annotation_tan.m

function [Int_ROI,ROI] = annotation_tan(brain_region)

% %----Description----%
% Create masks of user specified brain regions using the annotation
% template(ANO.nii) and the allen table in the templates folder. 

% FORMAT [Int_ROI,ROI] = annotation_tan(brain_region)
% 
% %----Input----%
% brain_region: name of brain region whose mask will be generated by this
% function.
% Please refer to manual to know how to give brain_region as an input. 

% %----Output----%
% Int: the allen intensities present in brain_region
% ROI: image volume of brain_region
%
% -----------------------------------------%
% Tanusree Chaudhuri
% Max Planck Institute of Psychiatry, Munich
% tanusree_chaudhuri@psych.mpg.de
% -----------------------------------------%


global TemplatesDir
global ROI_ResultsDir

% ---------- 1.  ANO table  ------------ %%%%%
ANO = readtable(strcat(TemplatesDir,'/ANO.xlsx'));
Regions = table2array(ANO(:,1));
Children = table2array(ANO(:,5));

% ---- 2. Obtaining intensities of region of interest ---- %%
Index_region = strfind(Regions,brain_region);
Index = find(not(cellfun('isempty',Index_region)));
Children_region = Children(Index);
Int_ROI = strsplit(Children_region{1,1},';') ;
Int_ROI = str2double(Int_ROI);
if(isnan(Int_ROI) == 1)
    Int_ROI = table2array(ANO(Index,4));
end
% ---------- 3. Creating Mask of region of interest ------------ %%%%%
ano_hdr = spm_vol(strcat(TemplatesDir,'/wANO.nii'));
ano = spm_read_vols(ano_hdr);
ROI = zeros(size(ano,1),size(ano,2),size(ano,3));

ind = {};
    for j = 1:length(Int_ROI)

        ind{end + 1} = find(ano == Int_ROI(j));
        ROI(ind{j}) = 1;
    end
    

no_of_words = numel(strsplit(brain_region));
if (no_of_words == 1)
    ano_hdr.fname = strcat(brain_region,'_ROI.nii');
    ano_hdr.fname = strcat(regexprep(brain_region,'/','_'),'_ROI.nii'); 
else
    ano_hdr.fname = strcat(regexprep(brain_region,' ','_'),'_ROI.nii');
    ano_hdr.fname = strcat(regexprep(brain_region,'/','_'),'_ROI.nii'); 
end
ano_hdr.fname = strcat(ROI_ResultsDir,'/',ano_hdr.fname);
spm_write_vol(ano_hdr,ROI);
disp(['ROI result is stored in ',ROI_ResultsDir]);
end