Making big data open: data sharing in neuroimaging (original) (raw)

• Van Essen, D.C. et al. The WU-Minn human connectome project: an overview. Neuroimage 80, 62–79 (2013).
  Article PubMed Google Scholar
• Poline, J.-B. et al. Data sharing in neuroimaging research. Front. Neuroinform. 6, 9 (2012).
  Article PubMed PubMed Central Google Scholar
• Keator, D.B. et al. Towards structured sharing of raw and derived neuroimaging data across existing resources. Neuroimage 82, 647–661 (2013).
  Article CAS PubMed Google Scholar
• Mennes, M., Biswal, B.B., Castellanos, F.X. & Milham, M.P. Making data sharing work: The FCP/INDI experience. Neuroimage 82, 683–691 (2013).
  Article PubMed Google Scholar
• Brakewood, B. & Poldrack, R.A. The ethics of secondary data analysis: considering the application of Belmont Principles to the sharing of neuroimaging data. Neuroimage 82, 671–676 (2013).
  Article PubMed Google Scholar
• Posner, M.I., Petersen, S.E., Fox, P.T. & Raichle, M.E. Localization of cognitive operations in the human brain. Science 240, 1627–1631 (1988).
  Article CAS PubMed Google Scholar
• Poldrack, R.A. Mapping mental function to brain structure: how can cognitive neuroimaging succeed? Perspect. Psychol. Sci. 5, 753–761 (2010).
  Article PubMed PubMed Central Google Scholar
• Lloyd, D. Functional MRI and the study of human consciousness. J. Cogn. Neurosci. 14, 818–831 (2002).
  Article PubMed Google Scholar
• Poldrack, R.A., Halchenko, Y.O. & Hanson, S.J. Decoding the large-scale structure of brain function by classifying mental states across individuals. Psychol. Sci. 20, 1364–1372 (2009).
  Article PubMed Google Scholar
• Schwartz, Y., Thirion, B. & Varoquaux, G. Mapping paradigm ontologies to and from the brain. Adv. Neural. Inf. Process. Syst. 26, 1673–1681 (2013).
  Google Scholar
• Poldrack, R.A. et al. Discovering relations between mind, brain, and mental disorders using topic mapping. PLoS Comput. Biol. 8, e1002707 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Anonymous. Announcement: reducing our irreproducibility. Nature 496, 398 (2013).
• Anonymous. How science goes wrong. The Economist (19 October 2013).
• Button, K.S. et al. Power failure: why small sample size undermines the reliability of neuroscience. Nat. Rev. Neurosci. 14, 365–376 (2013).
  Article CAS PubMed Google Scholar
• Ioannidis, J.P.A. Why most published research findings are false. PLoS Med. 2, e124 (2005).
  Article PubMed PubMed Central Google Scholar
• David, S.P. et al. Potential reporting bias in FMRI studies of the brain. PLoS ONE 8, e70104 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Medland, S.E., Jahanshad, N., Neale, B.M. & Thompson, P.M. Whole-genome analyses of whole-brain data: working within an expanded search space. Nat. Neurosci. 17, 791–800 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Carp, J. On the plurality of (methodological) worlds: estimating the analytic flexibility of fMRI experiments. Front. Neurosci. 6, 149 (2012).
  Article PubMed PubMed Central Google Scholar
• Ioannidis, J.P.A. Why most discovered true associations are inflated. Epidemiology 19, 640–648 (2008).
  Article PubMed Google Scholar
• Kriegeskorte, N., Lindquist, M.A., Nichols, T.E., Poldrack, R.A. & Vul, E. Everything you never wanted to know about circular analysis, but were afraid to ask. J. Cereb. Blood Flow Metab. 30, 1551–1557 (2010).
  Article PubMed PubMed Central Google Scholar
• Kriegeskorte, N., Simmons, W.K., Bellgowan, P.S.F. & Baker, C.I. Circular analysis in systems neuroscience: the dangers of double dipping. Nat. Neurosci. 12, 535–540 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Vul, E., Harris, C., Winkielman, P. & Pashler, H. Puzzlingly high correlations in fMRI studies of emotion, personality, and social cognition. Perspect. Psychol. Sci. 4, 274–290 (2009).
  Article PubMed Google Scholar
• Simmons, J.P., Nelson, L.D. & Simonsohn, U. False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant. Psychol. Sci. 22, 1359–1366 (2011).
