EEG02_channelPreprocessing.m

%% Preprocessing : phase 2
% - Remove EMG and AUX channels
% - Remove or interpolate bad channels (comment line 78 to remove and 79 to interpolate)
% - Save
% 
% Note that channel to remove should be indicated as channel number
%
% Tip: place a stopper at line 65 so that you can inspect channels before being
% asked which ones you would like to remove

close all;
clear all;
clc;

% Declare paths
pathData = '/Volumes/Seagate/project_rhythmicBrain/DATA/'; %Folder where all data is
addpath('/Users/claraziane/Documents/Académique/Informatique/MATLAB/eeglab2021.1'); %EEGLAB toolbox

% Load matrix where all rejected channels are stored (comment if running script for the 1st time)
load('/Volumes/Seagate/project_rhythmicBrain/Results/subAll/chanReject.mat')

 % Load file containing EEG electrode coordinates as some blocks do not have the right coordinates
load('/Volumes/Seagate/project_rhythmicBrain/DATA/chanLocs.mat')

Participants = {'sub-001'; 'sub-002'; 'sub-003'; 'sub-004'; 'sub-005'; 'sub-006'; 'sub-007'; 'sub-008'; 'sub-009'; 'sub-010'; 'sub-011'; 'sub-012'; 'sub-013'; 'sub-014'; 'sub-015'; 'sub-016'; 'sub-017'; 'sub-018'; 'sub-019'; 'sub-020'};
Blocks       = {'run-01'; 'run-02'; 'run-03'; 'run-04'; 'run-05'; 'run-06'; 'run-07'; 'run-08'; 'run-09'; 'run-10'; 'run-11'; 'run-12'; 'run-13'; 'run-14'; 'run-15'; 'run-16'; 'run-17'; 'run-18'; 'run-19'};

extensionRoot  = '.set';
extensionFinal = '_chanClean.set';

[ALLEEG EEG CURRENTSET ALLCOM] = eeglab;
for iParticipant = 1:length(Participants)
    directory = fullfile(pathData, Participants{iParticipant}, 'eeg');
    participantStr = strcat('SUB', Participants{iParticipant}(end-2:end));

    for iBlock = 1:length(Blocks)
        conditionStr = strcat('Run', Blocks{iBlock}(end-1:end));
        fileRead     = [Participants{iParticipant} '_task-AudioCueWalkingStudy_' Blocks{iBlock} extensionRoot];
        fileWrite    = [Participants{iParticipant} '_task-AudioCueWalkingStudy_' Blocks{iBlock} extensionFinal];

        % To deal with different number of blocks per participant
        if exist(fullfile(directory, fileRead), 'file') ~= 0

            EEG = pop_loadset('filename', fileRead,'filepath', directory); % Loads an EEG dataset
            [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 0,'gui','off'); % Edits/saves EEG dataset structure information

            % Keep only EEG channels
            if sum(strcmpi('EMG',{EEG.chanlocs.type})) ~= 0 || sum(strcmpi('AUX',{EEG.chanlocs.type})) ~= 0
                chanEEG = strcmpi('EEG',{EEG.chanlocs.type});
                nChan = sum(chanEEG);
                EEG = pop_select(EEG, 'nochannel', [nChan+1 : length(EEG.chanlocs)]);
                [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,'overwrite','on','gui','off');
                EEG = eeg_checkset(EEG);
            end

            % Use same EEG electrode coordinate system for all blocks
            if strcmpi(ALLEEG.chaninfo.filename, '/data/projects/ramon/johanna_eeg2bids/data_mfiles/channel_labels_plusEMG.locs')
                ALLEEG.chanlocs = chanLocs;
                EEG.chanlocs    = chanLocs;
            end

            % Identify bad channels
            iChan = 1;
            chanReject.(participantStr).(conditionStr)(iChan) = NaN;
            while(1)
                chanRemove = input('Should some channels be removed from the data ?, Y/N [Y]:', 's');
                if chanRemove == 'Y'
                    chanReject.(participantStr).(conditionStr)(iChan) = input('Which channel should be removed from the data ?');
                    iChan = iChan + 1;
                elseif chanRemove == 'N'
                    break
                end
            end

            % Remove/Interpolate identified bad channels
            if ~isnan(chanReject.(participantStr).(conditionStr)(1))
                chanReject.(participantStr).(conditionStr) = sort(chanReject.(participantStr).(conditionStr));
                EEG = pop_interp(EEG, chanReject.(participantStr).(conditionStr)(1:iChan-1), 'spherical'); %Comment this line if you want to remove bad channels without interpolating
                % EEG = pop_select( EEG, 'nochannel', chanReject.(participantStr).(conditionStr)(1:iChan-1)); %Comment this line if you want to interpolate bad channels
                [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,'overwrite','on','gui','off');
                EEG = eeg_checkset(EEG);

                % Rereference
                nChan = length(EEG.chanlocs);
                EEG = pop_reref(EEG, [],'exclude',[109-(length(chanReject.(participantStr).(conditionStr))-1):nChan]);
                [ALLEEG EEG CURRENTSET] = pop_newset(ALLEEG, EEG, 1,'overwrite','on','gui','off');
            end

            % Save new .set file
            EEG = pop_saveset(EEG, 'filename', fileWrite, 'filepath', [directory '/']); %pop_saveset saves one or more EEG dataset structures
            ALLEEG = [];

            save('/Volumes/Seagate/project_rhythmicBrain/Results/subAll/chanReject', 'chanReject');

        end

    end

end