File size: 5,978 Bytes
d7989aa | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | %% 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
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