% function MRI_quality(BIDS_path)
% Stefan J. Blaschke, Neurology Department, University Hospital Cologne
% VERSION 1.0., 31.12.2022
%
% matlab script to examine preprocessed fMRI dataset
% display of raw imaging
% overlay with registered atlas
% SNR and tSNR
% display of tSNR with mask outlines
% DVARS and FD
% -  Afyouni S. & Nichols T.E., Insights and inference for DVARS, 2017
%   http://www.biorxiv.org/content/early/2017/04/06/125021.1
% necessity of GSR (Chen et al., 2022, Magn Reson Med)

if exist("Mat","var")
% header
    addpath(".\scripts\toolbox\DVARS-master\")
    addpath(".\scripts\toolbox\DVARS-master\Nifti_Util\")
    addpath(".\scripts\toolbox\BCT\")
    addpath(".\scripts\toolbox\spm12")
    addpath(".\scripts\toolbox\fMRI-Quality-Checker-master")
    addpath(".\scripts\toolbox\spm12\matlabbatch")
    addpath(".\scripts\toolbox\nifti_utils-master\")
    addpath(".\scripts\toolbox\nifti_utils-master\external\NIFTI")
    addpath(".\scripts\toolbox\FSLNets\")
    addpath(".\scripts\")
%%
% create data table to store features

varnames = {'animal','ses','ID','MRI date','qualy', 'strenght','degree','modularity','CC','CPL','SW'};
vartype = repmat({'cellstr'},length(varnames),1);
Graphmaster = table('Size',[length(Mat), length(varnames)],'VariableTypes',vartype,'VariableNames',varnames);

%%
% loop through Data
%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%

for idx = 118:length(Mat) % start loop subjects

fprintf('running set #%u of %u\n',idx,length(Mat))

Graphmaster{idx,"animal"} = {Mat(idx).animal};
Graphmaster{idx,"ses"} = {Mat(idx).ses};

mNet = Mat(idx).mNet;
    if ~isempty(mNet)
        Graphmaster{idx,"ID"} = Mat(idx).ID;
        Graphmaster{idx,"MRI date"} = Mat(idx).date;
        Graphmaster{idx,'qualy'} = {Mat(idx).qualy}; 
        
        [degree, strength, modularity, CPL, CC, SW] = MRI_graph(mNet, AUC);
        
        Graphmaster{idx,'degree'} = {degree};
        Graphmaster{idx,'strenght'} = {strength}; 
        Graphmaster{idx,'modularity'} = {modularity}; 
        Graphmaster{idx,'CPL'} = {CPL}; 
        Graphmaster{idx,'CC'} = {CC}; 
        Graphmaster{idx,'SW'} = {SW}; 

    end
end
else
        disp('please load structure of matrices')

end