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EEG_Processing_Gorka_LST.m
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% EEG Processing Script for Gorka lab, James Glazer 3/7/23: glazerja1@gmail.com
%
% Processing Steps Simplified:
% 1. Load raw BDf, save raw .set/.fdt datset.
% 2. Resample, re-reference, filter.
% 3. Remove/interpolate bad channels (save _removedchans and _interp .set/.fdt datasets).
% 4. Create eventlist, binlister, segment/epoch w/baseline correction.
% 5. Ocular Correct, artifact reject, calculate average ERPs.
% 6. Save "completed" .set/.fdt dataset and .erp averaged erpset.
%
% How to use:
% 1. Place all raw BDF files in same folder and enter this path/location.
% 2. Put the name of each file in subName list.
% 3. Create empty folders where the data will go and enter their path/location in the script.
% Recommended folder structure:
% GorkaData\RawBDF\ .bdf raw files for all subjects
% GorkaData\Datasets\Raw: .set/.fdt datasets saved immediately after loading .bdf (raw data)
% GorkaData\Datasets\Processing: .set/.fdt datasets saved at intermediate processing steps (saved after important processing steps)
% GorkaData\Datasets\Completed: .set/.fdt datasets saved after completed preprocessing (ready for erp averaging)
% GorkaData\EventLists\Raw: .txt raw eventlists saved containing all trial/event code information
% GorkaData\EventLists\Processed: .txt processed eventlists saved containing all artifact/bin information
% GorkaData\Binlister\GorkaBinlister.txt: .txt file containing binlister information for epoching/segmenting/averaging
% GorkaData\Erpsets: .erp final fully processed erpset files ready for ERP plotting, data exporting, and grand averaging
% 4. Click "Run".
%
% Processing Steps Summary:
% Steps 1-4: Load raw BDF, edit/save .set/.fdt dataset, resample.
% Steps 5-7: Remove unused/double channels, re-reference, create VEOG/HEOG channels and remove VEO+/VEO-/HEOR/HEOL
% Steps 8-10: Filter and save .set/.fdt dataset with full channel information
% Steps 11-14: Remove VEOG/HEOG, detect bad channels, reload dataset above with full channels, remove bad channels, save dataset, interpolate removed channels
% Steps 15-19: Create eventlist/load binlist, epoch/segment (w/baseline correct), ocular correct, remove VEOG/HEOG
% Steps 20-23: Artifact detect/reject, export eventlist with artifact information, get channel locations, save fully processed dataset
% Steps 24-25: Compute average erps and save final .erp files ready for ERP plotting, data exporting, and grand averaging
%
% Processing Steps Detailed:
% 1. Load the raw .BDF file
% 2. Edit dataset name and save raw .set/.fdt file
% 3. Resample data PROPERLY, For SIFT to ease antialiasing filter slope, see code from Makoto:
% 4. Load channel locations from channelLocationFile
% 5. Channel Operations: Remove unused/double electrodes, reorder remaining channels: New Channel list: 0-34 = scalp, 35-38 = EOGs, 39-40 = Mastoids
% 5a. Remove following electrodes: ST1/ST2/EKG1/EKG2/PA1/PA2 (channels 33-38) and GSR1/GSR2/ERG1/ERG2/RESP/PLET/TEMP (channels 55-61)
% 5b. Remove double electrodes: VEO+/VEO-/HEOR/HEOL/M1/M2/FCz/Iz (channels 47-54)
% 5c. Move FCz/Iz to channels 33-34, Move external sensors (M1/M2/VEO+/VEO-/HEOR/HEOL) to end of channel list 35-40
% 6. Re-reference to average of mastoids (channels 39/40), remove M1/M2
% 7. Create VEOG & HEOG difference for Gratton & Coles Ocular Correction Regression performed later, remove VEO+/VEO-/HEOR/HEOL
% 8. Filter the Data: IIR Butterworth bandpass 0.1 to 30 Hz
% 9. Reload channel locations
% 10. Edit dataset name and save preprocessed .set/.fdt file with FULL channel information BEFORE removing channels
% 11. Automatic bad channel detection/rejection using clean_rawdata
