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P3_Canna_Pilot_Analysis_ComputeERP.m
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P3_Canna_Pilot_Analysis_ComputeERP.m
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ccc
%
exp = 'P3_Canna_Pilot';
subs = {'001';'002'; '003'; '005'; '006'};
%subs = {'006'}; %to test on just one sub
nsubs = length(subs);
conds = {'Pre';'Post'};
nconds = length(conds);
Pathname = 'M:\Data\P3_Canna_Pilot\';
[ALLEEG EEG CURRENTSET ALLCOM] = eeglab;
i_count = 0;
for i_sub = 1:nsubs
for i_cond = 1:nconds
i_count = i_count + 1;
Filename = [subs{i_sub} '_' exp '_' conds{i_cond}];
EEG = pop_loadset('filename',[Filename '_Corrected_Target.set'],'filepath','M:\Data\P3_Canna_Pilot\segments\');
[ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 );
EEG = pop_loadset('filename',[Filename '_Corrected_Standard.set'],'filepath','M:\Data\P3_Canna_Pilot\segments\');
[ALLEEG, EEG, CURRENTSET] = eeg_store( ALLEEG, EEG, 0 );
end
end
eeglab redraw
%compute grand average Erps
[erp1aw, erp2aw, diffaw] = pop_comperp( ALLEEG, 1, [1:6:i_sub*i_cond*2] ,[2:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
[erp1pw, erp2pw, diffpw] = pop_comperp( ALLEEG, 1, [3:6:i_sub*i_cond*2] ,[4:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
% [erp1ad, erp2ad, diffad, time] = pop_comperp( ALLEEG, 1, [5:6:i_sub*i_cond*2] ,[6:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
%subject erps
electrode = 5;
erp_out = [];
for i_sub = 1:nsubs
for i_cond = 1:nconds
erp_out(:,1,:,i_cond,i_sub) = mean(ALLEEG(1+ 2*((i_sub-1)*2+(i_cond-1))).data,3)';
erp_out(:,2,:,i_cond,i_sub) = mean(ALLEEG(2+ 2*((i_sub-1)*2+(i_cond-1))).data,3)';
end
end
%grand average plots + difference
erp_diff_out = squeeze(erp_out(:,1,:,:,:)-erp_out(:,2,:,:,:));
figure('Color',[1 1 1]);
for i_cond = 1:2
switch i_cond
case 1
colour = 'b';
case 2
colour = 'g';
case 3
colour = 'r';
end
subplot(2,2,i_cond);
boundedline(EEG.times,squeeze(mean(erp_out(:,1,electrode,i_cond,:),5)),squeeze(std(erp_out(:,1,electrode,i_cond,:),[],5))./sqrt(nsubs),colour,...
EEG.times,squeeze(mean(erp_out(:,2,electrode,i_cond,:),5)),squeeze(std(erp_out(:,2,electrode,i_cond,:),[],5))./sqrt(nsubs),'k');
set(gca,'Color',[1 1 1]);
set(gca,'YDir','reverse');
if i_cond == 2
legend({'Targets', 'Standards'},'Location','SouthEast');
end
axis tight; ylim([-2.5 8]);
line([-200 1000],[0 0],'color','k');
line([0 0],[-2.5 8],'color','k');
title(conds{i_cond});
xlabel('Time (ms)');
ylabel('Voltage (uV)');
subplot(2,2,2+i_cond);
boundedline(EEG.times,squeeze(mean(erp_diff_out(:,electrode,i_cond,:),4)),squeeze(std(erp_diff_out(:,electrode,i_cond,:),[],4))./sqrt(nsubs),colour);
set(gca,'Color',[1 1 1]);
set(gca,'YDir','reverse');
if i_cond == 2
legend('Targets-Standards','Location','SouthEast');
end
axis tight; ylim([-2.5 8]);
line([-200 1000],[0 0],'color','k');
line([0 0],[-2.5 8],'color','k');
title(conds{i_cond});
xlabel('Time (ms)');
ylabel('Voltage (uV)');
end
%%
%Difference Waves at any given electrodes.
figure('Color',[1 1 1]);
subplot(2,1,1);
electrode = 6;
boundedline(EEG.times,squeeze(mean(erp_diff_out(:,electrode,1,:),4)), squeeze(std(erp_diff_out(:,electrode,1,:),[],4))./sqrt(nsubs),'b',...
EEG.times,squeeze(mean(erp_diff_out(:,electrode,2,:),4)), squeeze(std(erp_diff_out(:,electrode,2,:),[],4))./sqrt(nsubs),'g'); %,...
% EEG.times,squeeze(mean(erp_diff_out(:,electrode,3,:),4)), squeeze(std(erp_diff_out(:,electrode,3,:),[],4))./sqrt(nsubs),'r');
set(gca,'Color',[1 1 1]);
set(gca,'YDir','reverse');
line('XData', [100 100], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','r')
line('XData', [175 175], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','r')
line('XData', [180 180], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','m')
line('XData', [275 275], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','m')
legend('Pre','Post','Location','SouthEast');
axis tight; ylim([-5 9]);
line([-200 1000],[0 0],'color','k');
line([0 0],[-5 9],'color','k');
title('Difference Wave, Fz');
xlabel('Time (ms)');
ylabel('Voltage (uV)');
subplot(2,1,2);
electrode = 3;
boundedline(EEG.times,squeeze(mean(erp_diff_out(:,electrode,1,:),4)), squeeze(std(erp_diff_out(:,electrode,1,:),[],4))./sqrt(nsubs),'b',...
EEG.times,squeeze(mean(erp_diff_out(:,electrode,2,:),4)), squeeze(std(erp_diff_out(:,electrode,2,:),[],4))./sqrt(nsubs),'g'); %,...
