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JIP fMRI Analysis Toolkit

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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.