mrVista WorkFlow

The zip files below contain snapshots (sometimes nightly) of the magnetic resonance imaging analysis software that we use in the Heeger and Wandell labs.

This code involves the work of many people from these labs. Please remember most modules are not yet stable. Thanks to the heroic recoding efforts of David Heeger and David Ress, the mrVista code is now much better than earlier versions. However, the bulk of this codebase was developed as an undisciplined growth, so it may contain many little problems and is not always easy to follow. Although we use it every day and have great confidence in the core routines, we are also familiar with its limitations. We are constantly working on revisions and improvements and just plain bug fixes.

As to the manual- well, there is no manual. However, in most packages there is a ReadMe file that describes some of the basic functionality of the software and brief installation notes.

Unless otherwise noted, all our code is released under the GPL . The authors of the code retain all copyrights. By downloading our code from the links below or from our CVS repository, you agree to be bound by the terms of the GPL.

mrVista.zip: The main analysis tools are packaged as mrVista.
mrGray.zip: The mrGray windows application for white-gray segmentation and 3-d viewing. The mrGray source code is also available (mrGraySrc.zip). You can also get a sample dataset for mrGray (mrGray_sampleData.zip).
mrFlatMesh.zip: The tools in mrFlatMesh are used for flattening cortex. These are included in mrVista- we provide them separately for those who just want to do flattening.
Anatomy.zip: Tools for managing our anatomical data. These are also included in mrVista. A new addition to Anatomy is mrMesh- a VTK/OpenGL 'server' that we call from matlab to do 3d visualization.
displayCode, exptTools, oceanOptics.zip: Tools are used for experimental display and calibration. The display code includes an example of how to create the stimuli for retinotopy.

CVS Snapshots:

You can also browse the CVS repository where we keep track of the software and modifications.

Pre-Introduction:
Before you start, you should be aware that this is all a bit complicated. You will need to be familiar with MATLAB, Macs and the Brainard/Peli Psychophysics toolbox. You should also know how to calibrate your monitor for best results. If any of the above mean nothing to you, stop now!

Introduction:
The code we distribute here is what we use for running retinotopy scans in our fMRI experiments. Broadly speaking, these stimuli can be grouped into
1) Expanding rings
2) Rotating wedges

Expanding rings are flickering annuli that start in the middle of the screen and move towards the edge. Rotating wedges are flickering sectors that move around the center of the screen. They are useful because they generate distinctive patterns of activation in the early visual areas that can be used to determine visual field angle and eccentricity. Once again, if you are lost by now then stop.

Overview:
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.

BP- Toolbox:
The first is the Brainard-Peli psychophysics toolbox which you can download and install from the same website you got this readme from.

Expt Tools:
The second library is our own set of tools built on this toolbox. We call this exptTools. You can download it from this website. http://white.stanford.edu/getRet.shtml

How to install Expt Tools:
Unzip the exptTools folder into your MATLAB toolbox directory. Then bring up the path browser in MATLAB (hit the button on the toolbar that looks like two folders on top of each other with barcodes to their right). From the path browser, click the 'default path' button. This will tell matlab to search the toolbox directory and include any new folders in there. See if exptTools has been installed by typing installCheckET

in matlab. you should see something on the command line telling you that the path is okay. Now be aware of this: To run psychophysics properly, you need to have a properly calibrated monitor. In fact, matlab needs to know a lot about your monitor: its frame rate, the color of its phosphors, its size, position, the number of bits in the video card and other things like that. We store all this information in a set of files, called displayParams.m gamma.mat spectra.mat These files are in a default folder on our machines:

exptTools expects these files to exist when it initiates. If they don't, you will get a set of errors. You might get something working (if exptTools defaults to something useful). More often than not, you will get garbage. We have included some sample display calibration files in the retinotopy code distribution. We have also changed the retinotopy code so that it uses these sample files rather than looking in the default folder above. But this is for demonstration purposes only. Our monitors are not your monitors and our frame rates will be different to yours as well. That means that the timings for the retinotopies will be wrong. Do not email us about this. Or anything. You are welcome to examine the code to see what we have done and modify it to your hearts' content but we cannot provide technical support on this. It is hard enough making it work on our >own< machines.

Once both these libraries are in place, you can run the retinotopy code. Extract the code in retinotopyCode.zip to a directory called 'ret' somewhere in your directory path. Change to this directory in MATLAB and type ret Now you can start debugging your installation.