MATLAB for the Behavioral Sciences: How to program your own experiment
2007 course notes

Ione Fine



Suitable for graduate students and advanced undergraduates considering graduate school in the behavioral sciences

Description: This class will be a tutorial for programming techniques in Matlab that are particularly relevant to researchers in behavioral sciences. The class will give a researcher with no or little experience in programming the tools they need to design and program their own experiment, do basic analysis, and plot their results. For example, we will include classes on experimental design, stimulus presentation, experimental timing, graphical user interfaces, curve fitting, randomization techniques, basic statistics, and customized data plotting, debugging and code optimization techniques.

Almost all experiments in the behavioral sciences have a certain structure.
Some sort of stimulus is displayed, the subject makes some sort of response, a new stimulus is presented that may or may not depend on the subjects' response. At the end of the experiment the data needs to be saved and analyzed. This class will step through these various stages of a typical program. By the end of the class, the student will not only have the programming knowledge she needs to develop a working program, she will have already written several working programs typical of a wide variety of behavioral science experiments.

In each class, I will explain basic techniques and commands and provide code examples. Homeworks will practice and build on these skills. Optional homeworks will include more advanced topics and techniques. Each class will build on the core material of the class before.

The class is based on a book that Ione Fine and Geoffrey Boynton are writing, and the notes for the class is the manuscript draft for the book.


The EPOST discussion group is HERE



Introduction (3/28/2007)
Chapter 1 (strings &  vectors, 3/28/2007)
Chapter 2 (matrices & calculations, 4/6/2007)
Chapter 3 (basic graphics, 4/9/2007)
       scaleif.m
Chapter 4 (beginning FaceAdaptation experiment, 4/3/2007)
    folder for male images
    folder for female images
    folder for morph images
Chapter 5 (functions, 4/7/2007)
Chapter 6 (Psychtoolbox, , 4/10/2007)

NOTES for Chapter 6.
Getting started with PsychToolbox Screen.m command
1. Start with just 1 monitor
2. See if
>ScreenTest
works. If it does then the screen command works. If not, then Psychtoolbox isn't working right on your computer and you should let me know.
3. Try DarkScreen
4. Try FunkyScreen
If you do it in this order it will be much easier to work out any problems.

Dealing with frozen blank screens
If you display stimuli on the main screen, as we often do, then the Screen window will hide the main menu bar and obscure Matlab’s command window. That can be a problem if your program stops (perhaps due to an error) before closing the window. The keyboard will seem to be dead because its output is directed to the front most window, which belongs to Screen not Matlab, so Matlab won’t be aware of your typing.
Remain calm.
Typing Ctrl-C will stop your program if hasn't stopped already. Typing:
command-zero (on the Mac)
Alt-Tab (on Windows)
Will bring Matlab’s command window forward. That will restore keyboard input. The screen might still be hard to make out, if you’ve been playing with the lookup table. Typing:
(hit Return key)
clear Screen
will then cause Matlab to flush Screen.mex. Screen.mex, as part of its exit procedure, cleans up everything it did, closing all its windows and restoring the lookup table of all its displays. And everything will be hunky dory again.

Chapter 7 (more FaceAdaptation experiment, 4/10/2007)
Chapter 8 (finishing FaceAdapt experiment, 4/15/2007)
Chapter 9  (keyboard input, RTs, 4/22/2007)
Chapter 10  (basic plotting, 4/22/2007)
Chapter 11  (more plotting, 4/29/2007 ***added Geoff's color illusion and notes on view***)
    logx2raw.m
    logy2raw.m
Chapter 12  (analyzing fake fmri data, 4/26/2007)
Chapter 13  (Data in, data out. reading and writing to excel and text files, 4/27/2007)
Chapter 14  (CosmoQuiz, example of using PT windows and key press commands to collect subject data, 4/29/2007)
Chapter 15  (Optimization, 5/7/2007)  
    You will also need the following functions:
    fit.m
    params2var.m
    var2params.m
    fitFun.m
    updateUI.m
    fitUI.m
Chapter 16  (sound, 5/17/2007)  
Chapter 17  (calibration, 5/22/2007)  
   
I'll bring copies of Chapter 11 to class