Software
Software
Software Wiki Page
Download VISTA Lab code on Git Hub!
We call the software tools mrVista (aka VISTASOFT). 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. Most of the software runs on Apple computers.
mrVista
The main analysis tools of are packaged as mrVista (‘VISTASOFT’ svn repository). ‘mrVista’ also refers to the set of tools for functional MRI data analysis. These tools include methods for analyzing retinotopic mapping data, general linear models, and modeling population receptive field sizes, among other functions.
For more information on the mrVista software, visit the Lab Wiki.
mrDiffusion
Download
mrDiffusion Wiki Page
mrDiffusion is our diffusion imaging analysis and visualization package. It is available as part of our open-source and freely distributed VISTASOFT package. The code is distributed as a nightly snapshot from our SVN repository. That means that the above link always points to the most current version of the software. Some parts of mrDiffusion also depend on routines in SPM (SPM2 or SPM5), so you should download that as well. mrDiffusion is useful for processing diffusion-weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, and RGB fiber direction maps. It is also useful for performing deterministic tractography. It will soon support probabilistic tractography through the ContTrack tools that Anthony Sherbony is developing. For more information, please visit the Lab Wiki.
Quench
QUENCH is an independent software component, developed by Anthony Sherbondy and David Akers in collaboration with our team, for visualization and segmentation of tractography results into meaningful fiber bundles. The interface is gesture based, not ROI based, which makes fiber segmentation easier and less dependent on crude ROI drawing (also much more fun).
The program is a C++ application. It is designed to work either independently or in coordination with mrDiffusion. You will need around 2GB of memory to run it. QUENCH runs under MAC, Windows and Linux. For more information, please visit the Lab Wiki.
ITKGray
ITKGray is a new segmentation tool that Dr. Robert Dougherty has developed. ITKGray is a branch of the ITKSnap project, and most of the hard work was done by the ITKSnap developers. We added some of the mrGray functionality, like topology checking/fixing and a new flood-fill paintbrush that is similar to the mrGray auto-segmentation methods, but is run on small sections of an image rather than the entire image at once. For more information about ITKGray, and for information on how to install the software and get it working on your Linux box or Windows machine, visit the Lab Wiki. If you’d like to get the source code and try to build it under your favorite platform, just contact bobd at stanford-dot-edu.
Retinotopy Stimulus
The retinotopy code comprises a set of MATLAB m-files. These files are in the Ret directory of the package that you downloaded along with this readme. The file that you use to call the stimuli is ret.m Once you have everything set up, you can type
ret
from the command line and a nice graphical interface will pop up to allow you to configure the stimuli for an fMRI scan. It will work out how many fMRI frames you have, how long the stimulus will last, what priority to run the stimulus at etc etc. It will also allow you to choose from a list of about 10 different variations on the basic themes of rotating wedges and expanding rings. The retinotopy code is built on two software libraries that you will also need – Psychtoolbox and Vistadisp.