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eegplugin_eye_eeg.m
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eegplugin_eye_eeg.m
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% eegplugin_eye_eeg() - Preprocess, synchronize, artifact-correct,
% and analyze simultaneously recorded eye tracking and EEG data
%
% Description:
% EYE-EEG is an extension for EEGLAB written to facilitate joint analyses
% of eye tracking and electroencephalographic (EEG) data. Among other
% things, it can be used for fixation control, objective eye artifact
% rejection, pupillometry, saccade and fixation detection, control of
% microsaccades, eye tracker-supported ICA component selection, basic
% oculomotor research, or computing fixation-related potentials (FRPs).
%
% EYE-EEG was developed by Olaf Dimigen and Ulrich Reinacher, 2009-2023
%
% >> web: http://www.eyetracking-eeg.org
%
% Copyright (C): Olaf Dimigen with major contributions by Ulrich Reinacher (until 2012)
% Any user feedback is highly welcome! Email: [email protected]
% If you use functions of this toolbox, please cite this reference:
% ------------------------------------------------------------------
% Dimigen, O., Sommer, W., Hohlfeld, A., Jacobs, A., & Kliegl, R. (2011).
% Coregistration of eye movements and EEG in natural reading: Analyses
% & Review, J Exp Psychol: General, Vol. 140 (4), 552-572.
%
% If you use the saccade/fixation detection, please additionally cite:
%
% Engbert, R., & Mergenthaler, K. (2006). Microsaccades are triggered
% by low retinal image slip, PNAS, Vol. 103 (18), 7192-7197
%
% If you select independent components based on the sac/fix variance
% ratio criterion, make sure to also cite:
%
% Plöchl, M., Ossandon, J.P., & König, P. (2012). Combining EEG and
% eye tracking: identification, characterization, and correction of
% eye movement artifacts in electroencephalographic data. Frontiers in
% Human Neuroscience, doi: 10.3389/fnhum.2012.00278
%
%
% Please clarify that you have used the implementation of these methods
% in EYE-EEG, as they may differ from the original versions in some
% regards
%
% If you combined EYE-EEG with deconvolution modeling in "UNFOLD" please
% cite the unfold toolbox paper (Ehinger & Dimigen, 2019, PeerJ) as well
% as the specialized paper by Dimigen & Ehinger, 2021, Journal of Vision
%
% Installation:
% Simply copy the folder called "eye_eegX.XX" containing the toolbox's m-files
% as a subdirectory into the EEGLAB plugin directory and restart EEGLAB.
%
% GUI functions
% ------------------------------------------------------------------
% <a href="matlab:helpwin pop_applytochannels">pop_applytochannels</a> - apply EEGLAB functions to selected channels
% <a href="matlab:helpwin pop_detecteyemovements">pop_detecteyemovements</a> - detect saccades and fixations
% <a href="matlab:helpwin pop_ploteyemovements">pop_ploteyemovements</a> - plot properties of saccades and fixations
% <a href="matlab:helpwin pop_importeyetracker">pop_importeyetracker</a> - import & synchronized eye tracking data
% <a href="matlab:helpwin pop_parseeyelink">pop_parseeyelink</a> - preprocess eye tracking data from SR Research
% <a href="matlab:helpwin pop_parsesmi">pop_parsesmi</a> - preprocess eye tracking data from Sensomot. Instr.