% 11a. First remove VEOG/HEOG BEFORE bad channel detection/removal: Final Channel list: 0-34 = SCALP chans
% 11b. Reload channel locations
% 11c. Automatically detect and remove bad SCALP chans using clean_rawdata default parameters
% 11d. Get list of full remaining "good" SCALP EEG channels
% 11e. Add VEOG/HEOG to trimChans list because these are "good" by default as we don't want to remove them
% 12. Remove bad channels, keep VEOG/HEOG for ocular correction later
% 12a: Reload dataset recently saved BEFORE removing bad channels that still has VEOG/HEOG
% 12b. Save original channels for all scalp electrodes, used to interpolate bad electrodes later
% 12c. get list of channels before channel rejection
% 12d. get list of bad/rejected channels by finding the difference between allChans and trimChans lists
% 12f. Actually remove the bad channels using badChansList
% 13. Edit dataset name and save preprocessed .set/.fdt file AFTER removing channels
% 14. Interpolate bad channels
% 15. Create & Save EventLists
% 16. Separate the trials into Bins by loading your BinLister file
% 17. Epoch the Data: Window and Baseline
% 18. Blink correction using Gratton & Coles ocular correction
% 19. Remove VEOG/HEOG after Ocular Correction: Final Channel list: 0-34 = scalp, Reload channel locations
% 20. Automatically detect & reject trials/epochs for each event code in each bin
% 20a. Artifact Rejection: ERPLAB Moving Window: Remove epochs exceeding voltage threshold as a moving window with a total amplitude, window size, and window step
% 20b. Artifact Rejection: ERPLAB Sample-to-Sample: Remove epochs exceeding voltage threshold between two sampling points
% 20c. Artifact Rejection: ERPLAB Flatline: Remove epochs with flatlined data lower than voltage threshold
% 21. Export EventList containing bin/artifact information
% 22. Look up channel locations again
% 23. Edit dataset name and save fully processed .set/.fdt file that is ready for averaging into erpset .erp file
% 24. Compuate average ERPs using erplab to create .erp file
% 25. Save the erpset .erp file
% ===== Manually enter the path location on your machine for the following folders =====
clear all; close all; clc;
% path containing raw .BDF files to load
raw_bdf_loadpath = 'C:\Users\glaze\Desktop\GorkaScripts\data\RawBDF\';
% path to save raw datasets as .set/.fdt eeglab format
raw_dataset_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\datasets\Raw\';
% path to save .set/.fdt datasets at intermediate processing steps: optional but strongly recommended
% example 1: datasets saved after bad channel rejection can be used to determine which channels were removed and interpolated
% example 2: datasets saved after artifact rejection can be used to determine which and how many epochs/trials/conditions were rejected
% Note: This is required to use SummaryScript.m to save details on bad channels/artifact rejection results
ongoing_dataset_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\datasets\Processing\';
% path to save fully processed .set/.fdt files before ERP averaging
processed_dataset_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\datasets\Completed\';
% path to save erpsets in erplab .erp format
erpset_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\Erpsets\';
% save raw and processed eventlist path:
raw_eventlist_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\EventLists\Raw\';
processed_eventlist_savepath = 'C:\Users\glaze\Desktop\GorkaScripts\data\EventLists\Processed\';
% binlister path: see https://github.com/lucklab/erplab/blob/master/pop_functions/pop_binlister.m
binlister_loadpath = 'C:\Users\glaze\Desktop\GorkaScripts\data\Binlister\LST_BinLister.txt';
