Why donate?

- Tutorials, follow the NBT course

**Follow us **

**Most popular pages**

You are here: Frontpage : Introduction » Tutorials » Granger causality analysis of EEG data » Part IV: Granger-causality indices

Table of Contents

In this tutorial we will use two popular linear indices that are based on the concept of Granger Causality:

These two indices are similar in the sense that both are expressed in the frequency domain and that both are _normalized_, i.e. they can take values from 0 to 1 with 0 meaning no flow and 1 meaning a maximal information flow.

A DTF and PDC analysis always start by fitting a VAR model to your data:

arfitObj = learn(var.arfit, eeg);

Then you can compute the DTF with the command:

dtfObj = compute(var.dtf, arfitObj, linspace(0,0.1,50));

Or the PDC with the command:

pdcObj = compute(var.pdc, arfitObj, linspace(0,0.1,50));

The last input argument to method `compute()`

is an array of normalized
frequencies at which the PDC and DTF will be computed. Remember that
a normalized frequency
is just the result of dividing
a real frequency by the sampling rate. This means that the commands
above will compute the PDC and DTF in a range of frequencies
starting at 0 Hz and ending at Hz. Within this
range the PDC and DTF values will be computed at 49 equidistant bins
(that is what function `linspace`

does).

You can plot the result of the DTF and PDC analyses using these commands:

figure; plot(dtfObj); set(gcf, 'Name', 'DTF analysis of the scalp EEG data'); figure; plot(pdcObj); set(gcf, 'Name', 'PDC analysis of the scalp EEG data');

The interpretation of the figures is as we explained during the lecture. Cell of the figure corresponds to the flow in the direction . The vertical axis of each cell is PDC or DTF value (ranging from 0 to 1). The horizontal axis of each cell is normalized frequency. You should be able to zoom into a cell element by clicking on it. You can then return to the original figure by clicking on the figure again.

Since both the PDC and DTF are just estimates, they are affected by
random estimation errors. Therefore, it is necessary to assess how large a
PDC or DTF value needs to in order to consider it *significantly* larger
than 0. This can be done using method `compute_significance()`

:

pdcObj = compute_significance(pdcObj, surrogator.var, 0.05) dtfObj = compute_significance(dtfObj, surrogator.var, 0.05)

where the last argument is the significance threshold. Computing the
significance thresholds may take a few minutes. Once done you can
display the thresholds by plotting again objects `pdcObj`

and `dtfObj`

:

figure; plot(dtfObj); set(gcf, 'Name', 'DTF analysis of the scalp EEG data'); figure; plot(pdcObj); set(gcf, 'Name', 'PDC analysis of the scalp EEG data');

which will generate the following two figures:

There is no point in trying to interpret the results of this analysis. The EEG data that you have been provided is just a very small chunk of data from a single subject and from just 7 (randomly chosen) EEG sensors (out of 257 sensors). Performing and interpreting the results of a real study is far beyond the scope of this tutorial. However, what you can conclude from the figures above is that there are significant flows at one frequency or another in almost any direction, i.e. the PDC (and even less the DTF) do not seem to be very specific. The probable reason for this is that information flows between scalp EEG signals is greatly affected by volume conduction effects.

`path`

-like topology). Then you can analyze
this artificial observations in the same way as we did above with the
scalp EEG data and draw some conclusions on the results provided by
the PDC and the DTF.

*direct flows* of information
while the other is also very sensitive to *indirect flows*. Which
one is which? In a network with many connections between nodes, do you think
that it is better to have an index that is sensitive to indirect flows, or
is it better to be sensitive only to direct flows?

We will now create a VAR model that emulates the model that we fitted to the scalp EEG in the sense that the generated observations will look like EEG signals. However, in our artificial model we will modify the pattern of information flow between EEG signals so that it matches our wishes. This can be done with the commands:

varObj = dynamics.var('VarCoeffs', arfitObj.Coeffs); varObj = set_topology(varObj, 'myTopo', 'randomize', false);

where `'myTopo`

' should be replaced by the topology that you want your
artificial EEG data to have. You can use any of the topologies that we
discussed in Part II of the tutorial, with the exception of
the `'random`

' topology.

Now you should draw in a paper the information flow diagram underlying
your synthetic EEG model. You can do this by inspecting the
model coefficients of your model (`varObj.VarCoeffs`

), as we described
in Part II of the tutorial.

Now you should generate some observations of the EEG-inspired VAR model that you just created:

[artificialEEG varObj] = generate(varObj, 10000);

Plot this artificial EEG and confirm that, contrary to the toy model that we used in Part II, these observations do look like real EEG:

eegplot(cell2mat(artificialEEG), 'srate', 1000);

In my case, the model observations look like this:

Now you can save your artificial EEG in a file called `myeeg.mat`

:

artificialEEG = cell2mat(artificialEEG); save myeeg.mat artificialEEG;

And finally, you can send this file to one of your fellow students and challenge him or her to guess the pattern of information flow underlying your artificial EEG data. For that, he or she will have to perform an analysis of your artificial EEG data in the same way as we did with the real EEG data.

You are allowed to read the help of the constructor of `dynamics.var`

objects:

help dynamics.var;

and build a more complicated VAR model (e.g. with noise, with non-equal innovation variances, etc…).

`myeeg.mat`

either via e-mail, with a USB
memory stick (ask your tutor for one) or via http://www.wetransfer.com.

**[1] Kaminski and Blinowska, 1991**, *A new method of the description of the
information flow in the brain structures*, Biol. Cybern. 65, 203-210,
doi: 10.1007/BF00198091

**[2] Baccala and Sameshima, 2001**, *Partial Directed Coherence: a new concept
in neural structure determination*, Biol. Cybern. 84, 463-474,
doi: 10.1007/PL00007990