MAGNETIC RESONANCE IMAGING; HUMAN; INDEPENDENT COMPONENT ANALYSIS; INFORMATION PROCESSING; INFORMATION SCIENCE; INTELLIGENCE; INTERNET; LICENSING; MENTAL FUNCTION; NEUROIMAGING; PSYCHOLOGICAL ASPECT; PUBLICATION; TASK PERFORMANCE;

EID: 84886752096     PISSN: 16625196     EISSN: None     Source Type: Journal    
DOI: 10.3389/fninf.2013.00012     Document Type: Article

References (58)

1. Alvarez, R., & Poldrack, R. A. (unpublished). A study of cross-language repetition priming in spanish-english bilinguals.
2. Aron, A. R., Behrens, T. E., Smith, S., Frank, M. J., & Poldrack, R. A. (2007). Triangulating a cognitive control network using di_usion-weighted magnetic resonance imaging (mri) and functional mri. J Neurosci, 27 (14), 3743-3752
3. Aron, A. R., Gluck, M. A., & Poldrack, R. A. (2006). Long-term test-retest reliability of functional mri in a classi_cation learning task. Neuroimage, 29 (3), 1000-1006
4. Beckmann, C. F., & Smith, S. M. (2004). Probabilistic independent component analysis for functional magnetic resonance imaging. IEEE Trans Med Imaging, 23 (2), 137-152
5. Biswal, B. B., Mennes, M., Zuo, X.-N., Gohel, S., Kelly, C., Smith, S. M., Beckmann, C. F., Adelstein, J. S., Buckner, R. L., Colcombe, S., Dogonowski, A.-M., Ernst, M., Fair, D., Hampson, M., Hoptman, M. J., Hyde, J. S., Kiviniemi, V. J., Kötter, R., Li, S.-J., Lin, C.-P., Lowe, M. J., Mackay, C., Madden, D. J., Madsen, K. H., Margulies, D. S., Mayberg, H. S., McMahon, K., Monk, C. S., Mostofsky, S. H., Nagel, B. J., Pekar, J. J., Peltier, S. J., Petersen, S. E., Riedl, V., Rombouts, S. A. R. B., Rypma, B., Schlaggar, B. L., Schmidt, S., Seidler, R. D., Siegle, G. J., Sorg, C., Teng, G.-J., Veijola, J., Villringer, A., Walter, M., Wang, L., Weng, X.-C., Whit-eld-Gabrieli, S., Williamson, P., Windischberger, C., Zang, Y.-F., Zhang, H.-Y., Castellanos, F. X., & Milham, M. P. (2010). Toward discovery science of human brain function. Proc Natl Acad Sci U S A, 107 (10), 4734-4739
6. Brakewood, B., & Poldrack, R. A. (2013). The ethics of secondary data analysis: Considering the application of belmont principles to the sharing of neuroimaging data. Neuroimage.
7. Carp, J. (2012). On the plurality of (methodological) worlds: estimating the analytic exibility of fmri experiments. Front Neurosci, 6, 149
8. Chang, C., & Lin, C. (2011). Libsvm: a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2, 1-27
9. Congdon, E., Mumford, J. A., Cohen, J. R., Galvan, A., Aron, A. R., Xue, G., Miller, E., & Poldrack, R. A. (2010). Engagement of large-scale networks is related to individual di_erences in inhibitory control. Neuroimage, 53 (2), 653-663
10. Dosenbach, N. U. F., Nardos, B., Cohen, A. L., Fair, D. A., Power, J. D., Church, J. A., Nelson, S. M., Wig, G. S., Vogel, A. C., Lessov-Schlaggar, C. N., Barnes, K. A., Dubis, J. W., Feczko, E., Coalson, R. S., Pruett, J. R., Jr, Barch, D. M., Petersen, S. E., & Schlaggar, B. L. (2010). Prediction of individual brain maturity using fmri. Science, 329 (5997), 1358-1361
11. Duncan, K. J., Pattamadilok, C., Knierim, I., & Devlin, J. T. (2009). Consistency and variability in functional localisers. Neuroimage, 46 (4), 1018-1026
12. Editorial, N. N. (2000). A debate over fmri data sharing. Nat Neurosci, 3 (9), 845-846
13. Fan, R. E., Chang, K., Hsieh, C., Wang, X., & Lin, C. (2008). Liblinear: A library for large linear classification. Journal of Machine Learning Research, 9, 1871-1874
14. Foerde, K., Knowlton, B. J., & Poldrack, R. A. (2006). Modulation of competing memory systems by distraction. Proc Natl Acad Sci U S A, 103 (31), 11778-11783
15. Gadde, S., Aucoin, N., Grethe, J. S., Keator, D. B., Marcus, D. S., Pieper, S., & Fbirn, Mbirn, Birn-Cc (2012). Xcede: an extensible schema for biomedical data. Neuroin- formatics, 10 (1), 19-32
16. Gardner, D., Akil, H., Ascoli, G. A., Bowden, D. M., Bug, W., Donohue, D. E., Goldberg, D. H., Grafstein, B., Grethe, J. S., Gupta, A., Halavi, M., Kennedy, D. N., Marenco, L., Martone, M. E., Miller, P. L., Müuller, H.-M., Robert, A., Shepherd, G. M., Sternberg, P. W., Van Essen, D. C., & Williams, R. W. (2008). The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics, 6 (3), 149-160
17. Gorgolewski, K. J., Margulies, D. S., & Milham, M. P. (2013a). Making data sharing count: a publication-based solution. Front Neurosci, 7, 9
18. Gorgolewski, K. J., Storkey, A., Bastin, M. E., Whittle, I. R., Wardlaw, J. M., & Pernet, C. R. (2013b). A test-retest fmri dataset for motor, language and spatial attention functions. Gigascience, 2 (1), 6
19. Greicius, M. D., Srivastava, G., Reiss, A. L., & Menon, V. (2004). Default-mode network activity distinguishes alzheimer's disease from healthy aging: evidence from functional mri. Proc Natl Acad Sci U S A, 101 (13), 4637-4642
20. Jimura, K., Stover, E., Cazalis, F., & Poldrack, R. A. (in prep). Skill acquisition and task switching in the mirror-reading task.
