scripts/Step1_PreProc.m

%% Step 1 - load Flankers data from OCD II Study
clear all; clc
addpath('Y:\EEG_Data\Flankers OCDII\');
datalocation='Y:\EEG_Data\Flankers OCDII\Raw Data\';   % Data are here
savedir='Y:\EEG_Data\Flankers OCDII\Processed Data\';  % Save processed data here
appledir='Y:\EEG_Data\Flankers OCDII\Processed Data\APPLE Outputs\';  
erpdir='Y:\EEG_Data\Flankers OCDII\Processed Data\ERPs\';  
locpath=('Y:\Programs\eeglab12_0_2_1b\plugins\dipfit2.2\standard_BESA\standard-10-5-cap385.elp'); % Generic EEGlab locs
cd(datalocation);

% Data are 67 chans.  1:64 are EEG, incl. M1/2 and CB1/2.  65=HEOG 66=VEOG 67=EKG
FILZ=dir('*.cnt');

for si=[21,32,45]    %1:length(FILZ)
    
    subname=FILZ(si).name;
    subno=str2num(subname(1:3));
    
    % Load .cnt file and import channel locations
    EEG = pop_loadcnt([datalocation,subname], 'dataformat', 'int32', 'keystroke', 'on');
    
    % Get Locs
    EEG = pop_chanedit(EEG,    'lookup', locpath);
    EEG = eeg_checkset( EEG );
    
    NUMSTIM=121:168;
    for ai=1:length(NUMSTIM)
        ALLSTIM{ai}=num2str(NUMSTIM(ai));
    end
    
    % Epoch
    EEG = pop_epoch( EEG, ALLSTIM, [-2 2], 'newname', 'Epochs', 'epochinfo', 'yes');
    EEG = eeg_checkset( EEG );
    
    % Remove mean
    EEG = pop_rmbase(EEG,[],[]);
    
    % Extract peripherals
    EEG.VEOG=squeeze(EEG.data(65,:,:)) ;
    EEG.HEOG=squeeze(EEG.data(66,:,:)) ;
    % EEG.EKG=squeeze(EEG.data(67,:,:)) ;
    EEG.MASTOIDS=squeeze(mean(cat(1,EEG.data(33,:,:),EEG.data(43,:,:)),1));
    
    % reref!
    EEG = pop_reref(EEG,[find(strcmpi('M1',{EEG.chanlocs.labels})) find(strcmpi('M2',{EEG.chanlocs.labels}))]);
    
    % Strip to 60: 33=M1, 43=M2, 60=CB1, 64=CB2, 65=HEOG, 66=VEOG
    EEG = pop_select(EEG,'nochannel',[find(strcmpi('CB1',{EEG.chanlocs.labels})) find(strcmpi('CB2',{EEG.chanlocs.labels})) ...
        find(strcmpi('HEOG',{EEG.chanlocs.labels})) find(strcmpi('EKG',{EEG.chanlocs.labels})) find(strcmpi('VEOG',{EEG.chanlocs.labels}))]);
    
    
    CONGRU=[121, 124, 125, 128, 131, 134, 135, 138, 141, 144, 145, 148, 151, 154, 155, 158, 161, 164, 165, 168];
    INCONGRU=[122, 123, 126, 127, 132, 133, 136, 137, 142, 143, 146, 147, 152, 153, 156, 157, 162, 163, 166, 167];
    NeedLeft=[121,123,126,128,131,133,136,138,141,143,146,148,151,153,156,158,161,163,166,168];
    NeedRight=[122,124,125,127,132,134,135,137,142,144,145,147,152,154,155,157,162,164,165,167];
    
