In this tutorial we will learn how simple intracerebral current sources can generate complicated patterns of EEG potentials at the scalp. We will then see how, under certain conditions, the underlying EEG sources can be effectively localized from the scalp measurements. However, the tutorial also aims to illustrate how the solution to the inverse EEG problem can be easily confounded e.g. by the presence of noisy background EEG activity.
Supporting materials:
Please download the tutorial and uncompress the .zip
file. Then simply add directory tutorial_dipoles and all its
subdirectories to your MATLAB's path.
To add a directory and all its subdirectories to MATLAB's path you can use MATLAB's command:
addpath(genpath('M:/mypath/tutorial_dipoles'))
where M:/mypath/tutorial_dipoles is the location where you uncompressed
the .zip file. In some occasions during this tutorial I will assume that
you are running MATLAB commands from the root directory of the tutorial
(i.e. from M:/mypath/tutorial_dipoles in the example above). To change your
working directory do this in MATLAB:
cd M:/mypath/tutorial_dipoles
where you will have to change M:/mypath/tutorial_dipoles for the path where
you downloaded the tutorial.
The tutorial should work under MATLAB R2010a or newer. It is likely to work also under not too much older MATLAB versions. The tutorial makes use of the following freely available MATLAB toolboxes:
For convenience, all dependencies have been included in the tutorial .zip package so that you don't need to download them separately.
Note: The tutorial uses the 3D rendering capabilities of the OpenGL implementation that is included with your operating system. As OpenGL support differ slightly between operating systems there is a small chance that some of the figures will display differently in different operating systems.
The tutorial instructions explain just a small fraction of the
tutorial scripts' features. You can always get a more detailed help of
individual MATLAB functions using the command help followed by the
name of the relevant function. For instance, the command:
help plot
will display the help of MATLAB's built-in plot command.
The tutorial makes use of MATLAB's classes. Do not get get
intimidated by the term. A class is just a user-defined data type. MATLAB
comes with lots of built-in data types. For instance double and single
are two types that can store numeric data:
x = 5;
The variable x above is now an instance (also called
an object) of class double. You can find out the classes of the variables
in your MATLAB's workspace using the command whos. The result could be
something like this:
>> whos
Name Size Bytes Class Attributes
myHead 1x1 2805970 head.mri
x 1x1 8 double
y 1x1 8 double
where you can see that variable x is an object of class double and variable
myHead is an object of class head.mri. The latter is a class that we
have defined specifically for the purposes of this tutorial.
It is important to realize the difference between a class and an object.
In the example above, x and y are two different objects of the same class.
One of the great advantages of using objects with MATLAB is that it allows you to overload function names. For instance, if you run the command:
plot(myHead);
MATLAB will first check whether a specialized method plot() has been defined
for class head.mri. If such method exists then it will run that method
instead of MATLAB's built-in function plot(). A head.mri object contains a
head model and a double object contains just numbers. Indeed, plotting such
different data types involve very different operations. Thus, it makes sense
that different versions of plot are called, depending on the class of what
you want to be plotted. Remember: the specialized version of plot() that
takes care of plotting mri.head objects is called a method of class
mri.head.
Imagine that you want to get some help on method plot() for objects of class
mri.head. You could try to do this:
help plot
but you will find that the help that is displayed corresponds to MATLAB's
built-in plot() instead of corresponding to method plot() of class
mri.head. Only if you read until the end of the help that is displayed you
will see a section that reads Overloaded methods: and that lists several
other functions that are also called plot(), and that will be called
instead of the built-in, depending on the type of the input argument.
If you already installed the tutorial scripts you should see in that list
a link reading head.mri. If you click that link you will get the help that
you were looking for. Alternatively, you could have just used the command:
help head.mri.plot
This documentation uses MathML to display inlined mathematics. Unfortunately
not all browsers support MathML natively, including Internet Explorer. In this
case you will not be able to see the mathematical expressions correctly.
While there is a plug-in available (MathPlayer) for adding this capability
to Internet Explorer, in our tests this combination crashed the browser when
viewing some of these pages. According to Wikipedia, some major web-browsers
that currently display MathML natively include Mozilla Firefox, Opera, and
Camino. At this point we can't do anything else than to direct you to use
these browsers to view these pages.
The tutorial code is also available at a public git repository. Feel free to fork the code and enhance it in any way you want.
This tutorial has been prepared for the course Advanced Human Neurophysiology, given at the VU University Amsterdam, and organized by Klaus Linkenkaer-Hansen. The author of the tutorial is German Gomez-Herrero.
As both code and documentation has been made from scratch for the year 2011 course, it is likely that you will find bugs and typos. Please report those to me so that I can fix them. I would also appreciate any feedback on the tutorial contents so that I can improve it.