SwitchingFCalongAtask/withinStagePLI.m

% get bump locations and define tempral windows for connectivity

clear all
close all
clc

buOff   = 2; % FC stges everything between bumps except fro bumps
blOff   = 40; % 400 milliseconds baseline
withBL  = true;
dimBL   = [10, 6]; % form 40 - 10 to onset - 6 samples -> BL with 25 samples, 250 millisecons
dataHSMM = '/hmmBu4RroiAveMap3StagBL.mat';


nSj     = 18;
fs      = 100;
nRoi    = 68;
nFC     = (nRoi^2)/2 - nRoi/2;

dataPath = './data';
dataMEG  = './data/thetaROIs_R.mat';
saveFile = './dataSave' ;
folderModel = dataHSMM(1:end-4);

load([dataPath dataHSMM], 'proBump','x','y')
load(dataMEG, 'roiaveR','xR', 'yR', 'subjtR')

nStage  = size(proBump, 3)+1;
nStageBL= nStage;
buOff_i = buOff * ones(1, nStage-1);
buOff_i = [0, buOff_i];
buOff_e = buOff * ones(1, nStage-1);
buOff_e = [buOff_e, 0];
if withBL, 
    nStageBL = nStage + 1; 
    buOff_i  = [dimBL(1), buOff_i];
    buOff_e  = [dimBL(2), buOff_e];
end

roiR = single(roiaveR);
xd = xR;
yd = yR;
subj = subjtR;
clear roiaveR xR yR subjtR 

pairs =  combnk([1:nRoi],2);
tooShort = [];

nTr     = length(x);
lens    = y - x + 1;
pliTr   = zeros(nStageBL, nFC, nTr, 'single');
maxN    = max(lens);
buSampl = ones(nTr, nStage,'single');
% location of bumps given by HsMM
for bu = 1:nStage-1
    buSampl(:,bu+1)   = round( [1:maxN] * squeeze(proBump(:,:,bu)) );
end
buSampl = horzcat(buSampl, lens);
buSampl = buSampl + blOff;
if withBL,
    buSampl = horzcat(ones(size(buSampl,1), 1), buSampl);
end
for tr = 1:nTr
    yTr = y(tr) - x(tr) + 1;
    data = hilbert(roiR(xd(tr):yd(tr),:));
    % common spectral density
    csd = data(:, pairs(:,1)) .* conj(data(:, pairs(:,2)));
    % sample phase differences sign
    siCsd = sign( imag( csd ));
     % stage mean PLI
    for s = 1:size(buSampl,2)-1  
        if (buSampl(tr,s+1)-buOff_e(s)) - (buSampl(tr,s)+buOff_i(s)) <= 0,
            pliTr(s,:,tr) = 0;
            tooShort = vertcat(tooShort, [s,tr]);
        end
        pliTr(s,:,tr) = mean( siCsd( buSampl(tr,s)+buOff_i(s):buSampl(tr,s+1)-buOff_e(s) ,:), 1);
    end
end
% average by subjects
pliSj   = zeros(nStageBL, nFC, nSj);
for sj = 1:nSj
    pliSj(:,:,sj) =  squeeze( mean(pliTr(:,:,subj==sj), 3) );  % mean over subjects
end
pliR = squeeze( mean(pliSj,3) );
 

save2path = [saveFile folderModel];
%save([save2path '/FCraw.mat'], 'pliR')