Vistasoft SVN

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The following sections describe the code repositories developed by the VISTA lab. All repositories are locally hosted and can be "checked out" using SVN. Some of the repositories can be browsed using Trac (click the title to browse with trac). Each repository section contains a "Get" section with details of how you can obtain the code. Importantly, some of the VISTA code packages (e.g., VISTASOFT) require external software to run (e.g., Matlab, SPM). Please see the section below for information about required software.

Contents

[edit] VISTASOFT

VISTASOFT is the MAIN software repository for the tools used in the VISTA Lab. The repository includes methods for processing anatomical, functional, and diffusion tensor imaging data. The software is written mainly in Matlab. The VISTASOFT package contains:

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. To run VISTASOFT you will need Matlab and tools from FSL and SPM (described below).

    Get VISTASOFT

    SVN
    Recommended for local users and those who want to contribute code or simply keep their software up to date. If you need help getting started using subversion, have a look at the SVN page.

     # Repo URL: 
     https://white.stanford.edu/repos/vistasoft
    # Linux Checkout Command: svn checkout https://white.stanford.edu/repos/vistasoft

    DOWNLOAD

    For those users who would like to quickly download a current version of the software. Clicking HERE will download a zip-file containing a current (hourly) snapshot of the entire VISTASOFT repository.

[edit] VISTADISP

Experimental control and display toolbox. A set of Matlab routines for controlling the experiment, particular for calibrating displays for vision experiments and managing the interface with the MR scanner. But also useful for straight psychophysics. This code relies on parts of the PsychToolBox.

    Get VISTADISP

    SVN

     # Repo URL: 
     https://white.stanford.edu/repos/vistadisp
    # Linux Checkout Command: svn checkout https://white.stanford.edu/repos/vistadisp

    DOWNLOAD

    For those users who would like to quickly download a current version of the software. Clicking HERE will download a zip-file containing a current (hourly) snapshot of the entire VISTADISP repository.

[edit] VISTADATA

The vistadata repository includes data sets that are used in conjunction with the tutorial scripts in mrScripts. These scripts run on multiple platforms and the tutorial scripts expect certain data sets to be in the vistadata repository.

    Get VISTADATA

    SVN

     # Repo URL: 
     https://white.stanford.edu/repos/vistadata
    # Linux Checkout Command: svn checkout https://white.stanford.edu/repos/vistadata

    DOWNLOAD

    Those users who would like to quickly download a current version of the repo can do so using the link above. This will download a zip-file containing a current (daily) snapshot of the entire VISTADATA repository.

    LOCAL USE
    Within the VISTA LAB there is no need to checkout a version because we maintain one checked-out copy of the vistadata in:

    /usr/local/vistadata
    

[edit] VISTAPROJ

We are working on a number of local projects that have software, experiments and analyses under development. These projects are not ready for sharing. It is convenient, however, to maintain a repository version of the project code. The vistaproj repository contains the code for these development projects VISTASOFT projects. Vistaproj is intended to be a working repository for local projects, unlike the relatively stable VISTASOFT repository.

    Get VISTAPROJ

    NOTE: VISTAPROJ is a private/secure repository - which means only members of the lab have access this repo. For this reason we did not set up the VISTAPROJ repository for trac browsing.
    SVN

     # Repo URL: 
     https://white.stanford.edu/srepos/vistaproj 
    # Linux Checkout Command: svn co https://white.stanford.edu/srepos/vistaproj

    You can just check out a portion of the repository, as well, by specifying the subdirectory. The way to do this is to create a directory, vistaproj, and then to use:

     svn co  https://white.stanford.edu/srepos/vistaproj/YOURPROJECT 
    

[edit] VISTASRC

VISTASRC is a repository containing the source code and compiled versions of mrMesh, related mex files (build mesh, smooth mesh and curvature), and an older version of QUENCH.

    Get VISTASRC

    SVN

     # Repo URL: 
      https://white.stanford.edu/repos/vistasrc 
    # Linux Checkout Command: svn co https://white.stanford.edu/repos/vistasrc

    DOWNLOAD

    For those users who would like to quickly download a current version of the software. Clicking HERE will download a zip-file containing a current (hourly) snapshot of the entire VISTASRC repository.

[edit] VISTADWI

VISTADWI (aka StanfordTools-DWI) is a repository containing only the source code for certain VISTA executables:

    Get VISTADWI

    SVN

     # Repo URL: 
      https://white.stanford.edu/repos/StanfordTools-DWI/ 
    # Linux checkout command: svn co https://white.stanford.edu/repos/StanfordTools-DWI/

    DOWNLOAD

    For those users who would like to quickly download a current version of the code. CLicking the above link will download a zip-file containing a current (hourly) snapshot of the entire VISTADWI repository.

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