% channelLocationFile: this path is found in your eeglab dipfit plugin folder: eeglab\plugins\dipfit\standard_BESA\standard-10-5-cap385.elp
channelLocationFile = 'C:\Users\glaze\Documents\MatLabPrograms\eeglab2020_0\plugins\dipfit\standard_BESA\standard-10-5-cap385.elp';
% Enter subject IDs here
subName = {'Subject001_LST', 'Subject002_LST','Subject003_LST'};
% load EEGlab
[ALLEEG EEG CURRENTSET ALLCOM] = eeglab;
% load ERPlab
ALLERP = buildERPstruct([]);
CURRENTERP = 0;
% Process data
for iSubject = 1:length(subName)
% ===== Steps 1-4: Load raw BDF, edit/save .set/.fdt dataset, resample =====
% 1. Load the raw .BDF file
EEG = pop_biosig([raw_bdf_loadpath subName{iSubject} '.bdf']);
% 2. Edit dataset name and save raw .set/.fdt file
EEG = pop_editset(EEG, 'setname', [subName{iSubject} '_Raw']);
EEG = pop_saveset(EEG, 'filename',[subName{iSubject} '_Raw.set'], 'filepath', raw_dataset_savepath);
% 3. Resample data PROPERLY, For SIFT to ease antialiasing filter slope, see code from Makoto:
% https://sccn.ucsd.edu/wiki/Makoto%27s_useful_EEGLAB_code
% https://eeglab.org/others/Firfilt_FAQ.html#Q._For_Granger_Causality_analysis.2C_what_filter_should_be_used.3F_.2804.2F26.2F2018_Updated.29
EEG = pop_resample(EEG, 256, 0.8, 0.4); % BioSemi
% 4. Load channel locations from channelLocationFile
EEG = pop_chanedit(EEG, 'lookup', channelLocationFile);
eeglab redraw;
% ===== Steps 5-7: Remove unused/double channels, re-reference, create VEOG/HEOG channels and remove VEO+/VEO-/HEOR/HEOL =====
% 5. Channel Operations: Remove unused/double electrodes, reorder remaining channels: New Channel list: 0-34 = scalp, 35-38 = EOGs, 39-40 = Mastoids
% 5a. Remove following electrodes: ST1/ST2/EKG1/EKG2/PA1/PA2 (channels 33-38) and GSR1/GSR2/ERG1/ERG2/RESP/PLET/TEMP (channels 55-61)
% 5b. Remove double electrodes: VEO+/VEO-/HEOR/HEOL/M1/M2/FCz/Iz (channels 47-54)
% 5c. Move FCz/Iz to channels 33-34, Move external sensors (M1/M2/VEO+/VEO-/HEOR/HEOL) to end of channel list 35-40
%
% WARNING: if data channels differ you will need to edit this section to match
% Note: to recreate this code using different channels, use erplab -> EEG channel operations
% -> click "Clear Equations" -> check "Create new dataset" -> click reference assistant
% -> enter 0 into "Ch_REF = ", check "Copy original label to new label"
% -> check "If a channel is not being re-referenced, include an equation for simply copying the channel (recommended for independent transformations)"
% -> check "All Channels" -> click "ok", channel equations will appear in the white box
% Now you can edit the equations so that they match the locations below, then -> click "Run"
% After it runs, type "EEG.history" into the command line to get your code (note: you can delete the " - ( 0 )")
EEG = pop_eegchanoperator(EEG, {...
'nch1 = ch1 Label Fp1', 'nch2 = ch2 Label AF3', 'nch3 = ch3 Label F7', 'nch4 = ch4 Label F3', 'nch5 = ch5 Label FC1',...
'nch6 = ch6 Label FC5', 'nch7 = ch7 Label T7', 'nch8 = ch8 Label C3', 'nch9 = ch9 Label CP1', 'nch10 = ch10 Label CP5',...
'nch11 = ch11 Label P7', 'nch12 = ch12 Label P3', 'nch13 = ch13 Label Pz', 'nch14 = ch14 Label PO3', 'nch15 = ch15 Label O1',...
'nch16 = ch16 Label Oz', 'nch17 = ch17 Label O2', 'nch18 = ch18 Label PO4', 'nch19 = ch19 Label P4', 'nch20 = ch20 Label P8',...
'nch21 = ch21 Label CP6', 'nch22 = ch22 Label CP2', 'nch23 = ch23 Label C4', 'nch24 = ch24 Label T8', 'nch25 = ch25 Label FC6',...
'nch26 = ch26 Label FC2', 'nch27 = ch27 Label F4', 'nch28 = ch28 Label F8', 'nch29 = ch29 Label AF4', 'nch30 = ch30 Label Fp2',...
'nch31 = ch31 Label Fz', 'nch32 = ch32 Label Cz', 'nch33 = ch45 Label FCz', 'nch34 = ch46 Label Iz', 'nch35 = ch39 Label VEO+',...
'nch36 = ch40 Label VEO-', 'nch37 = ch41 Label HEOR', 'nch38 = ch42 Label HEOL', 'nch39 = ch43 Label M1', 'nch40 = ch44 Label M2'},...
