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This manual defines the general methods and specific software tools that we use to acquire and process MR software.

In the Administrative section, we describe a variety of local procedures involving subject safety, signing up for scanning, and related topics.

The majojrity of this manual describes the software tools we use to process our measurements. We call the software tools mrVista (Mister Vista). The software includes methods for processing anatomical, functional, and diffusion tensor imaging data. The software is written mainly in Matlab. There are some additional utilities written in C++/VTK. All of the software runs on Windows/XP and on Linux (Red Hat). Most of the software runs on Apple computers.

The software capabilities are described in the separate sections accessed through the menu at the left. To download the software go to the Software section.

To see examples of how we use the software, consult some of our recent research papers.

  1. Visual Field Map Clusters in Human Cortex
    Wandell, A. A. Brewer and R.F. Dougherty (2005)
    Phil. Trans. of the Royal Society London, v. 360, pp. 693-707.

  2. Functional organization of human occipital-callosal fiber tracts.
    Robert F. Dougherty, Michal Ben-Shachar, Roland Bammer, Alyssa Brewer, Brian Wandell (2005).
    PNAS, v. 102, no. 20, pp. 7350-7355.

  3. Visual field representations and locations of visual areas V1/2/3 in human visual cortex
    R. F. Dougherty, V. M. Koch, A. A. Brewer, B. Fischer, J. Modersitzki and B. A. Wandell (2003).
    Journal of Vision, 3(10),586-598, DOI 10.1167/3.10.1.

We use the package every day, and we have confidence in the main computations. We are also familiar with its limitations and continue to work on additions and just plain bug fixes. We double check the calculations for sense, and if you use the code we hope you will do so as well.

Major contributions to the current version of the code were made by Robert Dougherty, David Heeger, William Press, David Ress, Rory Sayres, Alex Wade, and Brian Wandell. At various stages of development, Geoff Boynton, Stephen Engel, Rehan Kahn, and Allen Poirson contributed. If your name is missing please let me know.

In addition to our lab at Stanford, the code is being used at Royal Holloway (Morland), Smith-Kettlewell (Wade), UC Berkeley (Sobel) and perhaps other places. Heeger has branched a separate NYU version, and I believe Boynton and Engel have their own versions as well.

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