annotation_tan.m

%%%----- Annotation Task ------%%%
% NOTE: The variable 'TREE' is the hierarchical structure of brain regions.
% brain_region = input('Enter region of interest: ');

function [Int,mask,idxLUT] = annotation_tan(brain_region)

% ---------- 1. Obtaining intensity values of region of interest ------------ %%%%%
addpath(genpath('/home/tchaudhuri/toolboxes/antx-master/freiburgLight/allen'));
brain = load('TREE'); 
[table idxLUT] = buildtable(brain.tree);
Int = {};
Regions = extractfield(idxLUT,'name')';
    for i = 1:length(idxLUT)
        Int{end + 1} = extractfield(idxLUT(i),'children');
    end
Int = Int';

% brain_region = input('Enter region of interest: ');
    for a = 1:length(Regions)
        if(strcmp(Regions{a,1},brain_region) == 1)
            Int = Int{a,1}';
        end
    end
% disp(strcat('Allen intensities of ', brain_region, ' are in Int'));

% ---- How to search for the name of a region in the LUT? ---- %%
Index_region = strfind(Regions,brain_region);
Index = find(not(cellfun('isempty',Index_region)));
% disp(strcat('Index of ',brain_region,' in idxLUT: ',num2str(Index)));

% ---------- 2. Creating Mask of region of interest ------------ %%%%%
% MC_change_voxel_size;
ano = niftiread('ANO_x10.nii');
% ano = niftiread('ANOpcol.nii');
mask = zeros(size(ano,1),size(ano,2),size(ano,3));
ind = {};
    for j = 1:length(Int)
    
        ind{end + 1} = find(ano == Int(j));
        mask(ind{j}) = 1;
    end
%metadata = niftiinfo('ANO_x10.nii');
%x = pwd;
% cd('/home/tchaudhuri/code/matlab/Annotation_Task')
%niftiwrite(mask,strcat(brain_region,'_Mask'),metadata);
%cd(x);

end