'ErrorMsg', 'popup', 'Warning', 'off' );
% 6. Re-reference to average of mastoids (channels 39/40), remove M1/M2
% Note: to recreate this code using different channels, follow the steps above for Channel Operations but enter ((ch39 + ch40)/2) into "Ch_REF = "
% -> then remove the last two lines ('nch39 = nch39 - ((ch39 + ch40)/2) Label M1', 'nch40 = ch40 - ((ch39 + ch40)/2) Label M2')
% -> then click "Run" and afterwards type "EEG.history" into the command line to get your code
EEG = pop_eegchanoperator(EEG, {...
'nch1 = ch1 - ((ch39 + ch40)/2) Label Fp1', 'nch2 = ch2 - ((ch39 + ch40)/2) Label AF3', 'nch3 = ch3 - ((ch39 + ch40)/2) Label F7',...
'nch4 = ch4 - ((ch39 + ch40)/2) Label F3', 'nch5 = ch5 - ((ch39 + ch40)/2) Label FC1', 'nch6 = ch6 - ((ch39 + ch40)/2) Label FC5',...
'nch7 = ch7 - ((ch39 + ch40)/2) Label T7', 'nch8 = ch8 - ((ch39 + ch40)/2) Label C3', 'nch9 = ch9 - ((ch39 + ch40)/2) Label CP1',...
'nch10 = ch10 - ((ch39 + ch40)/2) Label CP5', 'nch11 = ch11 - ((ch39 + ch40)/2) Label P7', 'nch12 = ch12 - ((ch39 + ch40)/2) Label P3',...
'nch13 = ch13 - ((ch39 + ch40)/2) Label Pz', 'nch14 = ch14 - ((ch39 + ch40)/2) Label PO3', 'nch15 = ch15 - ((ch39 + ch40)/2) Label O1',...
'nch16 = ch16 - ((ch39 + ch40)/2) Label Oz', 'nch17 = ch17 - ((ch39 + ch40)/2) Label O2', 'nch18 = ch18 - ((ch39 + ch40)/2) Label PO4',...
'nch19 = ch19 - ((ch39 + ch40)/2) Label P4', 'nch20 = ch20 - ((ch39 + ch40)/2) Label P8', 'nch21 = ch21 - ((ch39 + ch40)/2) Label CP6',...
'nch22 = ch22 - ((ch39 + ch40)/2) Label CP2', 'nch23 = ch23 - ((ch39 + ch40)/2) Label C4', 'nch24 = ch24 - ((ch39 + ch40)/2) Label T8',...
'nch25 = ch25 - ((ch39 + ch40)/2) Label FC6', 'nch26 = ch26 - ((ch39 + ch40)/2) Label FC2', 'nch27 = ch27 - ((ch39 + ch40)/2) Label F4',...
'nch28 = ch28 - ((ch39 + ch40)/2) Label F8', 'nch29 = ch29 - ((ch39 + ch40)/2) Label AF4', 'nch30 = ch30 - ((ch39 + ch40)/2) Label Fp2',...
'nch31 = ch31 - ((ch39 + ch40)/2) Label Fz', 'nch32 = ch32 - ((ch39 + ch40)/2) Label Cz', 'nch33 = ch33 - ((ch39 + ch40)/2) Label FCz',...
'nch34 = ch34 - ((ch39 + ch40)/2) Label Iz', 'nch35 = ch35 - ((ch39 + ch40)/2) Label VEO+', 'nch36 = ch36 - ((ch39 + ch40)/2) Label VEO-',...
'nch37 = ch37 - ((ch39 + ch40)/2) Label HEOR', 'nch38 = ch38 - ((ch39 + ch40)/2) Label HEOL'}, 'ErrorMsg', 'popup', 'Warning', 'off' );
% 7. Create VEOG & HEOG difference for Gratton & Coles Ocular Correction Regression performed later, remove VEO+/VEO-/HEOR/HEOL
% To recreate using different channels, follow identical steps above for Channel Operations, Once the equations are created in the white box:
% Delete the last four lines (nch35 = ch35 Label VEO+, nch36 = ch36, Label VEO-, nch37 = ch37 Label HEOR, nch38 = ch38 Label HEOL)
% Add the following two lines:
% nch35 = ch35-ch36 Label VEOG
% nch36 = ch37-ch38 Label HEOG
% Click "Run", type EEG.history afterwards to get code
EEG = pop_eegchanoperator(EEG, {...
'nch1 = ch1 Label Fp1', 'nch2 = ch2 Label AF3', 'nch3 = ch3 Label F7', 'nch4 = ch4 Label F3',...