% <a href="matlab:helpwin pop_parsetobii">pop_parsetobii</a> - preprocess eye tracking data from Tobii
% <a href="matlab:helpwin pop_rej_eyecontin">pop_rej_eyecontin</a> - reject cont. data with out-of-range eye track
% <a href="matlab:helpwin pop_rej_eyeepochs">pop_rej_eyeepochs</a> - reject epochs with out-of-range eye track
% <a href="matlab:helpwin pop_checksync">pop_checksync</a> - assess quality of ET/EEG synchronization via cross-correlation
% <a href="matlab:helpwin pop_ploteventrate">pop_ploteventrate</a> - plot rate of saccades or fixations relative to the epoch time-locking event
% <a href="matlab:helpwin pop_overweightevents">pop_overweightevents</a> - create optimized dataset for training the ICA
% <a href="matlab:helpwin pop_eyetrackerica">pop_eyetrackerica</a> - identify ICs that covary with eye tracker
% <a href="matlab:helpwin pop_detecteyemovements">detecteogspikes</a> - estimate saccade onsets based on spikes in the radial EOG
% Non-GUI functions
% ----------------------------------------------------
% <a href="matlab:helpwin addevents">addevents</a> - add many events/urevents to cont. or epoched data
% <a href="matlab:helpwin applytochannels">applytochannels</a> - see pop function
% <a href="matlab:helpwin detecteyemovements">detecteyemovements</a> - see pop function
% <a href="matlab:helpwin detecteyemovements">detecteogspikes</a> - see pop function
% <a href="matlab:helpwin eyetrackerica">eyetrackerica</a> - see pop function
% <a href="matlab:helpwin geticvariance">geticvariance</a> - compute IC variance inside/outside saccades
% <a href="matlab:helpwin parseeyelink">parseeyelink</a> - see pop function
% <a href="matlab:helpwin parsesmi">parsesmi</a> - see pop function
% <a href="matlab:helpwin parsetobii">parsetobii</a> - see pop function
% <a href="matlab:helpwin rej_eyecontin">rej_eyecontin</a> - see pop function
% <a href="matlab:helpwin hist2d">hist2d</a> - 2-dimensional histogram
% <a href="matlab:helpwin cleantrigger">cleantrigger</a> - helper function
% <a href="matlab:helpwin findmatchingevents">findmatchingevents</a> - helper function
% <a href="matlab:helpwin findsequence2">findsequence2</a> - helper function
% <a href="matlab:helpwin ploteyemovements">ploteyemovements</a> - plot properties of saccades & fixations
% <a href="matlab:helpwin synchronize">synchronize</a> - synchronize ET/EEG data
% <a href="matlab:helpwin checksync">checksync</a> - assess quality of ET/EEG synchronization via cross-correlation
% <a href="matlab:helpwin overweightevents">overweightevents</a> - create optimized dataset for training the ICA
% Non-GUI functions for saccade & fixation detection
% ----------------------------------------------------
% <a href="matlab:helpwin vecvel">vecvel</a> - compute eye velocities (*)
% <a href="matlab:helpwin velthresh">velthresh</a> - compute relative velocity-thresholds (*)
% <a href="matlab:helpwin microsacc_plugin">microsacc_plugin</a> - detect (micro)saccades (*)
% <a href="matlab:helpwin binsacc">binsacc</a> - identify binocular saccades (*)
% <a href="matlab:helpwin saccpar">saccpar</a> - compute saccade parameters (*)
% <a href="matlab:helpwin mergesacc">mergesacc</a> - handle temporal saccade clusters
% <a href="matlab:helpwin mergesacc">filtSRP</a> - filter% rEOG (by convolution with SP template) (**)
%
% (*) Copyright: Ralf Engbert et al., University of Potsdam
% http://mbd.psych.uni-potsdam.de/~ralfweb, included with permission
% Notes:
% vecvel() was modified to include different data smoothing options
% velthresh() outsources code that was originally part of microsacc().
% microsacc() was therefore renamed to microsacc_plugin().
%
% (**) function written by Alon Keren, see Keren et al., 2010, NeuroImage
%
% Third-party helper functions
% ----------------------------------------------------
% <a href="matlab:helpwin parseq">parseq</a> - Copyright: R. Kliegl & J. Laubrock, University of Potsdam
% <a href="matlab:helpwin nearestpoint">searchclosest</a> - Copyright: Jos van der Geest, see included license file
%
% Functions that control GUI dialogues
% ----------------------------------------------------
% <a href="matlab:helpwin dlg_applytochannels">dlg_applytochannels</a>
% <a href="matlab:helpwin dlg_calcvisangle">dlg_calcvisangle</a>
% <a href="matlab:helpwin dlg_detecteyemovements">dlg_detecteyenovements</a>
% <a href="matlab:helpwin dlg_eyetrackerica">dlg_eyetrackerica</a>
% <a href="matlab:helpwin dlg_loadeyetracker">dlg_loadeyetracker</a>
% <a href="matlab:helpwin dlg_parser">dlg_parser</a>
% <a href="matlab:helpwin dlg_ploteyemovements">dlg_ploteyemovements</a>
% <a href="matlab:helpwin dlg_rej_eyecontin">dlg_rej_eyecontin</a>
