brainvis.m

clc
% Make sure to load the proper Ls and mus
% e.g. load RS_k6_Ls load RS_k6_mus

% Num of nodes according to atlas used
N = size(mus,1); % 90 (AAL)
%% Read Node file for BrainNet

if (N == 90)
    fid   = fopen('Node_AAL90.node');
    line1 = textscan(fid, '%f%f%f%f%f%s %*[^\n]','HeaderLines',1);
    fclose(fid);
elseif(N==360)
    line1 = cell(1,6);
end

%% Laplacian -> Adjacency

% given the Ls from the Algorithm take the W and plot them
prompt = 'Mean mu to visualize: ';
ind = input(prompt); % which mean to visualize

%L = L_final(:,:,ind);
L = Ls(:,:,ind);
W = diag(diag(L)) - L;
W(W<1e-4) = 0;
L = diag(sum(W)) - W;


% Thresholding W to reduce not relevant weigths
nozeros = W(W~=0);
th = prctile(nozeros, [10,50]);
W(W<th(2)) = 0;

% Thresholding W to avoid correlation between non-active nodes
indexes = mus(:,ind)> -0.01 ;

W(~indexes,~indexes) = 0;

%% Write edges
dlmwrite('W.edge', W, 'delimiter', ' ');

%% Create nodes file for mus
D = sum(W,2); % degrees


if (N == 360)
    codeBook = load('CodeBook_GLasser_360regions.mat');
    x = zeros(N,1);
    y = zeros(N,1);
    z = zeros(N,1);
    for i = 1:N
        x(i) = codeBook.codeBook.center{i}(1);
        y(i) = codeBook.codeBook.center{i}(2);
        z(i) = codeBook.codeBook.center{i}(3);
    end
    % set coordinates of nodes
    line1{1}(:,1) = x;
    line1{2}(:,1) = y;
    line1{3}(:,1) = z;
    
    line1{6} = num2str(zeros(N,1));
    line1{6}(:) = '-';
end

line1{4} = mus(:,ind); % COLORS 
line1{5} = mus(:,ind); %D; %% nodes size


data = [num2str(line1{1}), num2str(line1{2}),num2str(line1{3}), num2str(line1{4}), num2str(line1{5}), string(line1{6})];

fid = fopen('/Users/iricchi/Documents/MIP_LabImmersion/Nodes_output.node', 'wt');

for i = 1:N
    line = [data(i,1:3),' ',data(i,4:5),' ', data(i,6)];
    fprintf(fid,'%s%s%s%s%s%s%s%s\n',line);
end

fclose(fid);

%%
% Range : abs value of percentile +-
prc = prctile(line1{4}, [10,90]);
lim = max(abs(prc));

%%
load('conf.mat');
EC.nod.color_map_low = -lim;
EC.nod.color_map_high = lim;

save('EC','EC')

BrainNet_MapCfg('BrainMesh_ICBM152_smoothed.nv','Nodes_output.node','W.edge', 'EC.mat');

% savefig()