    % Get the good info out of the epochs
    for ai=1:size(EEG.epoch,2)
        EEG.epoch(ai).STIM=NaN;  EEG.epoch(ai).CONGRU=NaN;  EEG.epoch(ai).RightLeft=NaN;
        EEG.epoch(ai).RT=NaN;    EEG.epoch(ai).ACC=NaN;  EEG.epoch(ai).BlockStart=0;
        EEG.epoch(ai).TRIALNUM=NaN;
        BEH_VECTOR(ai,1:8)=NaN;
        for bi=1:size(EEG.epoch(ai).eventlatency,2)
            % Get STIMTYPE
            if EEG.epoch(ai).eventlatency{bi}==0 % If this bi is the event
                EEG.epoch(ai).TRIALNUM=ai;
                % ID what stimtype it was
                temp=str2num(EEG.epoch(ai).eventtype{bi});
                EEG.epoch(ai).STIM=temp;
                % And if it was congruent (1) or conflict (0)
                if any(temp==CONGRU)
                    EEG.epoch(ai).CONGRU=1;
                elseif any(temp==INCONGRU);
                    EEG.epoch(ai).CONGRU=0;
                end
                clear temp;
                % --- Now, find out what their next response was
                if bi<size(EEG.epoch(ai).eventlatency,2) && length(EEG.epoch(ai).eventtype{bi+1})==7 % IF something is next && it was a response
                    if strmatch(EEG.epoch(ai).eventtype{bi+1}(1:6),'keypad') % another verification
                        % ID what stimtype it was [Right=1, Left=2]
                        EEG.epoch(ai).RightLeft=str2num(EEG.epoch(ai).eventtype{bi+1}(7));
                        % And what the RT was
                        EEG.epoch(ai).RT=EEG.epoch(ai).eventlatency{bi+1};
                        % And if it was correct
                        temp=str2num(EEG.epoch(ai).eventtype{bi+1}(7));
                        if any(EEG.epoch(ai).STIM==NeedRight)
                            if temp==1, EEG.epoch(ai).ACC=1;
                            elseif temp==2, EEG.epoch(ai).ACC=0;
                            end
                        elseif any(EEG.epoch(ai).STIM==NeedLeft);
                            if temp==2, EEG.epoch(ai).ACC=1;
                            elseif temp==1, EEG.epoch(ai).ACC=0;
                            end
                        end
                        clear temp
                    end
                end
            end
            BEH_VECTOR(ai,1)=EEG.epoch(ai).TRIALNUM;
            BEH_VECTOR(ai,2)=EEG.epoch(ai).STIM;
            BEH_VECTOR(ai,3)=EEG.epoch(ai).CONGRU;
            BEH_VECTOR(ai,4)=EEG.epoch(ai).RightLeft;
            BEH_VECTOR(ai,5)=EEG.epoch(ai).RT;
            BEH_VECTOR(ai,6)=EEG.epoch(ai).ACC;
        end
        % Determine beginning of new blocks
        if ai==1, EEG.epoch(ai).BlockStart=1; toggle=1;
        else
            temp=num2str(EEG.epoch(ai).STIM); temp2=str2num(temp(3));
            if temp2<5
                newtoggle=1;
            elseif temp2>4
                newtoggle=2;
            end
            if newtoggle~=toggle
                EEG.epoch(ai).BlockStart=1;
                toggle=newtoggle;
            end
            clear temp temp2 newtoggle;
        end
        BEH_VECTOR(ai,7)=EEG.epoch(ai).BlockStart;
        % Determine if pre or post error
        if ai>1
            EEG.epoch(ai).PREVTRIAL.TRIALNUM=EEG.epoch(ai-1).TRIALNUM;
            EEG.epoch(ai).PREVTRIAL.STIM=EEG.epoch(ai-1).STIM;
            EEG.epoch(ai).PREVTRIAL.CONGRU=EEG.epoch(ai-1).CONGRU;
            EEG.epoch(ai).PREVTRIAL.RightLeft=EEG.epoch(ai-1).RightLeft;
            EEG.epoch(ai).PREVTRIAL.RT=EEG.epoch(ai-1).RT;
            EEG.epoch(ai).PREVTRIAL.ACC=EEG.epoch(ai-1).ACC;
            EEG.epoch(ai).PREVTRIAL.BlockStart=EEG.epoch(ai-1).BlockStart;
        end
    end
    