% <a href="matlab:helpwin dlg_rej_eyeepochs">dlg_rej_eyeepochs</a>
% <a href="matlab:helpwin dlg_syncsettings">dlg_syncsettings</a>
% <a href="matlab:helpwin dlg_ploteventrate">dlg_ploteventrate</a>
% <a href="matlab:helpwin dlg_checksync">dlg_checksync</a>
% <a href="matlab:helpwin dlg_detecteogspikes">dlg_detecteogspikes</a>
% ----------------------------------------------------
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
%
% Eyelink (TM) is a trademark of SR Research Ltd., Mississauga, Canada
% SMI (TM) is a trademark of SensoMotoric Instruments GmbH, Germany
% Tobii (TM) is a trademark of Tobii AB, Stockholm, Sweden
function vers = eegplugin_eye_eeg(fig,try_strings,catch_strings)
vers = 'eye_eeg_v1.00';
% add subfolder for dialogues and other helpers
addpath(fullfile(fileparts(which(mfilename)),'internal'));
%% callbacks for menu items
% PARSE EYE TRACKER RAW DATA
cb_parsesmi = [try_strings.no_check, '[ET LASTCOM] = pop_parsesmi; clear ET;', catch_strings.add_to_hist];
cb_parseeyelink = [try_strings.no_check, '[ET LASTCOM] = pop_parseeyelink; clear ET;', catch_strings.add_to_hist];
cb_parsetobii = [try_strings.no_check, '[ET LASTCOM] = pop_parsetobii; clear ET;', catch_strings.add_to_hist];
% IMPORT & SYNCHRONIZE EYE TRACK
cb_importeyetracker = [try_strings.check_cont, '[EEG LASTCOM] = pop_importeyetracker(EEG);', catch_strings.new_and_hist];
%cb_checksync = [try_strings.check_data, '[EEG LASTCOM] = pop_checksync(EEG);', catch_strings.add_to_hist];
% PREPROCESS EYE TRACK
cb_rej_eyeepochs = [try_strings.check_epoch, '[EEG LASTCOM] = pop_rej_eyeepochs(EEG);', catch_strings.new_and_hist];
cb_rej_eyecontin = [try_strings.check_cont, '[EEG LASTCOM] = pop_rej_eyecontin(EEG);', catch_strings.new_and_hist];
% APPLY EEGLAB FUNCTION TO SELECTED CHANNELS ONLY
check4chanlocs = '[EEG LASTCOM] = eeg_checkset(EEG,''chanloc''); if ~isempty(LASTCOM), if LASTCOM(1) == -1, LASTCOM = ''''; return; end; end;';
cb_envelope_f1 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_eegfilt(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f2 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_ERPLAB_butter1(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f3 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_ERPLAB_polydetrend(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f4 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_iirfilt(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f5 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_eegfiltnew(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f6 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_firma(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f7 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_firpm(EEG);'');', catch_strings.new_and_hist];
cb_envelope_f8 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_firws(EEG);'');', catch_strings.new_and_hist];
cb_envelope_2 = [try_strings.check_data, '[EEG tmp LASTCOM] = pop_epoch(EEG); clear tmp;' catch_strings.new_and_hist];
cb_envelope_3 = [try_strings.check_data, '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_rmbase(EEG);'');' catch_strings.new_and_hist];
cb_envelope_4 = [try_strings.check_data, check4chanlocs '[EEG LASTCOM] = pop_applytochannels(EEG,[],''pop_timtopo(EEG);'');' catch_strings.add_to_hist];
% DETECT SACCADES & FIXATIONS
cb_detectem_1 = [try_strings.no_check, '[EEG LASTCOM] = pop_detecteyemovements(EEG);', catch_strings.new_and_hist];
% PLOT SACCADES & FIXATIONS
cb_plotem_1 = [try_strings.no_check, '[EEG LASTCOM] = pop_ploteyemovements(EEG);', catch_strings.add_to_hist];
% PLOT SACCADES & FIXATIONS
cb_plotrate = [try_strings.no_check, '[LASTCOM] = pop_ploteventrate(EEG);', catch_strings.add_to_hist];
% CREATE OPTIMIZED ICA TRAINING DATA (OPTICAT)
% cb_overweight = [try_strings.no_check, '[EEG_overweighted LASTCOM] = pop_overweightevents(EEG);', catch_strings.add_to_hist];
cb_overweight = [try_strings.no_check, 'EEG_overweighted = pop_eegfiltnew(EEG); [EEG_overweighted LASTCOM] = pop_overweightevents(EEG); [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG_overweighted, size(ALLEEG,2),''setname'',''Overweighted training data'',''gui'',''off''); eeglab redraw;', catch_strings.add_to_hist];
% EYETRACKER-SUPPORTED ICA
cb_etICA = [try_strings.check_ica, '[EEG vartable LASTCOM] = pop_eyetrackerica(EEG);', catch_strings.add_to_hist];
% ADVANCED
cb_checksync = [try_strings.check_data, '[EEG LASTCOM] = pop_checksync(EEG);', catch_strings.add_to_hist];
cb_radialeog = [try_strings.check_data, '[EEG LASTCOM] = pop_detecteogspikes(EEG);', catch_strings.add_to_hist];
pause(0.001)
% Note: This pause is due to one of the weirdest bug I have ever tracked.
