atlas_split_3to4D.m

function atlas_split_3to4D(path_and_atlas, labels_txt)


%% Split any 3D atlas to 4D
% Radwan 08/01/2019
% This little function is designed to work for the aal atlas splitting it
% to 4D and gives you room to do some minor editing, e.g. smoothing,
% dilation etc. with fslmaths
% your atlas labels must be arranged as a single numbered column, using .
% after the no. like so: 1. ACC (Anterior Cingulate Cortex)
%                        2. PCC (Post...

%% Part 1 Define some stuff
% 
% clear all;
% clc


[a b c ] = fileparts(path_and_atlas);
dir_main = a;
atlas_labels = [dir_main filesep labels_txt];
atlas_nii = [dir_main filesep b c];
atlas_dir_4D = [dir_main filesep b '_4D'];

poolobj = gcp('nocreate');
delete(poolobj)
parpool(4);
%% Part 2
% loop to get your labels and indices from the labels.txt file (hopefully
% this is only 1 column with the indices representing the image intensity of each
% label

labels_f = fopen(atlas_labels);
lwip = textscan(labels_f,'%d %s', 'delimiter', '.'); % this is to get an index of the vois... kinda redundant actually
fclose(labels_f);
indices = lwip{1};
names = lwip{2};

clear aal;
aal = struct([]);

for i = 1:size(indices,1)
    aal(i).index = (lwip{1}(i));
    aal(i).name = strrep(names(i), ' ', '_'); 
    aal(i).name = char(strtok(aal(i).name, '('));
    aal(i).lt  = char(string((double(aal(i).index)) - 0.5));
    aal(i).ut = char(string((double(aal(i).index)) + 0.5));
%     aal(i).index = (aal(i).index);
%     aal(i).name = (aal(i).name);
end


%% Part 3 
% use fslroi in a for loop to split this 3D atlas into a 4D image

mkdir(atlas_dir_4D);

parfor i = 1:size(aal,2)
    
    % need to add values for min. t.dim and size in t.dim to fslroi
    % afterwards we will need fslmerge to produce a 4D nii
    unix(['source ~/.bash_profile ;  fslmaths ' atlas_nii ' -thr ' aal(i).lt ' -uthr '  aal(i).ut ' -bin ' atlas_dir_4D filesep b '_4D_' aal(i).name '.nii.gz ']);
    % If you want them smoothed just add a -s 2 or something.
    
end

    aal_4D_nii = ([dir_main filesep b '_4D_complete.nii']);
    new_order = sort({aal(:).name});
    sort_aal = fopen([dir_main filesep b '_labels_sorted.txt'] ,'w');
    fprintf(sort_aal,'%s\n',new_order{:});
    fclose(sort_aal);
    unix(['source ~/.bash_profile ; fslmerge -t ' aal_4D_nii ' ' atlas_dir_4D filesep '*' b '_4D_*']); 


poolobj = gcp('nocreate');
delete(poolobj)