  Article PubMed Google Scholar
• Wicherts, J.M., Bakker, M. & Molenaar, D. 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 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Biswal, B.B. et al. Toward discovery science of human brain function. Proc. Natl. Acad. Sci. USA 107, 4734–4739 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Tomasi, D. & Volkow, N.D. Functional connectivity density mapping. Proc. Natl. Acad. Sci. USA 107, 9885–9890 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Rubinov, M. & Sporns, O. Weight-conserving characterization of complex functional brain networks. Neuroimage 56, 2068–2079 (2011).
  Article PubMed Google Scholar
• Yan, C.-G., Craddock, R.C., Zuo, X.-N., Zang, Y.-F. & Milham, M.P. Standardizing the intrinsic brain: towards robust measurement of inter-individual variation in 1,000 functional connectomes. Neuroimage 80, 246–262 (2013).
  Article PubMed Google Scholar
• Zuo, X.-N. et al. Network centrality in the human functional connectome. Cereb. Cortex 22, 1862–1875 (2012).
  Article PubMed Google Scholar
• Yeo, B.T.T., Krienen, F.M., Chee, M.W.L. & Buckner, R.L. Estimates of segregation and overlap of functional connectivity networks in the human cerebral cortex. Neuroimage 88C, 212–227 (2013).
  Google Scholar
• Zalesky, A., Fornito, A., Cocchi, L., Gollo, L.L. & Breakspear, M. Time-resolved resting-state brain networks. Proc. Natl. Acad. Sci. USA 111, 10341–10346 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Webb, J.T., Ferguson, M.A., Nielsen, J.A. & Anderson, J.S. BOLD Granger causality reflects vascular anatomy. PLoS ONE 8, e84279 (2013).
  Article PubMed PubMed Central CAS Google Scholar
• Salimi-Khorshidi, G., Smith, S.M., Keltner, J.R., Wager, T.D. & Nichols, T.E. Meta-analysis of neuroimaging data: a comparison of image-based and coordinate-based pooling of studies. Neuroimage 45, 810–823 (2009).
  Article PubMed Google Scholar
• Laird, A.R., Lancaster, J.L. & Fox, P.T. BrainMap: the social evolution of a human brain mapping database. Neuroinformatics 3, 65–78 (2005).
  Article PubMed Google Scholar
• Yarkoni, T., Poldrack, R.A., Nichols, T.E., Van Essen, D.C. & Wager, T.D. Large-scale automated synthesis of human functional neuroimaging data. Nat. Methods 8, 665–670 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Van Horn, J.D. et al. The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies. Phil. Trans. R. Soc. Lond. B 356, 1323–1339 (2001).
  Article CAS Google Scholar
• Poldrack, R.A. et al. Toward open sharing of task-based fMRI data: the OpenfMRI project. Front. Neuroinform. 7, 12 (2013).
  Article PubMed PubMed Central Google Scholar
• Van Horn, J.D. & Gazzaniga, M.S. Why share data? lessons learned from the fMRIDC. Neuroimage 82, 677–682 (2013).
  Article PubMed Google Scholar
• Marques, J.P. et al. MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field. Neuroimage 49, 1271–1281 (2010).
  Article PubMed Google Scholar
• Hoge, R.D. Calibrated fMRI. Neuroimage 62, 930–937 (2012).
  Article PubMed Google Scholar
• Gauthier, C.J., Desjardins-Crépeau, L., Madjar, C., Bherer, L. & Hoge, R.D. Absolute quantification of resting oxygen metabolism and metabolic reactivity during functional activation using QUO2 MRI. Neuroimage 63, 1353–1363 (2012).
  Article CAS PubMed Google Scholar
• Hurko, O. et al. The ADNI publication policy: commensurate recognition of critical contributors who are not authors. Neuroimage 59, 4196–4200 (2012).
  Article PubMed Google Scholar
• Rohlfing, T. & Poline, J.-B. Why shared data should not be acknowledged on the author byline. Neuroimage 59, 4189–4195 (2012).
  Article CAS PubMed Google Scholar
• Gorgolewski, K.J., Margulies, D.S. & Milham, M.P. Making data sharing count: a publication-based solution. Front. Neurosci. 7, 9 (2013).
  Article PubMed PubMed Central Google Scholar
• Gorgolewski, K.J. et al. A test-retest fMRI dataset for motor, language and spatial attention functions. Gigascience 2, 6 (2013).
