Local software projects

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  • BW: We are no longer using the vistaproj SVN repository. The work in that repository has been moved into other imageval git repositories. There may be some historical directories in there, but we are no longer using SVN and we did not create a vistaproj git repository **
  • All the text below here should be eliminated once someone else confirms that what I am saying is true.
  • We should say where the vistastim code resides
  • We should make a link to the key vistalab project repositories here and people can read about the projects on github

TO BE DEPRECATED BELOW HERE

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.

This page is a list of some of the ongoing projects. Lab members are welcome to protect their code development using vistaproj, and to indicate roughly what is going on by maintaining some links to the new projects here. The links are generally restricted viewing. If you are in the VISTA lab and receive a restricted viewing message, contact Brian, Bob, Jon or someone who can change your user settings.

A kind of "sister repository" to vistaproj is vistastim. Vistaproj should contain code (mostly smal files). "Vistastim" was created to store images or other stimuli. Many of our projects, whether for psychophysics, neuroimaging, or computational modeling, use stored image files. Some of these image files, such as photos of individuals, may be protected. Lab members are welcome to check in stimuli. This should make it easier to run the same experiment on different machines.

Contents

[edit] Vistaproj checkout

To checkout the entire repository:

  • On the linux command line type: svn co https://white.stanford.edu/srepos/vistaproj
  • Using Tortoise SVN set up the repository fields using the link (above).

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

or the equivalent setting in Tortoise SVN.

We did not set up the vistaproj repository for trac browsing because we don't want our dirty laundry on the web. There is probably a way to set it up with restricted browsing. Someone?

[edit] Vision Experiments and Modeling

  • LedFlicker - Hiroshi Horiguchi is making measurements of the BOLD signal with a special device he and Bob Dougherty constructed. We hope this will clarify certain biophysical aspects of the BOLD signal. The device should also enable us to make measurements about color and time that were previously unreachable.
  • eCogPRFs - Jon Winawer and Andreas Rauschecker are making implanted electrode measurements in the visual pathways.
  • CertaintyFMRI - Jon Winawer is using classifiers to relate the BOLD signal with certain perceptual judgments.
  • Vismodel - Jon Winawer and Brian Wandell are developing physical simulations from cone encoding, ganglion cell spiking, and so forth. We hope to develop this into a biophysical simulator with physically accurate properties of the stimulus followed by plausible models of different stages in the visual pathways
  • v4 - For analyzing data and making figures for hV4 paper (Winawer, Horiguchi, Sayres, Amano, Wandell, 2010, Journal of Vision).
  • White matter mapping - Mapping retinotopy data on the white matter fascicles.


[edit] Neuroimaging Methods

  • AFQ - Jason Yeatman is creating tools for Automated fiber identification
  • microtrack - Brian Wandell is developing software for understanding the biophysics of the diffusion signal and the implications of these measures for axon size, density, membrane properties, and so forth.
  • Diffusion Simulator - Robert Dougherty and Bragi Sveinsson are modeling diffusion at the molecular level, to understand the meaning of diffusion signals.

[edit] Software tools

[edit] Vistastim

Vistastim is a protected repository, like vistaproj. Instructions for svn checkout are identical to those for vistaproj, except that "vistaproj" should be replaced with "vistastim". Contents

  • MRI Localizers Stimuli to run fMRI localizers. Currently contains faces and houses provided by Kai Miller, 400 x 400 pixels each. These can be used for experiments but the images themselves should not be in publications.
  • Your stimuli here
Personal tools