![Introduction to MATLAB
• MATLAB stands for Matrix Laboratory
• First of all, it is a calculator. For example, type 5 +
8*5 and press Enter
• A Matrix is an array (series) of data, stored in rows
and columns (2D). For example, type [1:5;6:10] and
press Enter.
• Variable is the way MATLAB stores data in the
working memory (workspace). Press arrow up and
make it A= [1:5;6:10]
Variable A now contains your matrix. Note that
variable ans will be overwritten.
7](https://image.slidesharecdn.com/analysingeegdatausingmatlab-170822205818/85/Analysing-EEG-data-using-MATLAB-7-320.jpg)
![Transpose and Text
• Type E=D’
• Transpose ‘
• T = ‘Text’;
• Price = ‘10CHF’
• randn function makes a vector with normally
distributed random numbers, which are the same on
each Matlab start up.
• X=randn(5)
• Y=[1:2:10]
• Y = [1:2:10;2:3:15]
9](https://image.slidesharecdn.com/analysingeegdatausingmatlab-170822205818/85/Analysing-EEG-data-using-MATLAB-9-320.jpg)
![Final datasets
• When you interpolated bad channels, you can
delete the trials containing artefacts
• In EEGLAB: Edit Select data Epoch range fill in
trials to reject e.g. [1 10] Click remove these and ok
• Save as P5_Final.set
27](https://image.slidesharecdn.com/analysingeegdatausingmatlab-170822205818/85/Analysing-EEG-data-using-MATLAB-27-320.jpg)
Analysing EEG data using MATLAB
- 1. From raw EEG data to ERP Eva A.M. van Poppel, MSc
- 2. Overview •What is EEG? •What is an ERP? •Introduction to MATLAB •Break •From raw EEG data to ERP in EEGLAB 2
- 3. What is EEG? EEG stands for Electro Encephalo Graphy It is the firing of neuronal pyromodal cells, measured by electrodes on the outside of the brain (scalp) in microvolts (µV). 3 Picture by Saint Luke's Health System
- 4. What is EEG? Can we measure the activity of inner brainstructures, like the hippocampus, with EEG? No, we can only measure the outer layer of neurons, the neocortex. To measure deeper brain structures, you need other brain imaging techniques, like MRI. But compared to MRI, EEG has a better timing. 4 Picture by Saint Luke's Health System
- 5. Frequencies
- 6. What is an ERP? ERP stands for Event Related Potential. It is the evoked brain response after a stimulus. The start of the stimulus is normally at time point 0 ms. 6
- 7. Introduction to MATLAB • MATLAB stands for Matrix Laboratory • First of all, it is a calculator. For example, type 5 + 8*5 and press Enter • A Matrix is an array (series) of data, stored in rows and columns (2D). For example, type [1:5;6:10] and press Enter. • Variable is the way MATLAB stores data in the working memory (workspace). Press arrow up and make it A= [1:5;6:10] Variable A now contains your matrix. Note that variable ans will be overwritten. 7
- 8. • Now, we want to know what is in row 2, column 3 of Variable A. We type: A(2,3) and press Enter • What happens when you forget one of the dimensions (row or column) and type A(4)? • Type B=4 (Enter) C=5 (Enter). Type B+C (Enter) • Sometimes, you don’t want to see all internal calculations (for example when you load in a complete EEG data set). In this case, you should use the semicolon ; • Type D=ones(1,10); • How does D look like? What happens when you make D=ones(10,1) ? • This is called a vector, which is just one row or column containing data (1D) 8
- 9. Transpose and Text • Type E=D’ • Transpose ‘ • T = ‘Text’; • Price = ‘10CHF’ • randn function makes a vector with normally distributed random numbers, which are the same on each Matlab start up. • X=randn(5) • Y=[1:2:10] • Y = [1:2:10;2:3:15] 9
- 10. Loops • Press the button «New script» in the left upper corner. • Type: for i = 1:length(Y) F(i) = Y(1,i)+1; end • What did you do? How does F look? 10
- 11. FOR & IF Loop for j = 1:length(Y) if F(j) > Y(1,j) G(j) = Y(1,j) end end 11
- 12. MATLAB tricks • Don’t show calculations ; • Transpose ‘ • Text ‘’ • Comments % • Paragraph %% • Run full script F5 • Ctrl + C abort run • Compare scripts • Clear G; Clear all 12
- 13. Break 13