'nch5 = ch5 Label FC1', 'nch6 = ch6 Label FC5', 'nch7 = ch7 Label T7', 'nch8 = ch8 Label C3',...
'nch9 = ch9 Label CP1', 'nch10 = ch10 Label CP5', 'nch11 = ch11 Label P7', 'nch12 = ch12 Label P3',...
'nch13 = ch13 Label Pz', 'nch14 = ch14 Label PO3', 'nch15 = ch15 Label O1', 'nch16 = ch16 Label Oz',...
'nch17 = ch17 Label O2', 'nch18 = ch18 Label PO4', 'nch19 = ch19 Label P4', 'nch20 = ch20 Label P8',...
'nch21 = ch21 Label CP6', 'nch22 = ch22 Label CP2', 'nch23 = ch23 Label C4', 'nch24 = ch24 Label T8',...
'nch25 = ch25 Label FC6', 'nch26 = ch26 Label FC2', 'nch27 = ch27 Label F4', 'nch28 = ch28 Label F8',...
'nch29 = ch29 Label AF4', 'nch30 = ch30 Label Fp2', 'nch31 = ch31 Label Fz', 'nch32 = ch32 Label Cz',...
'nch33 = ch33 Label FCz', 'nch34 = ch34 Label Iz', 'nch35 = ch35-ch36 Label VEOG', 'nch36 = ch37-ch38 Label HEOG'},...
'ErrorMsg', 'popup', 'Warning', 'off' );
% ===== Steps 8-10: Filter and save .set/.fdt dataset with full channel information =====
% 8. Filter the Data: IIR Butterworth bandpass 0.1 to 30 Hz
EEG = pop_basicfilter(EEG, 1:EEG.nbchan,...
'Boundary', 'boundary',... % Boundary events
'Cutoff', [ 0.1 30],... % High and low cutoff
'Design', 'butter',... % IIR Butterworth filter
'Filter', 'bandpass',... % Bandpass filter type
'Order', 2,... % Filter order
'RemoveDC', 'on' ); % Remove DC offset
% 9. Reload channel locations
EEG = pop_chanedit(EEG, 'lookup',channelLocationFile);
eeglab redraw;
% 10. Edit dataset name and save preprocessed .set/.fdt file with FULL channel information BEFORE removing channels
EEG = pop_editset(EEG, 'setname', [subName{iSubject} '_ChopResampFilt']);
EEG = pop_saveset(EEG, 'filename',[subName{iSubject} '_ChopResampFilt.set'], 'filepath', ongoing_dataset_savepath);
% ===== Steps 11-14: remove VEOG/HEOG, detect bad channels, reload dataset above with full channels, remove bad channels, save dataset, interpolate removed channels =====
% 11. Automatic bad channel detection/rejection using clean_rawdata
% 11a. First remove VEOG/HEOG BEFORE bad channel detection/removal: Final Channel list: 0-34 = SCALP chans
EEG = pop_select(EEG, 'nochannel',{'VEOG','HEOG'});
% 11b. Reload channel locations
EEG = pop_chanedit(EEG, 'lookup',channelLocationFile);
eeglab redraw;
% 11c. Automatically detect and remove bad SCALP chans using clean_rawdata default parameters
EEG = pop_clean_rawdata(EEG,...
