Learning EEG

Chang Liu February 28, 2024 March 09, 2024

EEG Tutorial

Where do we start: EEGLAB Tutorial
A clean/resting state human EEG dataset to test your rejection: R:\Ferris-Lab\liu.chang1\DATA\SampleData\2019-12-19_humanExampleData\Raw
Downey et al. 2023: iCanClean to remove motion artifacts with the dual-layer electrode design Paper on iCanClean

Overall flowchart

Some useful code blocks

High-pass filter at 1Hz

EEG = pop_eegfiltnew(EEG, 'locutoff',1,'chantype',{'EEG' 'EMG' 'Noise'});

Keep only a subset of chans

EEG_chans = find(strcmpi('EEG',{EEG.chanlocs.type})); %define channels
EMG_chans = find(strcmpi('EMG',{EEG.chanlocs.type}));
Noise_chans = find(strcmpi('Noise',{EEG.chanlocs.type}));

EEG = pop_select( EEG, 'channel', sort([EEG_chans, EMG_chans,Noise_chans])); %select subset of channels
EEG = pop_select( EEG, 'channel', sort([EEG_chans])); %select just EEG channels

%update channel labels again just in case
EEG_chans = find(strcmpi('EEG',{EEG.chanlocs.type})); 
EMG_chans = find(strcmpi('EMG',{EEG.chanlocs.type}));
Noise_chans = find(strcmpi('Noise',{EEG.chanlocs.type}));

Re-reference and do cleanline

EEG = rerefC2CN2NExt2Ext_func(EEG,fullRankAvRefBool);
EEG = pop_cleanline(EEG, 'bandwidth',2,'chanlist',[EEG_chans EMG_chans Noise_chans],'computepower',1,...
    'linefreqs',[60 120],'newversion',0,'normSpectrum',0,'p',0.01,'pad',2,'plotfigures',...
0,'scanforlines',1,'sigtype','Channels','taperbandwidth',2,'tau',100,'verb',1,'winsize',4,'winstep',1);

Useful preprocessing code block

Please send me an email to request access to the example code Example code

Step 1: Remove bad channels based on standard deviation and kurtosis:

EEG = autoRejCh_func_CL(EEG,threshold);

Step 2: Perform average re-reference of EEG, EMG, and Noice channels

fullRankAvRefBool = false;
EEG = rerefC2CN2NExt2Ext_func(EEG,fullRankAvRefBool);

Optional Step: Remove motion artifact with iCanClean

[EEG] = iCanClean(EEG,[EEG_chans], [Noise_chans], 0, params);

Optional Step: Remove muscle artifact with iCanClean

[EEG] = iCanClean(EEG,[EEG_chans], [EMG_chans], 0, params);

Optional Step: Use EEGLAB’s channel rejection/time rejection method with parameters

[EEG_clean,EEG_clean_timerej,p_frames_rej,p_chan_rej] = channelrejection_wrap(EEG,config);