scripts/Figure2_SFFT_TOPO.m

%% SFFT Topoplots of REST and PRE-CUE data
clear; clc; close all;
datalocation = ('D:\Project_EEG_CC\SFFT_TopoFigure\Data_Topo_new\');
cd(datalocation)

savedirOFF='D:\Project_EEG_CC\SFFT_TopoFigure\Data_Topo_new\OFF\';        % OFF Data are here
savedirON='D:\Project_EEG_CC\SFFT_TopoFigure\Data_Topo_new\ON\';          % ON Data are here
savedirCTL='D:\Project_EEG_CC\SFFT_TopoFigure\Data_Topo_new\Control\';    % Control Data are here

load('D:\Project_EEG_CC\mFiles\ONOFF.mat','ONOFF')

BigN=size(ONOFF,1)./2;

off = [2 1 1 2 2 1 1 1 2 2 2 1 2 2 1 1 2 1 1 2 2 1 1 2 2 1 1 1];
on = [ 1 2 2 1 1 2 2 2 1 1 1 2 1 1 2 2 1 2 2 1 1 2 1 1 1 2 2 2];

%%%%% OFF and Control data
for mi=1:28
   
    %%%%%%%%%%     OFF data       %%%%%%%%%%%%%%%%%%%%%%%
   PDsx=[801:811,813:829];        
   load([savedirOFF,num2str(PDsx(1,mi)),'_Session_',num2str(off(1,mi)),'_PDDys_CC_ALL_TOPO.mat']);
   mData_Cue_OFF = cell2mat(mData_Cue);
   CueDataOFF{mi,:} = mData_Cue_OFF;
   
   mData_REST_OFF = cell2mat(mData_REST);
   RESTDataOFF{mi,:} = mData_REST_OFF;
   clear mData_Cue mData_Cue_OFF mData_REST mData_REST_OFF
   
   %%%%%%%%%%%%      ON data        %%%%%%%%%%%%%%%%%%%%%% for 824 off= on
   %%%%%%%%%%%%    
   load([savedirON,num2str(PDsx(1,mi)),'_Session_',num2str(on(1,mi)),'_PDDys_CC_ALL_TOPO.mat']);
   mData_Cue_ON = cell2mat(mData_Cue);
   CueDataON{mi,:} = mData_Cue_ON;
  
   mData_REST_ON = cell2mat(mData_REST);
   RESTDataON{mi,:} = mData_REST_ON;
   clear mData_Cue mData_Cue_ON mData_REST mData_REST_ON
   
   
   %%%%%%%%%%%%%   Control        %%%%%%%%%%%%%%%%%%%%%%%%%
   CTLsx=[8010,8070,8060,890:914];  
   load([savedirCTL,num2str(CTLsx(1,mi)),'_Session_1','_PDDys_CC_ALL_TOPO.mat']);
   mData_Cue_CTL = cell2mat(mData_Cue);
   CueDataCTL{mi,:} = mData_Cue_CTL;
   
   mData_REST_CTL = cell2mat(mData_REST);
   RESTDataCTL{mi,:} = mData_REST_CTL;
   clear mData_Cue mData_Cue_CTL mData_REST mData_REST_CTL

end

clearvars  -except CueDataOFF RESTDataOFF CueDataON RESTDataON CueDataCTL RESTDataCTL
tx2disp =-1500:2:4998;

%% #############################%%%%%%%%%%%%%  REST DATA  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

fs = 500;
% define analysis parameters
xlen = length(RESTDataOFF{1,:}(:,1));  % length of the signal
wlen = 128;                      % window length (recomended to be power of 2)
nop = [];                       % hop size (recomended to be power of 2)
nfft = 256;                      % number of fft points (recomended to be power of 2)

for n=1:28
    for ch = 1:60
       [sNr,fyr,txr] = spectrogram(RESTDataON {n,:}(:,ch),wlen,nop,nfft,fs, 'yaxis');  sON_All_Rt {n,:}.sub{ch,:} =  abs(sNr).^2; %
       [sCr,fyr,txr] = spectrogram(RESTDataCTL{n,:}(:,ch),wlen,nop,nfft,fs, 'yaxis');  sCTL_All_Rt{n,:}.sub{ch,:} =  abs(sCr).^2; %
    end
end
clear sFr sNr sCr 


