The JIP Toolkit was developed primarily for analysis of preclinical fMRI data, because the widely available neuro-imaging packages proved to be consistently bad at such tasks, although they may have become more flexible in recent years. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable
- automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step,
- visualization of 4-dimensional data using either mosaic or tri-planar display, and integration of general linear models for graphical display of time series analysis,
- a simple and flexible 1st-order GLM for fMRI time series analysis,
- a GLM for PET analysis within the framework of the simplified reference tissue model,
- a 2nd-order GLM analysis following the Worsley 2002 scheme,
- a tool for performing smoothing, registration, mapping (etc). using a command interpreter,
- MRI templates to place your data into standardized neuro-imaging spaces.
All tools use the Linux/Unix environment. The current distribution includes executables for
- Linux i686 (32-bit),
- Linux x86_64 (64-bit),
- Darwin for Mac OS X (universal binary), and
- Cygwin/X (32-bit) for Windows.
The code is distributed as open source to enable creation of executables for other systems. For any system, the essential components are Linux or Unix plus X11 graphic capabilities.
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Acknowledgement of Support
Like most software developed for scientific research, this work was funded indirectly through projects that required or benefited from its functionality. Support was derived from NIH grants to the developer of this software (Joseph B. Mandeville) and from grants to collaborators. Additional funding came from the Athinoula A. Martinos Center for Biomedical Imaging, a collaboration of the Massachusetts General Hospital, the Massachusetts Institute of Technology, and the Harvard Medical School. Explicit support for the distribution of this software came from the National Institute for Biomedical Imaging and Bioengineering (NIBIB @ NIH) through grant R03EB008134.
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