'FlatlineCriterion', 5,... % Maximum tolerated flatline duration in seconds (Default: 5)
'ChannelCriterion', 0.85,... % Minimum channel correlation with neighboring channels (default: 0.85)
'LineNoiseCriterion', 4,... % Maximum line noise relative to signal in standard deviations (default: 4)
'Highpass','off','BurstCriterion','off','WindowCriterion','off','BurstRejection','off','Distance','Euclidian');
eeglab redraw;
% 11d. Get list of full remaining "good" SCALP EEG channels
trimChans = {};
for channel = 1:EEG.nbchan
trimChans{end+1} = EEG.chanlocs(channel).labels;
end
% 11e. Add VEOG/HEOG to trimChans list because these are "good" by default as we don't want to remove them
trimChans{end+1} = 'VEOG';
trimChans{end+1} = 'HEOG';
% 12. Remove bad channels, keep VEOG/HEOG for ocular correction later
% 12a: Reload dataset recently saved BEFORE removing bad channels that still has VEOG/HEOG
EEG = pop_loadset('filename',[subName{iSubject} '_ChopResampFilt.set'], 'filepath', ongoing_dataset_savepath);
% 12b. Save original channels for all scalp electrodes, used to interpolate bad electrodes later
originalEEG = EEG;
% 12c. get list of channels before channel rejection
allChans = {};
for channel = 1:EEG.nbchan
allChans{end+1} = EEG.chanlocs(channel).labels;
end
% 12d. get list of bad/rejected channels by finding the difference between allChans and trimChans lists
badChansList = {};
for channel = 1:length(allChans)
badChan = strcmp(trimChans, allChans(channel));
if sum(badChan) == 0
badChansList{end+1} = allChans{channel};
end
end
eeglab redraw;
% 12f. Actually remove the bad channels using badChansList
for channel = 1:length(badChansList)
EEG = pop_select(EEG, 'nochannel',{badChansList{channel}});
end
eeglab redraw;
% 13. Edit dataset name and save preprocessed .set/.fdt file AFTER removing channels
EEG = pop_editset(EEG, 'setname', [subName{iSubject} '_ChopResampFilt_removedchans']);
EEG = pop_saveset(EEG, 'filename',[subName{iSubject} '_ChopResampFilt_removedchans.set'], 'filepath', ongoing_dataset_savepath);
% 14. Interpolate bad channels, resave dataset
EEG = pop_interp(EEG, originalEEG.chanlocs, 'spherical');
eeglab redraw;
EEG = pop_chanedit(EEG, 'lookup',channelLocationFile);
eeglab redraw;
EEG = pop_editset(EEG, 'setname', [subName{iSubject} '_ChopResampFilt_Interp']);
EEG = pop_saveset(EEG, 'filename',[subName{iSubject} '_ChopResampFilt_Interp.set'], 'filepath', ongoing_dataset_savepath);
eeglab redraw;
% ===== Steps 15-19: create eventlist/load binlist, epoch/segment (w/baseline correct), ocular correct, remove VEOG/HEOG =====
% 15. Create & Save EventLists
% See: https://jennifervendemia.files.wordpress.com/2013/03/very-simple-notes-on-event-lists-file-formats-in-erplab.pdf
EEG = pop_creabasiceventlist(EEG,...
'AlphanumericCleaning', 'on',... % Replace Letters with Numbers
'BoundaryNumeric', { -99 },... % Boundary event marker
'BoundaryString', { 'boundary' },... % Boundary string marker
'Eventlist', [raw_eventlist_savepath 'Raw_EventList_' subName{iSubject} '.txt']);
% 16. Separate the trials into Bins by loading your BinLister file
% See: https://socialsci.libretexts.org/Bookshelves/Psychology/Book%3A_Applied_Event-Related_Potential_Data_Analysis_(Luck)/02%3A_Processing_the_Data_from_One_Participant_in_the_ERP_CORE_N400_Experiment/2.06%3A_Exercise-_Assigning_Events_to_Bins_with_BINLISTER
EEG = pop_binlister(EEG ,...
'BDF', binlister_loadpath,...
'IndexEL', 1,... % Event List Index
'SendEL2', 'Workspace&EEG',... % Send the new Bins to the workplace and the EEG file
'UpdateEEG', 'on',... % Update the EEG file
'Voutput', 'EEG' );
% 17. Epoch the Data: Window and Baseline
EEG = pop_epochbin(EEG,...
[-500.0 1000.0],... % Window for Epoch
'-500 -300'); % Baseline window
% 18. Blink correction using Gratton & Coles ocular correction
% Regression-based method to remove blink and horizontal eye movements using the difference between VEO and HEO EOG electordes
% === WARNING 1: VEOG and HEOG must be channels 35 and 36, respectively. If they are not, refer to above to recreate them and enter their channel number below
% Note: this plugin is currently unavailable: contact glazerja1@gmail.com or Matthias Ihrke <mihrke@uni-goettingen.de> (Copyright (C) 2007)
EEG = pop_gratton(EEG, 35, 'chans', 1:EEG.nbchan); % Correct blinks using channel 35 = VEOG
EEG = pop_gratton(EEG, 36, 'chans', 1:EEG.nbchan); % Correct horizontal eye movements using channel 36 = HEOG
% === WARNING 2: Sometimes pop_gratton will give an error because the data length does not divide evenly into the ocular correction time windows.