% If ERPLAB is also in the plugins folder, the menu order gets messed up
% of the main EEGLAB menus (File, ..., ..., Help etc.) causing EYE-EEG's
% EyeTracker menu (created below) to be also in the wrong place. Inserting this
% "pause" solves this issue, possible by forcing a display update (?)
% between addition of the ERPLAB menu and the "Eyetracker" menu
% OD, May 2020
%% create GUI menus
W_MAIN = findobj('tag','EEGLAB');
% "EYETRACKER"
% attempt to make "Eyetracker" the last menu item before "Help"
% (note: menu position may change if more plugins are added, e.g. "ERPLAB")
eyetracker_m = uimenu( W_MAIN, 'Label', 'Eyetracker', 'tag','eyetracker');
try
nitems = get(eyetracker_m,'position');
set(eyetracker_m,'position',nitems-1);
catch
set(eyetracker_m,'position',nitems);
end
% set "Eyetracker" menu to default color for plugin menus
icadefs; % get PLUGINMENUCOLOR
set(eyetracker_m, 'foregroundcolor', PLUGINMENUCOLOR);
% "PARSE EYETRACKER RAW DATA"
parseEyetracker_m = uimenu( eyetracker_m, 'Label', 'Parse eyetracker raw data', 'Separator', 'on');
%uimenu( parseEyetracker_m, 'Label', 'EDF file from Eyelink', 'CallBack', cb_parseeyelink_edf);
uimenu( parseEyetracker_m, 'Label', 'text file from Eyelink', 'CallBack', cb_parseeyelink);
uimenu( parseEyetracker_m, 'Label', 'text file from SMI', 'CallBack', cb_parsesmi);
uimenu( parseEyetracker_m, 'Label', 'text file from Tobii', 'CallBack', cb_parsetobii);
% "IMPORT & SYNCHRONIZE ET"
uimenu( eyetracker_m, 'Label', 'Import & synchronize ET', 'CallBack', cb_importeyetracker, 'Separator', 'off', 'userdata', 'epoch:off; ');
%uimenu(eyetracker_m, 'Label', 'Evaluate synchronization (cross-corr.)', 'CallBack', cb_checksync, 'Separator', 'off', 'userdata', 'startup:off;'); % epoch:off;'
% APPLY FUNCTION TO SELECTED CHANNELS
helpers_m = uimenu( eyetracker_m, 'Label', 'Apply function to selected channels', 'Separator', 'on', 'userdata', 'startup:off;');
filters_m = uimenu( helpers_m, 'Label', 'Filter the data (selected channels)', 'Separator', 'on', 'userdata', 'startup:off;');
uimenu( filters_m, 'Label', 'Basic FIR filter (legacy)', 'CallBack', cb_envelope_f1, 'Separator', 'off', 'userdata', 'startup:off;');
% test whether filter functions from bundled plugins are available
% ...from ERPLAB
if exist('pop_ERPLAB_butter1','file')
uimenu( filters_m, 'Label', 'ERPLAB Butterworth filter' , 'CallBack', cb_envelope_f2, 'Separator', 'on', 'userdata', 'startup:off; ');
end
if exist('pop_ERPLAB_polydetrend','file')
uimenu( filters_m, 'Label', 'ERPLAB Polynomial Detrending', 'CallBack', cb_envelope_f3, 'Separator', 'off', 'userdata', 'startup:off; ');
end
% ...from other plugins (not yet added to EEGLAB path)
eegplugpath = fullfile(fileparts(which('eeglab')),'/plugins');
try
placeHolder = '';
% placeHolder = ' '; % use this if error occurs with exotic MacOS/Unix versions
% folders for IIR and FIR filter plugins
dir_iir = dir([eegplugpath placeHolder '/iirfilt*']);
dir_fir = dir([eegplugpath placeHolder '/firfilt*']);
% iirfilt plugin installed? if so, add menu entry
if ~isempty(dir_iir)
filtName = 'iirfilt.m';
if exist(fullfile(eegplugpath,dir_iir(1).name,filtName),'file')
uimenu( filters_m, 'Label', 'Short non-linear IIR filter', 'CallBack', cb_envelope_f4, 'Separator', 'on', 'userdata', 'startup:off; ');
end
else
%warning('iirfilt plugin not found in plugin folder)')