21. Kelley, C., & Milham, M. P. (unpublished). An fmri study of the simon task.
22. Kelly, A. M. C., Uddin, L. Q., Biswal, B. B., Castellanos, F. X., & Milham, M. P. (2008). Competition between functional brain networks mediates behavioral variability. Neu- roimage, 39 (1), 527-537
23. Laird, A. R., Lancaster, J. L., & Fox, P. T. (2005). Brainmap: the social evolution of a human brain mapping database. Neuroinformatics, 3 (1), 65-78
24. Lloyd, D. (2002). Functional mri and the study of human consciousness. J Cogn Neurosci, 14 (6), 818-831
25. Marcus, D. S., Olsen, T. R., Ramaratnam, M., & Buckner, R. L. (2007). The extensible neuroimaging archive toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, 5 (1), 11-34
26. Marenco, L., Ascoli, G. A., Martone, M. E., Shepherd, G. M., & Miller, P. L. (2008). The nif linkout broker: a web resource to facilitate federated data integration using ncbi identi_ers. Neuroinformatics, 6 (3), 219-227
27. Mechelli, A., Price, C. J., Noppeney, U., & Friston, K. J. (2003). A dynamic causal modeling study on category e_ects: bottom-up or top-down mediation? J Cogn Neurosci, 15 (7), 925-934
28. Mennes, M., Biswal, B. B., Castellanos, F. X., & Milham, M. P. (2012). Making data sharing work: The fcp/indi experience. Neuroimage.
29. Miller, M. B., Donovan, C.-L., Van Horn, J. D., German, E., Sokol-Hessner, P., & Wolford, G. L. (2009). Unique and persistent individual patterns of brain activity across di_erent memory retrieval tasks. Neuroimage, 48 (3), 625-635
30. Moran, J. M., Jolly, E., & Mitchell, J. P. (2012). Social-cognitive de_cits in normal aging. J Neurosci, 32 (16), 5553-5561
31. Nooner, K. B., Colcombe, S. J., Tobe, R. H., Mennes, M., Benedict, M. M., Moreno, A. L., Panek, L. J., Brown, S., Zavitz, S. T., Li, Q., Sikka, S., Gutman, D., Bangaru, S., Schlachter, R. T., Kamiel, S. M., Anwar, A. R., Hinz, C. M., Kaplan, M. S., Rachlin, A. B., Adelsberg, S., Cheung, B., Khanuja, R., Yan, C., Craddock, C. C., Calhoun, V., Courtney, W., King, M., Wood, D., Cox, C. L., Kelly, A. M. C., Di Martino, A., Petkova, E., Reiss, P. T., Duan, N., Thomsen, D., Biswal, B., Co-ey, B., Hoptman, M. J., Javitt, D. C., Pomara, N., Sidtis, J. J., Koplewicz, H. S., Castellanos, F. X., Leventhal, B. L., & Milham, M. P. (2012). The nki-rockland sample: A model for accelerating the pace of discovery science in psychiatry. Front Neurosci, 6, 152
32. Park, M., Koyejo, O., Ghosh, J., Poldrack, R., & JW, P. (2013). Bayesian structure learning for functional neuroimaging. Sixteenth International Conference on Artificial Intelligence and Statistics (AISTATS).