% Use below alternative code if above gives error (will not significantly change results):
% EEG = pop_gratton(EEG, 35, 'chans', 1:EEG.nbchan - 1, 'blinkcritwin', '22', 'blinkcritvolt', '200');
% EEG = pop_gratton(EEG, 36, 'chans', 1:EEG.nbchan, 'blinkcritwin', '22', 'blinkcritvolt', '200');
% If still gives error, play with 'blinkcritwin' and 'blinkcritvolt' values from 17-23 and 190-210 respectively, for example:
% EEG = pop_gratton(EEG, 35, 'chans', 1:EEG.nbchan - 1, 'blinkcritwin', '21', 'blinkcritvolt', '198');
% 19. Remove VEOG/HEOG after Ocular Correction: Final Channel list: 0-34 = scalp, Reload channel locations
EEG = pop_select(EEG, 'nochannel',{'VEOG','HEOG'});
EEG = pop_chanedit(EEG, 'lookup',channelLocationFile);
eeglab redraw;
% ===== Steps 20-23: artifact detect/reject, export eventlist with artifact information, get channel locations, save fully processed dataset =====
% 20. Automatically detect & reject trials/epochs for each event code in each bin
% 20a. Artifact Rejection: ERPLAB Moving Window: Remove epochs exceeding voltage threshold as a moving window with a total amplitude, window size, and window step
EEG = pop_artmwppth(EEG ,...
'Channel', 1:EEG.nbchan,... % Set of channels to be tested
'Flag', [ 1 2],... % Flag rejected trials onto the Event List
'Threshold', 75,... % Amplitude threshold for rejection
'Twindow', [ -200 1000],... % Test window
'Windowsize', 200,... % Moving window size
'Windowstep', 100 ); % Moving window step
% 20b. Artifact Rejection: ERPLAB Sample-to-Sample: Remove epochs exceeding voltage threshold between two sampling points
EEG = pop_artdiff(EEG ,...
'Channel', 1:EEG.nbchan,... % Set of channels to be tested
'Flag', [ 1 3],... % Flag rejected trials onto the Event List
'Threshold', 50,... % Threshold for rejection
'Twindow', [ -200 1000] ); % Test window
% 20c. Artifact Rejection: ERPLAB Flatline: Remove epochs with flatlined data lower than voltage threshold
EEG = pop_artflatline(EEG ,...
'Channel', 1:EEG.nbchan,... % Set of channels to be tested
'Duration', 498,... % Duration of test window
'Flag', [ 1 4],... % Flag rejected trials onto the Event List
'Threshold', [ -0.5 0.5],... % Threshold for low amplitude rejection
'Twindow', [ -200 1000] ); % Test window
% 21. Export EventList containing bin/artifact information
EEG = pop_exporteegeventlist(EEG,...
'Filename', [processed_eventlist_savepath 'Processed_EventList_' subName{iSubject} '.txt']);
% 22. Look up channel locations again
EEG = pop_chanedit(EEG, 'lookup',channelLocationFile);
eeglab redraw;
% 23. Edit dataset name and save fully processed .set/.fdt file that is ready for averaging into erpset .erp file
EEG = pop_editset(EEG, 'setname', [subName{iSubject} '_ChOpResamp_FiltElist_BinEpochOC_ChanRejInterp']);
EEG = pop_saveset(EEG, 'filename',[subName{iSubject} '_ChOpResamp_FiltElist_BinEpochOC_ChanRejInterp.set'], 'filepath', processed_dataset_savepath);
eeglab redraw;
% ===== Steps 24-25: Compute average erps and save final .erp files ready for ERP plotting, data exporting, and grand averaging =====
% 24. Compuate average ERPs using erplab to create .erp file
ERP = pop_averager(EEG, 'Criterion', 'good', 'ExcludeBoundary', 'on');
% 25. Save the erpset .erp file
ERP = pop_savemyerp(ERP,...
'erpname', [subName{iSubject} '_erpset'],... % Name the ERP set
'filename', [subName{iSubject} '_erpset.erp'],... % Name the file
'filepath', erpset_savepath,... % Path to save ERP set
'Warning', 'off');
% update erplab
CURRENTERP = CURRENTERP + 1;
ALLERP(CURRENTERP) = ERP;
end