scripts/Step1_CC_PreProcess_TASK.m

%% Step1: PreProcess CC Task
clear; clc; close all;
addpath('D:\Project_EEG_CC\CC_PD_Figures_Manuscript\CC_Manuscript\Manuscript_Scripts_PREDICT\Data\');
datalocation=('D:\Project_EEG_CC\CC_PD_Figures_Manuscript\CC_Manuscript\Manuscript_Scripts_PREDICT\Data\');
savedire = ('D:\Project_EEG_CC\CC_PD_Figures_Manuscript\CC_Manuscript\Manuscript_Scripts_PREDICT\Data\');
cd(datalocation);

PDsx=[801:811,813:829];     % 824 S2 is bad EEG!
CTLsx=[8010,8070,8060,890:914];

%% ##########################   TRN = training; TST = testing; FB = Reward and punishment
for subj=[PDsx,CTLsx]
    for session=1:2          
        if (subj>850 && session==1) || subj<850  % If not ctl, do session 2
            if exist([num2str(subj),'_Session_',num2str(session),'_PDDys_CC.mat'])~=2
                
                disp(['Do CC --- Subno: ',num2str(subj),'      Session: ',num2str(session)]); disp(' ');
                                
                TRN_STIM={'S111','S112','S113','S114','S121','S122','S123','S124','S211','S212','S213','S214','S221','S222','S223','S224'};
                TRN_RESP={'S101','S102','S103','S104'};
                TRN_FB={'S  8','S  9'};
                TST_STIM={'S 12','S 13','S 14','S 21','S 23','S 24','S 31','S 32','S 34','S 41','S 42','S 43'};
                TST_RESP={'S  1','S  2','S  3','S  4'};
                All_STIM={'S111','S112','S113','S114','S121','S122','S123','S124','S211','S212','S213','S214','S221','S222','S223','S224','S  8','S  9'...
                    'S 12','S 13','S 14','S 21','S 23','S 24','S 31','S 32','S 34','S 41','S 42','S 43'};
                
                % Data are 68 chans: 1=63 is EEG, 64 is VEOG, 66-68 is XYZ.  Ref'd to CPz - - will want to retrieve that during re-referencing
                % Load BrainVision data
                EEG = pop_loadbv(datalocation,[num2str(subj),'_',num2str(session),'_CC.vhdr']);
                
                % Get Locs
                locpath= ('D:\Matlab_Files\Matlab_toolbox\eeglab_current\eeglab14_1_1b\plugins\dipfit2.3\standard_BESA\standard-10-5-cap385.elp');
                
                EEG = pop_chanedit(EEG,    'lookup', locpath);
                EEG = eeg_checkset( EEG );  %% get the epoch information from EEG.event
                
                % Get event types
                for ai=2:length(EEG.event); temp=EEG.event(ai).type; TYPES(ai)=str2num(temp(2:end)) ; clear temp; end
                UNIQUE_TYPES=unique(TYPES);
                for ai=1:length(UNIQUE_TYPES); UNIQUE_TYPES_COUNT(ai)=sum(TYPES==UNIQUE_TYPES(ai)); end
                clc; TRIGGERS=[UNIQUE_TYPES;UNIQUE_TYPES_COUNT]; % Trigger type, Frequency
                
                % Epoch ---To TRN stim, TRN FB, and TST stim..NO RESPONSE
                
                EEG = pop_epoch( EEG, All_STIM, [-1.5         5], 'newname', 'Epochs', 'epochinfo', 'yes');
                EEG = eeg_checkset( EEG );
                
                % Remove X,Y,Z & VEOG
                EEG.VEOG=squeeze(EEG.data(64,:,:));
                EEG.X=squeeze(EEG.data(65,:,:));
                EEG.Y=squeeze(EEG.data(66,:,:));
                EEG.Z=squeeze(EEG.data(67,:,:));
                EEG.data=EEG.data(1:63,:,:);
                EEG.nbchan=63;
                EEG.chanlocs(67)=[];  EEG.chanlocs(66)=[]; EEG.chanlocs(65)=[]; EEG.chanlocs(64)=[];
                % Fix BV-specific issue - - - only needed for APPLE
                for ai=1:size(EEG.urevent,2), EEG.urevent(ai).bvtime=EEG.urevent(ai).bvmknum; end
                for ai=1:size(EEG.event,2), EEG.event(ai).bvtime=EEG.event(ai).bvmknum; end
                for ai=1:size(EEG.epoch,2), EEG.epoch(ai).eventbvtime=EEG.epoch(ai).eventbvmknum; end
                % Add CPz
                EEG = pop_chanedit(EEG,'append',63,'changefield',{64 'labels' 'CPz'});
                EEG = pop_chanedit(EEG,'lookup', locpath);
                % Re-Ref to Average Ref and recover CPz
                EEG = pop_reref(EEG,[],'refloc',struct('labels',{'CPz'},'type',{''},'theta',{180},'radius',{0.12662},'X',{-32.9279},'Y',{-4.0325e-15},'Z',{78.363},...
                    'sph_theta',{-180},'sph_phi',{67.208},'sph_radius',{85},'urchan',{64},'ref',{''}),'keepref','on');
                % Remove everything else NOW that CPz has been reconstructed from the total
                EEG.MASTOIDS = squeeze(mean(EEG.data([10,21],:,:),1));
                EEG.data = EEG.data([1:4,6:9,11:20,22:26,28:64],:,:);
                EEG.nbchan=60;
                EEG.chanlocs(27)=[];  EEG.chanlocs(21)=[];   EEG.chanlocs(10)=[];   EEG.chanlocs(5)=[];  % Have to be in this order!
                % Should probably re-ref to average again now that the contaminated channels are gone
                EEG = pop_reref(EEG,[]);
                % Remove mean
                EEG = pop_rmbase(EEG,[],[]);
                
                %%%%%%%%%%%%%%%%%%%%%%% ----------------------
                % Setup APPLE to interp chans, reject epochs, & ID bad ICs.  Output will be Avg ref'd and ICA'd.
                TASK='CC';
                eeg_chans=1:60;
                Do_ICA=1;
                ref_chan=36;  % 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 (will re-ref data to avg ref)
                [EEG,bad_chans,bad_epochs,bad_ICAs]=APPLE_PDDys_CC(EEG,eeg_chans,ref_chan,Do_ICA,subj,EEG.VEOG,session,TASK);
                
                % Save
                save([savedire,num2str(subj),'_Session_',num2str(session),'_PDDys_CC.mat'],'EEG','bad_chans','bad_epochs','bad_ICAs');
                
                % -----------------------------------------------------------------
                
                clearvars -except subj session  datalocation;
            end
        end
    end
end