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Skandha4 and Brain Mapper
University of Washington
  Skandha4 is a general purpose graphics toolkit, which combines a subset of Common Lisp - useful for fast interactive programming and prototyping - with the ability to add pre-compiled C-based primitive functions that significantly accelerate computationally demanding routines. Skandha4 supports 3D graphics, with drivers for IRIX GL and OpenGL available. It includes a module for processing and storing MRI data, with support for the Montreal MINC 3-D image volume file format added recently. Server capabilities make it possible to use Skandha4 as a backend graphics server for web-based applications (e.g. Brain Visualizer), in which the server is used to generate images from 3D models.
   Visual Brain Mapper (VBM) is an application based on Skandha4 toolkit. VBM was developed for visual mapping of functional brain data acquired at neurosurgery, and integration of that data with image-based functional data.   It is currently used to:
  Reconstruct patient-specific 3D models of the cortical surface, veins and arteries.
  Map onto these models cortical stimulation mapping (CSM) data obtained at neurosurgery.
  Map fMRI language activation onto the models.
  Visualize the combined CSM/fMRI data, both locally and on the web.

NIfTI-1 support
Jim Brinkley, Jeff Prothero, Kevin Hinshaw, Andrew Poliakov, Structural Informatics Group
Andrew Poliakov
Tutorial, Demos
How to get
Contact Andrew Poliakov
Current version
Current version release date
Open source
Available free of charge
Available on IRIX and Linux. 256M RAM. (Linux version utilizes software rendering of 3D scenes, and not as robust as IRIX version)
Technical publications
  • Hinshaw, K.P. and J.F. Brinkley, Incorporating constraint-based shape models into an interactive system for functional brain mapping, in Proceedings, American Medical Informatics Association Fall Symposium. 1998 pp. 921-925.
  • A. V. Poliakov, K. P. Hinshaw, C. Rosse and J. F. Brinkley, Integration and Visualization of Multimodality Brain Data for Language Mapping, Proceedings, American Medical Informatics Association Fall Symposium Washington, D.C., 1999.
  • J. F. Brinkley and J. S. Prothero, Slisp: A flexible software toolkit for hybrid, embedded and distributed applications, Software -- Practice and Experience, vol. 27, pp. 33-48, 1997.
Applications publications
  • Corina, D.P., McBurney, S.L., Dodrill, C., Hinshaw, K., Brinkley, J. and Ojemann, G. 1999 Functional roles of Broca's Area and SMG: Evidence from cortical stimulation mapping in a deaf signer. Neuroimage. 10:570-581.
  • Corina, D.P., Poliakov, A.V., Steury, K., Martin, R.F., Brinkley, J.F., Mulligan, K.A. and Ojemann, G.A. 2000 Correspondences between language cortex identified by cortical stimulation mapping and fMRI, Human Brain Mapping Annual Meeting, June 12-16, 2000, San Antonio, Texas. Neuroimage 11(5):S295.
Other information
Applications are stable and reasonably easy to use. However, they have not been "productorized" yet, and therefore should be considered BETA quality (will require fairly good knowledge of Unix OS to set up and run). Documentation is good for core modules of Skandha4, but may be insufficient for Brain Mapper (will require support from us).
functional, HBP supported, surface analysis, visualization, volume
IRIX, Linux
IATR listing last updated
30 May 2003