- 14. EEGLAB • Download on https://sccn.ucsd.edu/eeglab/downloadtoolbox.php • Extract for example in Documents • Click Set Path in Matlab Add folder eeglab • Save the path, but don’t save this on a shared server e.g. Rekenbeest • Type eeglab in the command window and press Enter 14
- 16. Import data • Go to File Manage EEGLAB extensions Data processing extensions • Choose the amplifier / EEG data recording software you use and install • Go to File Import data Using EEGLAB functions and plugins and choose your data type 16
- 17. Names Edit Channel locations. Use a template with XYZ coordinates and channel names for the EEG cap you used. 17
- 18. Reference • The ERP value at electrode X is the value of electrode X with respect to the location of the reference electrode. 18 • Therefore, we re-reference the recorded data to the average of the mastoid electrodes behind the ears.
- 19. Re-reference • In EEGLAB, click Tools Re-reference Re- reference data to channel(s): M1 M2 • Exclude channels containing non-EEG data, like EMG, EOG or trigger channels. • Add current reference channel back to the data when you want to restore the data of the physical reference electrode. You cannot use this when you recorded with average reference (TMSi & ANT). 19
- 20. Filter • A high-pass filter passes signals with a frequency higher than a certain cutoff frequency. For EEG data, you should use a high-pass filter of at least 0.1 Hz to remove the lower drift noise. • A low-pass filter passes signals with a frequency lower than a certain cutoff frequency. For ERP analysis, we typically use a low-pass band from 35 Hz. • A filter shifts the signal. Therefore, we first run a high-pass filter, and afterwards run the low-pass filter to shift it back. 20
- 21. Filter • A filter never cuts off at the given band exactly. • The slope is dependent of the filter order. • EEGLAB uses a basic FIR filter as a default (Finite Impulse Response) • The line noise (electricity network in Europe) is at 50 Hz. You need a notch filter of at least 48-52Hz to filter this out. 21
- 22. Filter • Because of filter artifacts at the end and beginning of the data, it is important you filter the data before epoching (cutting) • In EEGLAB, Tools Filter the data Basic FIR filt Lower edge of the frequency pass band 0.1 Hz • In EEGLAB, Tools Filter the data Basic FIR filt Higher edge of the frequency pass band 35 Hz 22
- 23. Epoch • Now, we want to aline our data, to make sure all trials start at 0 ms at the start of the stimulus. Therefore we “cut” our data -1000 ms before the stimulus and lasting 2500 ms after. • In EEGLAB, Tools Extract epochs Epoch limits in seconds -1 2.5 23
- 24. Baseline correction • Baseline correction is the procedure of relativizing the brain signal of interest (evoked response) with respect to a control (baseline) signal • In wake data, you normally use -200 to 0 ms before the stimulus onset as the baseline • In (deep) sleep data, we use -1000 to 0 ms as the baseline • EEGLAB automatically asks for the baseline period in ms after the epoch settings 24
- 25. Artefact rejection • Plot Channel data scroll • Settings Time range to display 1 Epoch • In wake data, EEG values > 75µV are considered artefacts and those trials are marked for rejection. In (deep) sleep data, this rule does not apply • Mark trials containing movements and artefacts for rejection, write the trial number in an Excel • You need at least 25 correct trials per subject for a nice ERP without noise • Normally, 5 -10% of trials contain artefacts 25
- 26. Interpolation • Some channels are noisy. In this case, we don’t reject the whole trial, but interpolate the channel affected • Interpolation is an artificial reconstruction of the channel, using the data of the surrounding channels • Run the script Eva_Interpolation.m to interpolate certain channels per trial • When you want to interpolate a bad channel in all trials, you have to do this before the epoching using Tools Interpolate electrodes 26
