SSVEP_Lrrk2/Matlab scripts/preproc_frequency_spectra_pfe.m

%% Load Ind mat files
% calls accuplot_mini requiring the Accusleep from Zeke Barger
% each mat file contains four animals channels 1-4 -> first animal channels 5-8 -> second animal etc.
% ch 1 = visual cortex right side, ch 2 = superior colliculus right side
% ch 3 = superior colliculus left side, ch 4 = visual cortex left side

base_dir=uigetdir(pwd); % point to directory of matfiles
mat=dir(fullfile(base_dir,'*.mat')); % list of files
nfiles=length(mat);
%%
% initiates arrays for visual cortex (VC) and superior colliculus (SC)
VC=[];
SC=[];

for thisF=1:nfiles
    in_mat=fullfile(base_dir,mat(thisF).name); 
    data=load(in_mat);
    EEG=data.d; % d1,d2,d3,d4 (four animals per file)  EEG=data x chan
    spectra=[];
    %loop for channels 1:4
    %accuplot function ==> G.spectrogram for each channel
    for ii=1:4
        [G,fAxis,showFreqs]=accuplot_mini(EEG, ii, 1000); %takes EEG, ch, fs
        % spektrum
        spe=mean(G.spectrogram,1);
        m=mean(spe);
        normSpe=spe/m; % normalisation to mean power
        %plot(fAxis(showFreqs),normSpe) 
        spectra=cat(1,spectra,normSpe);
    end
    % division into VC and SC
    VC=cat(3,VC,spectra([1,4],:));
    SC=cat(3,SC,spectra([2,3],:));
end

%%
% dividing each file into group_treatment
KO_veh=[1,5,9,26,30,34,37,41,45,39,43,47,15,19,23,51,55,59,52,56,60,62,66,70,64,68,72,...
    90,94,98,100,104,108,103,107,111,137,141,145,161,165,169,163,167,171];
KO_pfe=[3,7,11,13,17,21,16,20,24,50,54,58,74,78,82,76,80,84,...
    88,92,96,113,117,121,124,128,132,126,130,134,102,106,110,138,142,146,139,143,147,149,153,157,151,155,159];
WT_veh=[28,32,36,38,42,46,14,18,22,49,53,57,61,65,69,...
    89,93,97,91,95,99,112,116,120,114,118,122,127,131,135,150,154,158,160,164,168,162,166,170,172:174];
WT_pfe=[2,6,10,4,8,12,25,29,33,27,31,35,40,44,48,63,67,71,73,77,81,75,79,83,85:87,...
    115,119,123,125,129,133,101,105,109,136,140,144,148,152,156];

%% Mean and figures
mKOve_vc=mean(VC(:,:,KO_veh),3);
mKOpf_vc=mean(VC(:,:,KO_pfe),3);
mWTve_vc=mean(VC(:,:,WT_veh),3);
mWTpf_vc=mean(VC(:,:,WT_pfe),3);

figure(1)
subplot(211)
hold on
plot(fAxis(showFreqs),mWTve_vc','k')
plot(fAxis(showFreqs),mWTpf_vc','b')
subplot(212)
hold on
plot(fAxis(showFreqs),mKOve_vc','k')
plot(fAxis(showFreqs),mKOpf_vc','b')


mKOve_sc=mean(SC(:,:,KO_veh),3);
mKOpf_sc=mean(SC(:,:,KO_pfe),3);
mWTve_sc=mean(SC(:,:,WT_veh),3);
mWTpf_sc=mean(SC(:,:,WT_pfe),3);


figure(2)
subplot(211)
hold on
plot(fAxis(showFreqs),mWTve_sc','k')
plot(fAxis(showFreqs),mWTpf_sc','b')
subplot(212)
hold on
plot(fAxis(showFreqs),mKOve_sc','k')
plot(fAxis(showFreqs),mKOpf_sc','b')
% average of spectra

%% save spectrum for each group
s.VCko=VC(:,:,KO_veh);
s.VCwt=VC(:,:,WT_veh);
s.SCko=SC(:,:,KO_veh);
s.SCwt=SC(:,:,WT_veh);
s.VCkoP=VC(:,:,KO_pfe);
s.VCwtP=VC(:,:,WT_pfe);
s.SCkoP=SC(:,:,KO_pfe);
s.SCwtP=SC(:,:,WT_pfe);

path1='C:\Users\...'; % path to output
IDs=strcat(path1,'\SSVEPspectra.mat'); % name of output file
save(IDs, 's');