DFBIdb: A Software Package for Neuroimaging Data Management
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We present DFBIdb: a suite of tools for efficient management of neuroimaging project data. Specifically, DFBIdb was designed to allow users to quickly perform routine management tasks of sorting, archiving, exploring, exporting and organising raw data. DFBIdb was implemented as a collection of Python scripts that maintain a project-based, centralised database that is based on the XCEDE 2 data model. Project data is imported from a filesystem hierarchy of raw files, which is an often-used convention of imaging devices, using a single script that catalogues meta-data into a modified XCEDE 2 data model. During the import process data are reversibly anonymised, archived and compressed. The import script was designed to support multiple file formats and features an extensible framework that can be adapted to novel file formats. An ACL-based security model, with accompanying graphical management tools, was implemented to provide a straightforward method to restrict access to raw and meta-data. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria. The command-line interface was implemented to allow users to incorporate database commands into more complex scripts that may be utilised to automate data management tasks. By using DFBIdb, neuroimaging laboratories will be able to perform routine data management tasks in an efficient manner.
KeywordsData management Python XCEDE 2 Neuroimaging Archiving
We acknowledge the help of R. Beare and J. Chen in providing bug-testing support.
In order to develop the software in a swift manner, we utilised externally developed libraries and software packages. Table 4 shows the externally developed libraries and software packages that were utilised in DFBIdb.
Conflict of Interest Statement
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
- IEEE (2001a) 1003.1 standard for information technology—portable operating system interface (POSIX) base definitions, Issue 6. IEEE Std 1003.1-2001. Base Definitions, Issue 6, p. 448.Google Scholar
- IEEE (2001b) 1003.1 standard for information technology—portable operating system interface (POSIX) shell and utilities, Issue 6. IEEE Std 1003.1-2001. Shell and Utilities, Issue 6, p. 1090.Google Scholar
- IEEE (2001c) 1003.1 standard for information technology—portable operating system interface (POSIX) system interfaces, Issue 6. IEEE Std 1003.1-2001. System Interfaces, Issue 6, p. 1690.Google Scholar
- Keator, D., Wei, D., Gadde, S., Bockholt, H. J., Grethe, J. S., Marcus, D., et al. (2009) Derived data storage and exchange workflow for large-scale neuroimaging analyses on the BIRN Grid. Frontiers in Neuroinformatics.Google Scholar
- Lohrey, J. M., Killeen, N. E. B., & Egan, G. F. (2009) An integrated object model and method framework for subject-centric e-Research applications. Frontiers in Neuroinformatics.Google Scholar
- Marcus, D. S., Olsen, T., Ramaratnam, M., & Buckner, R. L. (2005). The Extensible Neuroimaging Archive Toolkit (XNAT): An informatics platform for managing, exploring, and sharing neuroimaging data. Neuroinformatics, 5, 11–34.Google Scholar
- Shepler, S., Callaghan, B., Robinson, D., Thurlow, R., Beame, C., Eisler, M., et al. (2003) NFS Version 4 Protocol.Google Scholar