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Calculate_Coherence.m
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Calculate_Coherence.m
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clear all
tic
disp('Initializing Files')
filepath = 'C:\Users\user\Documents\MATLAB';
cd(filepath)
load('SpkInfo.mat')
Fs = 1250; % Sampling Frequency; needed for filtering and plotting
% Theta/Delta state to analyze
TD = 2; %High 1, Low 2, Full 3
%%%%%%%%%%%%%%%%%%%%%%%%%
% Group, Band, LR, Animal, Layer/layer
Co = zeros(6,4,2,12,4,4);
%% Stroke group to analyze
% 1:4 6 ref Spk Info
for group = [1:4 6]
%% 1.Load the right and left side signals
%load H/L TD indexes
count = 0;
for animal = 1: length(SpkInfo{group,2})
REM = ['C:\Users\user\Documents\MATLAB\Data' filesep SpkInfo{group,1} '_' num2str(animal) filesep 'cREM.mat'];
try
load(REM);
catch
disp('Missing REM File')
continue
end
if isempty(cREM.R.start) || isempty(cREM.R.end)
disp('Missing REM Start or End Times for Right Side')
cd ..
continue
end
if isempty(cREM.L.start) || isempty(cREM.L.end)
disp('Missing REM Start or End Times for Left Side')
cd ..
continue
end
if isempty(SpkInfo{group,2}(animal).L_chn{3}) || isempty(SpkInfo{group,2}(animal).R_chn{3})
disp('Missing SpkInfo')
continue
end
activefilepath = ['C:\Users\user\Documents\MATLAB\Data' filesep SpkInfo{group,1} '_' num2str(animal) filesep 'concatenatedLFP.mat'];
load(activefilepath);
disp(['Loaded ' SpkInfo{group,1} '_' num2str(animal)])
% mkdir(['C:\Users\ipzach\Documents\MATLAB\Comodulograms' filesep SpkInfo{group,1} '_' num2str(animal)])
% % % % % % % % % % % % %
count = count +1;
for layer = 1:6
switch layer
case 1
A = 1;
B = 2;
compare = 'Cortex-SLM';
case 2
A = 1;
B = 3;
compare = 'Cortex-Pyr';
case 3
A = 1;
B = 4;
compare = 'Cortex-Oriens';
case 4
A = 2;
B = 3;
compare = 'SLM-Pyr';
case 5
A = 2;
B = 4;
compare = 'SLM-Oriens';
case 6
A = 3;
B = 4;
compare = 'Pyr-Oriens';
end
disp(compare)
AL_LFP = cLFP(:, SpkInfo{group,2}(animal).L_chn{A}(1));
AR_LFP = cLFP(:, SpkInfo{group,2}(animal).R_chn{A}(1));
BL_LFP = cLFP(:, SpkInfo{group,2}(animal).L_chn{B}(1));
BR_LFP = cLFP(:, SpkInfo{group,2}(animal).R_chn{B}(1));
for iBand = 1:4
switch iBand
case 1
range = [0.1 3];
case 2
range = [4 7];
case 3
range = [30 58];
case 4
range = [62 200];
end
AL_LFP = BPfilter(AL_LFP, Fs, range(1), range(2));
AR_LFP = BPfilter(AR_LFP, Fs, range(1), range(2));
BL_LFP = BPfilter(BL_LFP, Fs, range(1), range(2));
BR_LFP = BPfilter(BR_LFP, Fs, range(1), range(2));
% Loading Right Side LFPs
TDIdx = []; % Array for relevant data points indices
% disp('grabbing indices')
switch TD
case 1
% Get indices of High Theta/Delta
for iRem = 1:length(cREM.R.start)
TDIdx = [TDIdx (round(cREM.R.start(iRem)*Fs)):(round(cREM.R.end(iRem)*Fs))];
end
REMtitle = 'H';
% Get indices of Low Theta/Delta
case 2
LowRightStart = cREM.R.end(1:end-1);
LowRightEnd = cREM.R.start(2:end);
for iRem = 1:length(LowRightStart)
TDIdx = [TDIdx (round(LowRightStart(iRem)*Fs)):(round(LowRightEnd(iRem)*Fs))];
end
REMtitle = 'L';
% For entire reading
case 3
TDIdx = 1 : length(cLFP);
REMtitle = 'F';
end
ARH_LFP = AR_LFP(TDIdx);
BRH_LFP = BR_LFP(TDIdx);
% 'Loading left side LFPs'
TDIdx = []; % Array for relevant data points indices
switch TD
case 1
%Get indices of High Theta/Delta
for iRem = 1:length(cREM.L.start)
TDIdx = [TDIdx (round(cREM.L.start(iRem)*Fs)):(round(cREM.L.end(iRem)*Fs))];
end
case 2
% Get indices of Low Theta/Delta
LowLeftStart = cREM.L.end(1:end-1);
LowLeftEnd = cREM.L.start(2:end);
for iRem = 1:length(LowLeftStart)
TDIdx = [TDIdx (round(LowLeftStart(iRem)*Fs)+1):(round(LowLeftEnd(iRem)*Fs))];
end
case 3
%For entire reading
TDIdx = 1 : length(cLFP);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creat an array of the relevant data points
ALH_LFP = AL_LFP(TDIdx);
BLH_LFP = BL_LFP(TDIdx);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
try
Co(group,iBand,1,count,A,B) = mean(mscohere(ALH_LFP,BLH_LFP));
catch
disp(['Coherence for ' SpkInfo{group,1} num2str(animal) ' Left not calculated'])
end
try
Co(group,iBand,2,count,A,B) = mean(mscohere(ARH_LFP,BRH_LFP));
catch
disp(['Coherence for ' SpkInfo{group,1} num2str(animal) ' Right not calculated'])
end
end % band
end % layer
for iB = 1:4
for iH = 1:2
% Group, Band, LR, Animal, Layer/layer
heatmap(squeeze(Co(group,iB,iH,animal,:,:)));
pause(1)
end
end
end % animal
end % group
switch TD
case 1
name = 'HTD';
case 2
name = 'LTD';
case 3
name = 'Full';
end
save(['C:\Users\user\Documents\MATLAB\Coherence Data\' name],'Co')