  Article PubMed PubMed Central Google Scholar
• Hanke, M. et al. A high-resolution 7-tesla fMRI dataset from complex natural stimulation with an audio movie. Sci. Data 1, 140003 (2014).
  Article PubMed PubMed Central Google Scholar
• Anonymous. Using someone else's data. practiCal fMRI: the nuts & bolts http://practicalfmri.blogspot.com/2014/02/using-someone-elses-data.html (2014).
• Meehl, P. Theory testing in psychology and physics: a methodological paradox. Philos. Sci. 34, 103–115 (1967).
  Article Google Scholar
• Monogan, J.E. III. A case for registering studies of political outcomes: an application in the 2010 house elections. Polit. Anal. 21, 21–37 (2013).
  Article Google Scholar
• HD-200 Consortium. The ADHD-200 consortium: a model to advance the translational potential of neuroimaging in clinical neuroscience. Front. Syst. Neurosci. 6, 62 (2012).
• Guyon, I., Hur, A.B., Gunn, S. & Dror, G. Result analysis of the NIPS 2003 feature selection challenge. Adv. Neural Inf. Process. Syst. 17, 545–552 (2004).
  Google Scholar
• Marshall, E. Bermuda rules: community spirit, with teeth. Science 291, 1192 (2001).
  Article CAS PubMed Google Scholar
• Gardner, D. et al. The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics 6, 149–160 (2008).
  Article PubMed PubMed Central Google Scholar
• Marenco, L., Ascoli, G.A., Martone, M.E., Shepherd, G.M. & Miller, P.L. The NIF LinkOut broker: a web resource to facilitate federated data integration using NCBI identifiers. Neuroinformatics 6, 219–227 (2008).
  Article PubMed PubMed Central Google Scholar
• Langille, M.G.I. & Eisen, J.A. BioTorrents: a file sharing service for scientific data. PLoS ONE 5, e10071 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Gadde, S. et al. XCEDE: an extensible schema for biomedical data. Neuroinformatics 10, 19–32 (2012).
  Article PubMed Google Scholar
• Turner, J.A. & Laird, A.R. The cognitive paradigm ontology: design and application. Neuroinformatics 10, 57–66 (2012).
  Article PubMed PubMed Central Google Scholar
• Poldrack, R.A. et al. The cognitive atlas: toward a knowledge foundation for cognitive neuroscience. Front. Neuroinform. 5, 17 (2011).
  Article PubMed PubMed Central Google Scholar
• Marcus, D.S., Olsen, T.R., Ramaratnam, M. & Buckner, R.L. The extensible neuroimaging archive toolkit: an informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics 5, 11–34 (2007).
  Article PubMed Google Scholar
• Van Horn, J.D. & Toga, A.W. Is it time to re-prioritize neuroimaging databases and digital repositories? Neuroimage 47, 1720–1734 (2009).
  Article PubMed Google Scholar
• Das, S., Zijdenbos, A.P., Harlap, J., Vins, D. & Evans, A.C. LORIS: a web-based data management system for multi-center studies. Front. Neuroinform. 5, 37 (2011).
  PubMed Google Scholar
• Scott, A. et al. COINS: an innovative informatics and neuroimaging tool suite built for large heterogeneous datasets. Front. Neuroinform. 5, 33 (2011).
  Article PubMed PubMed Central Google Scholar
• Marcus, D.S. et al. Human connectome project informatics: quality control, database services, and data visualization. Neuroimage 80, 202–219 (2013).
  Article PubMed Google Scholar
• Rex, D.E., Ma, J.Q. & Toga, A.W. The LONI pipeline processing environment. Neuroimage 19, 1033–1048 (2003).
  Article PubMed Google Scholar
• Dinov, I. et al. Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline. PLoS ONE 5, e13070 (2010).
  Article PubMed PubMed Central CAS Google Scholar
• Gorgolewski, K. et al. Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. Front. Neuroinform. 5, 13 (2011).
  Article PubMed PubMed Central Google Scholar
• MacKenzie-Graham, A.J., Van Horn, J.D., Woods, R.P., Crawford, K.L. & Toga, A.W. Provenance in neuroimaging. Neuroimage 42, 178–195 (2008).
  Article PubMed Google Scholar
• Bellec, P. et al. The pipeline system for octave and MATLAB (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front. Neuroinform. 6, 7 (2012).
  Article PubMed PubMed Central Google Scholar