% % %%%%%%%%%%%%%%%%%%%%%   For REST Data 0-50 Hz frequncy band  %%%%%%%%%%%%%%%%%%%%%
band1= (find(fyr==0));  band2 = find(fyr<51, 1, 'last' );  %
ch = 21; % channel Cz

for n = 1:28
          %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONbandRt(n,:).band = sON_All_Rt{n, 1}.sub{ch, 1}(band1:band2,:) ;
            %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLbandRt(n,:).band = sCTL_All_Rt{n, 1}.sub{ch, 1}(band1:band2,:) ;
end

% %
for n = 1:28
          %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONRt_fband{n} = double(mean(ONbandRt(n).band,2));
            %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLRt_fband{n} = double(mean(CTLbandRt(n).band,2));
end

%
ONRt_fband = cell2mat(ONRt_fband);
CTLRt_fband = cell2mat(CTLRt_fband);

fyL2 = round (double(fyr(band1:band2)) );
tnR = size(ONRt_fband,2);
sONRt  = double(log10(ONRt_fband)); 
sCTLRt  = double(log10(CTLRt_fband));

subplot(2,4,[1 5])
shadedErrorBar(fyL2,mean(sCTLRt,2),std(sCTLRt,0,2)/sqrt(tnR),'k',1);  hold on;
shadedErrorBar(fyL2,mean(sONRt,2), std(sONRt,0,2)/sqrt(tnR), 'r',1);  hold on;

% %% T test for FFT data
TEMP_ON = ONRt_fband';
TEMP_CTL = CTLRt_fband';
%%%% ON vs CTL
[~,P1,~,STATS1]=ttest2(TEMP_ON,TEMP_CTL);
P1(P1>=.05)=NaN;  P1(P1<.05)=1; 
plot(fyL2,log10(15*P1),'*b','MarkerSize',5); hold off; clear TEMP_ON TEMP_CTL

xlim([0 50]); box off; ylim([0 5]);
xlabel('Frequency (Hz)'); ylabel('Log power(\muV^2)');  title ('REST(Black=CTL; Red = PD ON)');

% % %%%               for TOPO REST data

Thr1= min(find(fyr>4));  Thr2 = max(find(fyr<8));  % Theta
Alr1= min(find(fyr>8));  Alr2 = max(find(fyr<13)); % Alpha

for n = 1:28
  for ch  = 1:60
            %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONfreqbandRt{n,ch}.Theta = double( mean2(sON_All_Rt{n, 1}.sub{ch, 1}(Thr1:Thr2, :)) ) ;
      ONfreqbandRt{n,ch}.Alpha = double( mean2(sON_All_Rt{n, 1}.sub{ch, 1}(Alr1:Alr2, :)) ) ;
      
      
      %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLfreqbandRt{n,ch}.Theta = double( mean2(sCTL_All_Rt{n, 1}.sub{ch, 1}(Thr1:Thr2, :)) ) ;
      CTLfreqbandRt{n,ch}.Alpha = double( mean2(sCTL_All_Rt{n, 1}.sub{ch, 1}(Alr1:Alr2, :)) ) ;
           
  end
end

%% #############################################  Pre-Cue Data    ###########################################################

fs = 500;
% define analysis parameters
xlen = length(CueDataOFF{1,:}(:,1));  % length of the signal
wlen = 128;                           % window length (recomended to be power of 2)
nop = [];                             % hop size (recomended to be power of 2)
nfft = 256;                           % number of fft points (recomended to be power of 2)

for n=1:28
    for ch = 1:60
        %%%%%%%%%%%%% Pre Cue Data
        [sF,fy,tx] = spectrogram(CueDataOFF{n,:}(:,ch),wlen,nop,nfft,fs, 'yaxis'); sOFF_All{n,:}.sub{ch,:} =  abs(sF).^2; % in power
        [sN,fy,tx] = spectrogram(CueDataON{n,:} (:,ch),wlen,nop,nfft,fs, 'yaxis'); sON_All {n,:}.sub{ch,:} =  abs(sN).^2; %
        [sC,fy,tx] = spectrogram(CueDataCTL{n,:}(:,ch),wlen,nop,nfft,fs, 'yaxis'); sCTL_All{n,:}.sub{ch,:} =  abs(sC).^2; %
    end
end
clearvars sF sN sC


