Cluster_Overlap_main.m~

function [ClusterTable] = Cluster_Overlap_main(ImageFiles)

%%%% ----- Cluster Overlap Task ----- %%%%
%---------------------------------------------------------------------------------------------------------------%

% 'CodeDir' contains the fullpath to the folder into which the Toolbox is copied.
% 'DataDir' is the fullpath to the directory whose data needs to be analysed
% by this pipeline.
%
% %----Description----%
% Run this script to obtain proportion of brain regions detected in the cluster images. 

% FORMAT [ClusterTable] = Cluster_Overlap_main(ImageFiles)
% 
% %----Input----%
% ImageFiles: Filename of cluster image. 

% %----Output----%
% ClusterTable: Table array showing per
%
% -----------------------------------------%
% Tanusree Chaudhuri
% Max Planck Institute of Psychiatry, Munich
% tanusree_chaudhuri@psych.mpg.de
% -----------------------------------------%

%---------------------------------------------------------------------------------------------------------------%

global DataDir;
global TemplatesDir;

cd(DataDir);

% ----- Binarizing cluster image ------ %
ImagesToBeMasked = ImageFiles;
InputFilename = cellstr(ImagesToBeMasked);
[pth,nam,ext] = spm_fileparts(ImageFiles);
OutputFilename = strcat(pth,'/Mask_',nam,ext);
MaskingClusterImages(InputFilename,OutputFilename);

% ------ Cluster Labelling.------ %
ClusterMask = spm_vol(OutputFilename);
ClusterMask = spm_read_vols(ClusterMask);
CC = bwconncomp(ClusterMask);
NumberOfClusters = CC.NumObjects;


for img_cluster = 1:NumberOfClusters

    [ClusterLabels,ClusterParents,ClusterLabelsPercent] = ClusterProportionInPercentages(TemplatesDir,CC,img_cluster);
    if(isempty(ClusterLabels))
        Cluster_blob_num = cellstr(repmat(['Cluster',' ',num2str(img_cluster)],[1, 1]));
        ClusterLabels{end + 1} = [];
        ClusterLabelsPercent = 100;
        ClusterParents{end + 1} = [];
    end
    Cluster_blob_num = cellstr(repmat(['Cluster',' ',num2str(img_cluster)],[length(ClusterLabels) 1]));
    ClusterParents = ClusterParents';
    ClusterImageInfo = table(Cluster_blob_num,ClusterLabels,ClusterParents,ClusterLabelsPercent);
    disp(strcat('Blob','_',num2str(img_cluster),'_','done'));
    
    
    if(img_cluster == 1)
        ClusterTable = ClusterImageInfo;
    else
        ClusterTable = [ClusterTable;ClusterImageInfo];
    end
        
end



end