33. Pedregosa, F., Gramfort, A., Varoquaux, G., Cauvet, E., Pallier, C., & Thirion, B. (2012). Learning to rank from medical imaging data. In 3rd International Workshop on Machine Learning in Medical Imaging. Nice, France: INRIA. URL http://hal.inria.fr/hal-00717990
34. Poldrack, R. A. (2006). Can cognitive processes be inferred from neuroimaging data? Trends Cogn Sci, 10 (2), 59-63
35. Poldrack, R. A., Clark, J., Par-e-Blagoev, E. J., Shohamy, D., Creso Moyano, J., Myers, C., & Gluck, M. A. (2001). Interactive memory systems in the human brain. Nature, 414 (6863), 546-550
36. Poldrack, R. A., Fletcher, P. C., Henson, R. N., Worsley, K. J., Brett, M., & Nichols, T. E. (2008). Guidelines for reporting an fmri study. Neuroimage, 40 (2), 409-14
37. Poldrack, R. A., Halchenko, Y. O., & Hanson, S. J. (2009). Decoding the large-scale structure of brain function by classifying mental states across individuals. Psychol Sci, 20 (11), 1364-1372
38. Poldrack, R. A., Kittur, A., Kalar, D., Miller, E., Seppa, C., Gil, Y., Parker, D. S., Sabb, F. W., & Bilder, R. M. (2011a). The cognitive atlas: Towards a knowledge foundation for cognitive neuroscience. submitted.
39. Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011b). Handbook of Functional MRI Data Analysis. Cambridge University Press.
40. Poline, J.-B., Breeze, J. L., Ghosh, S., Gorgolewski, K., Halchenko, Y. O., Hanke, M., Haselgrove, C., Helmer, K. G., Keator, D. B., Marcus, D. S., Poldrack, R. A., Schwartz, Y., Ashburner, J., & Kennedy, D. N. (2012). Data sharing in neuroimaging research. Front Neuroinform, 6, 9
41. Rizk-Jackson, A., Aron, A. R., & Poldrack, R. A. (unpublished). Test-retest study of classi_cation learning and stop-signal tasks.
42. Salimi-Khorshidi, G., Smith, S. M., Keltner, J. R., Wager, T. D., & Nichols, T. E. (2009). Meta-analysis of neuroimaging data: a comparison of image-based and coordinate-based pooling of studies. Neuroimage, 45 (3), 810-823
43. Schonberg, T., Fox, C. R., Mumford, J. A., Congdon, E., Trepel, C., & Poldrack, R. A. (2012). Decreasing ventromedial prefrontal cortex activity during sequential risk-taking: an fmri investigation of the balloon analog risk task. Front Neurosci, 6, 80
44. Smith, S. M., Fox, P. T., Miller, K. L., Glahn, D. C., Fox, P. M., Mackay, C. E., Filippini, N., Watkins, K. E., Toro, R., Laird, A. R., & Beckmann, C. F. (2009). Correspondence of the brain's functional architecture during activation and rest. Proc Natl Acad Sci U S A, 106 (31), 13040-13045
45. Tom, S. M., Fox, C. R., Trepel, C., & Poldrack, R. A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315 (5811), 515-518
46. Tomasi, D., & Volkow, N. D. (2010). Functional connectivity density mapping. Proc Natl Acad Sci U S A, 107 (21), 9885-9890
47. Turner, J. A., & Laird, A. R. (2011). The cognitive paradigm ontology: Design and application. Neuroinformatics.
48. Uncapher, M. R., Hutchinson, J. B., & Wagner, A. D. (2011). Dissociable e_ects of topdown and bottom-up attention during episodic encoding. J Neurosci, 31 (35), 12613-12628
49. Van Horn, J. D., & Gazzaniga, M. S. (2002). Opinion: Databasing fmri studies towards a 'discovery science' of brain function. Nat Rev Neurosci, 3 (4), 314-318
50. Van Horn, J. D., & Gazzaniga, M. S. (2012). Why share data? lessons learned from the fmridc. Neuroimage.
51. Van Horn, J. D., Grethe, J. S., Kostelec, P., Woodward, J. B., Aslam, J. A., Rus, D., Rockmore, D., & Gazzaniga, M. S. (2001). 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 (1412), 1323-1339
52. Van Horn, J. D., & Ishai, A. (2007). Mapping the human brain: new insights from fmri data sharing. Neuroinformatics, 5 (3), 146-153
53. Varoquaux, G., Gramfort, A., & Thirion, B. (2012). Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering. In L. John, & P. Joelle (Eds.) International Conference on Machine Learning. Edimbourg, Royaume- Uni: Andrew McCallum. URL http://hal.inria.fr/hal-00705192
54. Wager, T. D., Davidson, M. L., Hughes, B. L., Lindquist, M. A., & Ochsner, K. N. (2008). Prefrontal-subcortical pathways mediating successful emotion regulation. Neuron, 59 (6), 1037-1050
55. Wicherts, J. M., Bakker, M., & Molenaar, D. (2011). Willingness to share research data is related to the strength of the evidence and the quality of reporting of statistical results. PLOS One, 6, e26828
56. Xue, G., Aron, A. R., & Poldrack, R. A. (2008). Common neural substrates for inhibition of spoken and manual responses. Cereb Cortex, 18 (8), 1923-1932
57. Xue, G., & Poldrack, R. A. (2007). The neural substrates of visual perceptual learning of words: implications for the visual word form area hypothesis. J Cogn Neurosci, 19 (10), 1643-1655
58. Yarkoni, T., Poldrack, R. A., Nichols, T. E., Van Essen, D. C., & Wager, T. D. (2011). Large-scale automated synthesis of human functional neuroimaging data. Nature Meth- ods.