% % %%%%%%%%%%%%%%%%%%%%%   For Pre-Cue Data 0-50 Hz frequncy band: -0.5 to 0 ms  %%%%%%%%%%%%%%%%%%%%%
band1= (find(fy==0));  band2 = find(fy<51, 1, 'last' );  %
xp1 = max(find(tx<1.0)); xp2 = find(tx==1.5 | tx < 1.6, 1, 'last' ); %%% for Pre-Cue Data
ch = 21; % channel Cz

for n = 1:28
          %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONbandPC(n,:).band = sON_All{n, 1}.sub{ch, 1}(band1:band2, xp1:xp2) ;
            %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLbandPC(n,:).band = sCTL_All{n, 1}.sub{ch, 1}(band1:band2, xp1:xp2) ;
end
  
for n = 1:28
          %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONPC_fband{n} = nanmean(ONbandPC(n).band,2);
            %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLPC_fband{n} = nanmean(CTLbandPC(n).band,2);
end
  
ONPC_fband = cell2mat(ONPC_fband);
CTLPC_fband = cell2mat(CTLPC_fband);

fyL = round (double(fy(band1:band2)) );
tnP = size(ONPC_fband,2);
sONPC  = double(log10(ONPC_fband)); 
sCTLPC  = double(log10(CTLPC_fband)); 

subplot(2,4,[3 7])
shadedErrorBar(fyL,mean(sCTLPC,2),std(sCTLPC,0,2)/sqrt(tnP),'k',1);  hold on;
shadedErrorBar(fyL,mean(sONPC,2), std(sONPC,0,2)/sqrt(tnP), 'r',1);  hold on;


% %% T test for FFT data
TEMP_ON = ONPC_fband';
TEMP_CTL = CTLPC_fband';
%%%% ON vs CTL
[~,P2,~,STATS2]=ttest2(TEMP_ON,TEMP_CTL);
P2(P2>=.05)=NaN;  P2(P2<.05)=1; 
plot(fyL2,log10(10*P2),'*b','MarkerSize',5); hold off; clear TEMP_ON TEMP_CTL

xlim([0 50]); box off; ylim([-1 5]);
xlabel('Frequency (Hz)'); ylabel('Log power(\muV^2)');  title ('Pre-Cue -500 -0(Black=CTL; Red = PD ON)');


%%%%%           Get Frequency bands info for PreCue for TOPO

Th1= min(find(fy>4));  Th2 = max(find(fy<8));  % Theta
Al1= min(find(fy>8));  Al2 = max(find(fy<13)); % Alpha

%%%%%%%%%%%%%%%%%%%%%%%   For Pre-Cue Data  %%%%%%%%%%%%%%%%%%%%%  

for n = 1:28
  for ch  = 1:60
          %%%%%%%%%%%%%%%%  ON  %%%%%%%%%%%%%%%%
      ONfreqbandPC{n,ch}.Theta = double( mean2(sON_All{n, 1}.sub{ch, 1}(Th1:Th2, xp1:xp2)) ) ;
      ONfreqbandPC{n,ch}.Alpha = double( mean2(sON_All{n, 1}.sub{ch, 1}(Al1:Al2, xp1:xp2)) ) ;
      
      %%%%%%%%%%%%%%%%  CONTROL  %%%%%%%%%%%%%%%%
      CTLfreqbandPC{n,ch}.Theta = double( mean2(sCTL_All{n, 1}.sub{ch, 1}(Th1:Th2, xp1:xp2)) ) ;
      CTLfreqbandPC{n,ch}.Alpha = double( mean2(sCTL_All{n, 1}.sub{ch, 1}(Al1:Al2, xp1:xp2)) ) ;
           
  end
end

%% FOR TOPO
% clearvars  -except OFFfreqbandPC ONfreqbandPC CTLfreqbandPC OFFfreqbandRs ONfreqbandRs CTLfreqbandRs OFFfreqbandRt ONfreqbandRt CTLfreqbandRt

% % Export data according to the band
for n = 1:28
    for ch  = 1:60
        %%%%%%%%% CONTROL   %%%%%%%%%%%%%%%%%%%%
        %%%%% PreCue
       CTL.Theta.PC(n,ch) = CTLfreqbandPC{n, ch}.Theta;
       CTL.Alpha.PC(n,ch) = CTLfreqbandPC{n, ch}.Alpha;
       
       %%%% REST
       CTL.Theta.Rt(n,ch) = CTLfreqbandRt{n, ch}.Theta;
       CTL.Alpha.Rt(n,ch) = CTLfreqbandRt{n, ch}.Alpha;
       
