scripts/Step1_PreProcess_REST.m

%% PD Rest
startup
clear all; clc
addpath('Y:\EEG_Data\PDDys\EEG\PD REST Scripts');
datalocation='Y:\EEG_Data\PDDys\EEG\Raw EEG Data\';   % Data are here
cd(datalocation);
savedir='Y:\EEG_Data\PDDys\EEG\Processed EEG Data\';

PDsx=[801 802 803 804 805 806 807 808 809 810 811 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 ];  % 803 S1 is garbage
CTLsx=[894 908 890 891 892 893 895 896 897 898 899 900 901 902 903 904 905 906 907 909 910 911 912 913 914 8010 8060 8070 ];

for subj=[PDsx,CTLsx]
    for session=1:2
        if (subj>850 && session==1) || subj<850  % If not ctl, do session 2
            if ~(exist([savedir,num2str(subj),'_',num2str(session),'_PDDys_REST.mat'])==2)
                disp(['Do Rest --- Subno: ',num2str(subj),'      Session: ',num2str(session)]); disp(' ');
                
                % 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),'_ODDBALL.vhdr']);
                % Get Locs
                locpath=('Y:\Programs\eeglab12_0_2_1b\plugins\dipfit2.2\standard_BESA\standard-10-5-cap385.elp');
                EEG = pop_chanedit(EEG,    'lookup', locpath);
                EEG = eeg_checkset( EEG );
                % 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
                All_STIM={'S  1','S  3'};  % Open, Closed
                EEG = pop_epoch( EEG, All_STIM, [-2         2], '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='REST';
                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,EEG.bad_chans,EEG.bad_epochs,EEG.bad_ICAs]=APPLE_PDDys(EEG,eeg_chans,ref_chan,Do_ICA,subj,EEG.VEOG,session,TASK);
                
                % Save
                save([savedir,num2str(subj),'_',num2str(session),'_PDDys_REST.mat'],'EEG');
                clear EEG bad* UNIQUE* TYPES TRIGGERS
                % ----------------------
            end
        end
    end
end