Unobtrusive integration of data management with fMRI analysis
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This note describes a software utility, called X-batch which addresses two pressing issues typically faced by functional magnetic resonance imaging (fMRI) neuroimaging laboratories (1) analysis automation and (2) data management. The first issue is addressed by providing a simple batch mode processing tool for the popular SPM software package (http://www.fil.ion. ucl.ac.uk/spm/; Welcome Department of Imaging Neuroscience, London, UK). The second is addressed by transparently recording metadata describing all aspects of the batch job e.g., subject demographics, analysis parameters, locations and names of created files, date and time of analysis, and so on). These metadata are recorded as instances of an extended version of the Protégé-based Experiment Lab Book ontology created by the Dartmouth fMRI Data Center. The resulting instantiated ontology provides a detailed record of all fMRI analyses performed, and as such can be part of larger systems for neuroimaging data management, sharing, and visualization. The X-batch system is in use in our own fMRI research, and is available for download at http://X-batch.sourceforge.net/.
Index EntriesfMRI SPM ontology neuroimaging data management analysis automation
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- Bales, N., Brinkley, J. F., et al. (2005) A Framework for XML-based Integration of Data, Visualization and Analysis in a Biomedical Domain. Proceedings, XSym 2005, pp. 207–221, Trondheim, Norway.Google Scholar
- Brinkley, J. F. and Rosse, C. (2002) Imaging Informatics and the Human Brain Project: the Role of Structure, Review Yearbook of Medical Informatics, 111–128. Pub Med ID: 12425235.Google Scholar
- Frackowiak, R. S. J., Friston, K. J., Frith, C. D., Dolan, R. J., and Mazziotta, J.C. (eds.) (1997) Human Brain Function. Academic Press, USA.Google Scholar
- Grethe, J. S., Baru, C., Gupta, A., et al. (2005) Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud. Health Technol. Inf. 112, 100–109.Google Scholar
- Jakobovits, R. M., Modayur, B, Brinkley, J. F. (1996) AWeb-based repository manager for brain mapping data. Proc. AMIA Annu. Fall Symp. pp. 309–313.Google Scholar
- Moore, E. B., Poliakov, A. V., and Brinkley, J. F. (2004) Brain Visualization in Java3D. Proceedings, MedInfo 2004 San Francisco, CA, p. 1761.Google Scholar
- Poliakov, A. V., Hinshaw, K. P., Rosse, C., and Brinkley, J. F. (1999) Integration and Visualization of Multimodality Brain Data for Language Mapping, Proceedings AMIAAnnu. Fall Symp pp. 349–353.Google Scholar
- Wong, B. A. and Brinkley, J. F. (1998) Dynamic 3-D scene navigation in web-based anatomy atlases, Proceedings AMIAAnnu. Fall Symp. pp. 1100–1104.Google Scholar