% #bugfix OD: removed this warning in v0.44, since iirfilt.m is not "shipped" with EEGLAB per default anymore
end
% firfilt plugin installed? if so, add menu entries
if ~isempty(dir_fir)
filtName = { 'pop_eegfiltnew.m' 'pop_firws.m' 'pop_firpm.m' 'pop_firma.m'};
filtMenuLabel = { 'Basic FIR filter (new)', 'Windowed sinc FIR filter' 'Parks-McClellan (equiripple) FIR filter' 'Moving average FIR filter'};
filtMenuCb = { cb_envelope_f5 cb_envelope_f8 cb_envelope_f7 cb_envelope_f6 };
for loop = 1:length(filtName)
if exist(fullfile(eegplugpath,dir_fir(1).name,filtName{loop}),'file')
uimenu( filters_m, 'Label', filtMenuLabel{loop}, 'CallBack', filtMenuCb{loop}, 'Separator', 'off', 'Position' , loop);
end
end
else
warning('firfilt plugin not found in plugin folder')
end
catch dir_error
fprintf('\n%s(): Could not add filter functions to plugin menu. Skipping this step.\n',mfilename)
end
uimenu( helpers_m, 'Label', 'Extract epochs (without baseline removal)', 'CallBack', cb_envelope_2, 'Separator', 'off', 'userdata', 'startup:off;');
uimenu( helpers_m, 'Label', 'Remove baseline (selected channels)' , 'CallBack', cb_envelope_3, 'Separator', 'off', 'userdata', 'startup:off;');
uimenu( helpers_m, 'Label', 'Channel ERPs - with scalp maps' , 'CallBack', cb_envelope_4, 'Separator', 'off', 'userdata', 'startup:off;');
% "REJECT DATA BASED ON ET"
rejectEyetrack_m = uimenu( eyetracker_m, 'Label', 'Reject data based on eye track' , 'Separator', 'on', 'userdata', 'startup:off; ');
uimenu( rejectEyetrack_m, 'Label', 'Reject bad cont. data', 'CallBack', cb_rej_eyecontin, 'Separator', 'off', 'userdata', 'startup:off; epoch:off;');
uimenu( rejectEyetrack_m, 'Label', 'Reject bad epochs', 'CallBack', cb_rej_eyeepochs, 'Separator', 'off', 'userdata', 'startup:off; continuous:off;');
% "DETECT SACCADES & FIXATIONS"
uimenu( eyetracker_m, 'Label', 'Detect saccades & fixations', 'CallBack', cb_detectem_1, 'Separator', 'off', 'userdata', 'startup:off; ');
% "PLOT SACCADES & FIXATIONS"
uimenu( eyetracker_m, 'Label', 'Plot eye movement properties', 'CallBack', cb_plotem_1, 'Separator', 'off', 'userdata', 'startup:off; ');
% "PLOT SACCADES & FIXATIONS"
uimenu( eyetracker_m, 'Label', 'Plot eye movement rate', 'CallBack', cb_plotrate, 'Separator', 'off', 'userdata', 'startup:off; ');
% "REJECT COMPONENTS WITH ET"
uimenu( eyetracker_m, 'Label', 'Create overweighted ICA training data (OPTICAT)', 'CallBack', cb_overweight, 'Separator', 'off', 'userdata', 'startup:off; ');
% "REJECT COMPONENTS WITH ET"
uimenu( eyetracker_m, 'Label', 'Reject components with eyetracker', 'CallBack', cb_etICA, 'Separator', 'off', 'userdata', 'startup:off; ');
% SPECIAL PURPOSE FUNCTIONS
advanced_m = uimenu( eyetracker_m, 'Label', 'Special-purpose functions', 'Separator', 'on', 'userdata', 'startup:off;');
uimenu(advanced_m, 'Label', 'Evaluate ET/EEG synchronization (cross-corr.)', 'CallBack', cb_checksync, 'Separator', 'off', 'userdata', 'startup:off;'); % epoch:off;'
uimenu(advanced_m, 'Label', 'Detect saccade onsets based on (radial) EOG spikes', 'CallBack', cb_radialeog, 'Separator', 'off', 'userdata', 'startup:off;'); % epoch:off;'
% "ABOUT THE TOOLBOX"
uimenu( eyetracker_m, 'Label', 'About this toolbox', 'CallBack', 'pophelp(''eegplugin_eye_eeg.m'');', 'Separator', 'on', 'userdata', 'startup:on;');