function run_dice_coeff_numk_does_not_matter
% Script to show that the number of clusters in the parcellation does not
% matter when looking at connectivity at the level of functinal families.
% Useing 3 preference values recommended by Frey & Dueck on their website: 
% https://www.psi.toronto.edu/affinitypropagation/faq.html#clusters 
% 
% If S is the similarity matrix, trying
% 1. min(S)
% 2. median(S)
% 3. min(S)-(max(S)-min(S))

% Step 1: 
make_matrices_for_dice

% Step 2:
make_8_branch_func_files_for_dice

%======== IMPORTANT ==========
fprintf('\n \n');
fprintf('IMPORTANT: \n');
fprintf('Since hierarchical clustering assigns random branch numbers to the clusters,\n');
fprintf('make sure that you have the best possible overlap between regions and branch numbers.\n');
fprintf('\n For example, \n');
fprintf('If region_1 in func_1 is numbered 1, \n');
fprintf('see to it that func_2.gii region that is the most similar to region_1 of func_1.gii is also numbered 1. \n');
fprintf('and so on for all branch numbers.');
fprintf('\n \n');
fprintf('TIP: Use calculate_max_dic.m to permutate through branch numbers and find maximum dice coefficient.');
fprintf('\n \n');
%=============================

error('Read above message. And run following steps 3 and 4 manually, after relabelling branches.')

% Step 3:
make_dice_coeff_calculation

% Step 4:
make_dice_coeff_plots

end