- 27. Final datasets • When you interpolated bad channels, you can delete the trials containing artefacts • In EEGLAB: Edit Select data Epoch range fill in trials to reject e.g. [1 10] Click remove these and ok • Save as P5_Final.set 27
- 28. Create ERP • File Create study Simple ERP study • Load in all final datasets • One row means the same subject, so two files on the same row means a within subject design, where each subject on a seperate row means a between subject design 28
- 29. ERP Statistics • Download the Fieldtrip toolbox and save it in your path • Or go to File Manage EEGLAB extensions Data processing extensions Fieldtrip-lite • Choose the “Montecarlo/Permutation based” statistics with “Cluster correction (CC)” 29
- 30. Sources Discovering Statistics Using SPSS, Andy Field, 3rd edition, 2009, SAGE Publications Ltd. Discovering Statistics Using R, Andy Field, 1st edition, 2012, SAGE Publications Ltd. https://ch.mathworks.com/help/matlab/matlab_prog/loop- control-statements.html https://sccn.ucsd.edu/eeglab/downloadtoolbox.php http://www.fieldtriptoolbox.org/download
Editor's Notes
- #8: vector is just one row or column containing data (1D). A Variable is capital sensitive and can contain multiple characters. MATLAB license problem? Make sure you’re connected to the Unifr network via secure-uni WLAN or the Cisco VPN.
- #16: The ground is used for common mode rejection. The primary purpose of the ground is to prevent power line noise from interfering with the small biopotential signals of interest. By design, amplifiers should not be affected by large changes in potential at both the active and reference sites. A ground electrode for EEG recordings is often placed on the forehead (but could be placed anywhere else on the body; the location of the ground on the subject is generally irrelevant). https://www.biopac.com/knowledge-base/ground-vs-reference-for-eeg-recording/
- #17: The ground is used for common mode rejection. The primary purpose of the ground is to prevent power line noise from interfering with the small biopotential signals of interest. By design, amplifiers should not be affected by large changes in potential at both the active and reference sites. A ground electrode for EEG recordings is often placed on the forehead (but could be placed anywhere else on the body; the location of the ground on the subject is generally irrelevant). https://www.biopac.com/knowledge-base/ground-vs-reference-for-eeg-recording/
- #18: The ground is used for common mode rejection. The primary purpose of the ground is to prevent power line noise from interfering with the small biopotential signals of interest. By design, amplifiers should not be affected by large changes in potential at both the active and reference sites. A ground electrode for EEG recordings is often placed on the forehead (but could be placed anywhere else on the body; the location of the ground on the subject is generally irrelevant). https://www.biopac.com/knowledge-base/ground-vs-reference-for-eeg-recording/
- #19: The ground is used for common mode rejection. The primary purpose of the ground is to prevent power line noise from interfering with the small biopotential signals of interest. By design, amplifiers should not be affected by large changes in potential at both the active and reference sites. A ground electrode for EEG recordings is often placed on the forehead (but could be placed anywhere else on the body; the location of the ground on the subject is generally irrelevant). https://www.biopac.com/knowledge-base/ground-vs-reference-for-eeg-recording/
- #20: The ground is used for common mode rejection. The primary purpose of the ground is to prevent power line noise from interfering with the small biopotential signals of interest. By design, amplifiers should not be affected by large changes in potential at both the active and reference sites. A ground electrode for EEG recordings is often placed on the forehead (but could be placed anywhere else on the body; the location of the ground on the subject is generally irrelevant). https://www.biopac.com/knowledge-base/ground-vs-reference-for-eeg-recording/