    % ----------------------
    % Setup APPLE to interp chans, reject epochs, & ID bad ICs.  Output will be Avg ref'd and ICA'd.
    eeg_chans=1:60;
    Do_ICA=1;
    ref_chan=19;  % Re-Ref to FCz   [WEIRD STEP, BUT THIS IS FOR FASTER, which is a part of APPLE]
    % % EEG = pop_reref(EEG,ref_chan,'keepref','on');
    
    % Run APPLE
    [EEG,EEG.bad_chans,EEG.bad_epochs,EEG.bad_ICAs]=APPLE_OCDII(EEG,eeg_chans,ref_chan,Do_ICA,subno,EEG.VEOG,appledir);
    
    % Save
    save([savedir,num2str(subno),'_FLANKERS.mat'],'EEG');
    save([savedir,num2str(subno),'_BEH_VECTOR.mat'],'BEH_VECTOR');
    
    
    % Let's just do this for display
    dims=size(EEG.data);
    EEG.data=eegfilt(EEG.data,500,[],20);
    EEG.data=reshape(EEG.data,dims(1),dims(2),dims(3));
    
    % Set Params
    tx=-2000:2:1998;
    b1=find(tx==-200);  b2=find(tx==0);
    t1=find(tx==-500);  t2=find(tx==1000);
    N2topo1=find(tx==200); N2topo2=find(tx==350);  N2toporangetot=200:2:350;
    P3topo1=find(tx==400); P3topo2=find(tx==600);  P3toporangetot=400:2:600;
    tx2disp=-500:2:1000;
    
    % Basecor your ERPs here so they are pretty.
    BASE=squeeze(  mean(EEG.data(:,b1:b2,:),2)  );
    for ai=1:dims(1)
        EEG.data(ai,:,:)=squeeze(EEG.data(ai,:,:))-repmat( BASE(ai,:),dims(2),1 );
    end
    
    % --------------
    for ai=1:length(EEG.epoch)
        CONDIS(ai)=EEG.epoch(ai).CONGRU;
    end
    % ------------------
    figure; 
    subplot(2,4,1:3); hold on
    site=19;  % FCz 
    ERP4topo=mean(EEG.data(site,N2topo1:N2topo2,:),3);
    topomax_N2=N2toporangetot(find(ERP4topo==min(ERP4topo)));
    topotoplot_N2=find(tx==topomax_N2);
    plot(tx2disp,mean(EEG.data(site,t1:t2,CONDIS==1),3),'b');
    plot(tx2disp,mean(EEG.data(site,t1:t2,CONDIS==0),3),'r');
    plot([topomax_N2 topomax_N2],[-4 4],'m');
    title(['FCz   Subno: ',num2str(subno)]);
    subplot(2,4,4); hold on
    TOPLOT=mean(EEG.data(:,topotoplot_N2,CONDIS==0),3) - mean(EEG.data(:,topotoplot_N2,CONDIS==1),3);
    topoplot( TOPLOT, EEG.chanlocs);  cbar
    % ------------------
    subplot(2,4,5:7); hold on
    site=46;  % Pz 
    ERP4topo=mean(EEG.data(site,P3topo1:P3topo2,:),3);
    topomax_P3=P3toporangetot(find(ERP4topo==max(ERP4topo)));
    topotoplot_P3=find(tx==topomax_P3);
    plot(tx2disp,mean(EEG.data(site,t1:t2,CONDIS==1),3),'b');
    plot(tx2disp,mean(EEG.data(site,t1:t2,CONDIS==0),3),'r');
    plot([topomax_P3 topomax_P3],[-4 4],'m');
    title(['Pz   Subno: ',num2str(subno)]);
    subplot(2,4,8); hold on
    TOPLOT=mean(EEG.data(:,topotoplot_P3,CONDIS==0),3) - mean(EEG.data(:,topotoplot_P3,CONDIS==1),3);
    topoplot( TOPLOT, EEG.chanlocs);  cbar
    
    saveas(gcf, [erpdir,num2str(subno),'_ERPs.png'],'png');
    close all;
    
    
    clear BEH_VECTOR EEG ai bi subno toggle CONDIS TOPLOT topomax_P3 topotoplot_P3 topomax_N2 topotoplot_N2 ERP4topo;
    
end

% ----------------------

%%