            %%%%%%%%%%%%%%  ON %%%%%%%%%%%%%%
       
       %%%%% PreCue
       ON.Theta.PC(n,ch) = ONfreqbandPC{n, ch}.Theta;
       ON.Alpha.PC(n,ch) = ONfreqbandPC{n, ch}.Alpha;
             
       %%%% REST
       ON.Theta.Rt(n,ch) = ONfreqbandRt{n, ch}.Theta;
       ON.Alpha.Rt(n,ch) = ONfreqbandRt{n, ch}.Alpha;
           
    end
end

%% statistics analysis for REST and Pre Cue...Theta and Alpha bands
ch = 21; % channel Cz
[~,Prt,~,STATSrt]=ttest2(CTL.Theta.Rt(:,ch), ON.Theta.Rt(:,ch));   Theta_state_RT = ['Theta REST: t value = ',num2str(STATSrt.tstat ),'; p value = ' num2str(Prt)]; disp(Theta_state_RT);
[~,Pra,~,STATSra]=ttest2(CTL.Alpha.Rt(:,ch), ON.Alpha.Rt(:,ch));   Alpha_state_RT = ['Alpha REST: t value = ',num2str(STATSra.tstat ),'; p value = ' num2str(Pra)]; disp(Alpha_state_RT);

[~,Ppt,~,STATSpt]=ttest2(CTL.Theta.PC(:,ch), ON.Theta.PC(:,ch));   Theta_state_PC = ['Theta PreCue: t value = ',num2str(STATSpt.tstat ),'; p value = ' num2str(Ppt)]; disp(Theta_state_PC);
[~,Ppa,~,STATSpa]=ttest2(CTL.Alpha.PC(:,ch), ON.Alpha.PC(:,ch));   Alpha_state_PC = ['Alpha PreCue: t value = ',num2str(STATSpa.tstat ),'; p value = ' num2str(Ppa)]; disp(Alpha_state_PC);

%% plot topo
load('D:\Project_EEG_CC\mFiles\BV_Chanlocs_60.mat'); chanlocs = BV_Chanlocs_60;
%%%% CONTROL - ON
% %%%%%%%%  for REST data
cad =[-100000 100000]; cat =[-5000 5000]; caa = [-500 500]; cab = [-40 40]; cag = [-20 20]; 

subplot(242);[~,P,~,~]=ttest2(CTL.Theta.Rt, ON.Theta.Rt); P(P>=.05)=NaN; P(P<.05)=1; P(isnan(P))=0; 
topoplot((mean(CTL.Theta.Rt)- mean(ON.Theta.Rt)),chanlocs,'maplimits',[-3 3],'emarker2', {find(P),'d','k',5,1}); clear P; title ('REST:Theta (CTL-PD ON)');caxis(cat);colormap jet;

subplot(246);[~,P,~,~]=ttest2(CTL.Alpha.Rt, ON.Alpha.Rt); P(P>=.05)=NaN; P(P<.05)=1; P(isnan(P))=0; 
topoplot((mean(CTL.Alpha.Rt)- mean(ON.Alpha.Rt)),chanlocs,'maplimits',[-3 3],'emarker2', {find(P),'d','k',5,1}); clear P; title ('REST:Alpha (CTL-PD ON)');caxis(caa);colormap jet;

% %%%%%%%%  for Pre-Cue data
cad =[-20000 20000]; cat =[-500 500]; caa = [-30 30]; cab = [-20 20]; cag = [-10 10]; 

subplot(244);[~,P,~,~]=ttest2(CTL.Theta.PC, ON.Theta.PC); P(P>=.05)=NaN; P(P<.05)=1; P(isnan(P))=0; 
topoplot((mean(CTL.Theta.PC)- mean(ON.Theta.PC)),chanlocs,'maplimits',[-3 3],'emarker2', {find(P),'d','k',5,1}); clear P; title ('PreCue:Theta (CTL-PD ON)');caxis(cat);colormap jet;

subplot(248);[~,P,~,~]=ttest2(CTL.Alpha.PC, ON.Alpha.PC); P(P>=.05)=NaN; P(P<.05)=1; P(isnan(P))=0; 
topoplot((mean(CTL.Alpha.PC)- mean(ON.Alpha.PC)),chanlocs,'maplimits',[-3 3],'emarker2', {find(P),'d','k',5,1}); clear P; title ('PreCue:Alpha (CTL-PD ON)');caxis(caa);colormap jet;

suptitle ('Control and PD ON')