% EEG.times,squeeze(mean(erp_diff_out(:,electrode,3,:),4)), squeeze(std(erp_diff_out(:,electrode,3,:),[],4))./sqrt(nsubs),'r');
set(gca,'Color',[1 1 1]);
set(gca,'YDir','reverse');
line('XData', [100 100], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','r')
line('XData', [175 175], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','r')
line('XData', [180 180], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','m')
line('XData', [275 275], 'YData', [9.25 -7], 'LineStyle', '-','LineWidth', 2, 'Color','m')
legend('Pre','Post','Location','SouthEast');
axis tight; ylim([-5 9]);
line([-200 1000],[0 0],'color','k');
line([0 0],[-5 9],'color','k');
title('Difference Wave, Pz');
xlabel('Time (ms)');
ylabel('Voltage (uV)');
%%
%Comparing targets and standards on the same plot
electrode = 5;
erp_out = [];
for i_sub = 1:nsubs
for i_cond = 1:nconds
erp_out(:,1,:,i_cond,i_sub) = mean(ALLEEG(1+ 2*((i_sub-1)*2+(i_cond-1))).data,3)';
erp_out(:,2,:,i_cond,i_sub) = mean(ALLEEG(2+ 2*((i_sub-1)*2+(i_cond-1))).data,3)';
end
end
figure('Color',[1 1 1]);
boundedline(EEG.times,squeeze(mean(erp_out(:,1,electrode,:,:),5)),squeeze(std(erp_out(:,1,electrode,:,:),[],5))./sqrt(nsubs),'r',...
EEG.times,squeeze(mean(erp_out(:,2,electrode,:,:),5)),squeeze(std(erp_out(:,2,electrode,:,:),[],5))./sqrt(nsubs),'g');
%EEG.times,squeeze(mean(erp_out(:,2,electrode,i_cond,:),5)),squeeze(std(erp_out(:,2,electrode,i_cond,:),[],5))./sqrt(nsubs),'k');
set(gca,'Color',[1 1 1]);
set(gca,'YDir','reverse');
if i_cond == 2
legend({'Targets', 'Standards'},'Location','SouthEast');
end
axis tight; ylim([-2.5 8]);
line([-200 1000],[0 0],'color','k');
line([0 0],[-2.5 8],'color','k');
title(conds{i_cond});
xlabel('Time (ms)');
ylabel('Voltage (uV)');
%%
%difference topographys
time_window = find(EEG.times>250,1)-1:find(EEG.times>450,1)-2;
figure('Color',[1 1 1]);
for i_cond = 1:2
subplot(1,2,i_cond);
set(gca,'Color',[1 1 1]);
temp = mean(mean(erp_diff_out(time_window,:,i_cond,:),4),1)';
temp(16:18) = NaN;
topoplot(temp,'M:\Analysis\VR_P3\BrainAMP_EOG_VR.ced', 'whitebk','on','plotrad',.6,'maplimits',[-4 4] )
title(conds{i_cond});
t = colorbar('peer',gca);
set(get(t,'ylabel'),'String', 'Voltage Difference (uV)');
end
%%
% for i_set = 1:48; trial_count(i_set) = ALLEEG(i_set).trials; end
% trial_count = reshape(trial_count,[2,3,8]);
% min(trial_count,[],3)
% mean(trial_count,3)
% max(trial_count,[],3)
%
% %mean and sd
% mean(mean(erp_diff_out(time_window,7,1:3,:),1),4)
% std(mean(erp_diff_out(time_window,7,1:3,:),1),[],4)
%
%
%
% % ttest of each condition
% [h p ci stat] = ttest(squeeze(mean(erp_diff_out(time_window,7,1,:),1)),0,.05,'right',1)
% [h p ci stat] = ttest(squeeze(mean(erp_diff_out(time_window,7,2,:),1)),0,.05,'right',1)
% [h p ci stat] = ttest(squeeze(mean(erp_diff_out(time_window,7,3,:),1)),0,.05,'right',1)
%plot difference
%uncorrected
% pop_comperp( ALLEEG, 1, 4,5,'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
% %corrected
% [erp1aw, erp2aw, diffaw] = pop_comperp( ALLEEG, 1, [1:6:i_sub*i_cond*2] ,[2:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
% [erp1pw, erp2pw, diffpw] = pop_comperp( ALLEEG, 1, [3:6:i_sub*i_cond*2] ,[4:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
% [erp1ad, erp2ad, diffad, time] = pop_comperp( ALLEEG, 1, [5:6:i_sub*i_cond*2] ,[6:6:i_sub*i_cond*2],'addavg','on','addstd','off','subavg','on','diffavg','off','diffstd','off','tplotopt',{'ydir' -1});
% [erp1aw, erp2aw, diffaw] = pop_comperp( ALLEEG, 1, [4:15:i_sub*i_cond*5] ,[5:15:i_sub*i_cond*5],'addavg','off','addstd','off','subavg','off','substd','off','diffavg','on','diffstd','on','tplotopt',{'ydir' -1});
% [erp1pw, erp2pw, diffpw] = pop_comperp( ALLEEG, 1, [9:15:i_sub*i_cond*5] ,[10:15:i_sub*i_cond*5],'addavg','off','addstd','off','subavg','off','substd','off','diffavg','on','diffstd','on','tplotopt',{'ydir' -1});
% [erp1ad, erp2ad, diffad, time] = pop_comperp( ALLEEG, 1, [14:15:i_sub*i_cond*5] ,[15:15:i_sub*i_cond*5],'addavg','off','addstd','off','subavg','off','substd','off','diffavg','on','diffstd','on','tplotopt',{'ydir' -1});
eeglab redraw