get_neuron_list.m

function[connections, list] = get_neuron_list(connections) 
    % Create a list of all MSN, FSI, and D1 / D2 neuron IDs (without connections)
    % Column 1 is the unique neuron ID in the striatum generated by MatLab
    % Column 2 is the neuron's ID within that group required by SpineCreator
    list.msn = unique(connections.msnmsn(:, 1));
    list.d1  = [list.msn(1 : ceil(length(list.msn) / 2))'    ; 0 : ceil(length(list.msn)  / 2) - 1]';
    list.d2  = [list.msn(length(list.d1) + 1 : end)'         ; 0 : floor(length(list.msn) / 2) - 1]';    
    list.fsi = sort(unique([unique(connections.fsifsi(:, 1)) ; unique(connections.fsimsn(:, 1))]));
    list.fsi(:,2) = 0:length(list.fsi) - 1;   
       
    % Separate all MSN connections into D-type lists
    connections.d1.all = connections.msnmsn((connections.msnmsn(:, 1) <= max(list.d1(:, 1))), :);
    connections.d1.d1  = connections.d1.all((connections.d1.all(:, 2) <= max(list.d1(:, 1))), :);
    connections.d1.d2  = connections.d1.all((connections.d1.all(:, 2) >  max(list.d1(:, 1))), :);

    connections.d2.all = connections.msnmsn((connections.msnmsn(:, 1) >  max(list.d1(:, 1))), :);
    connections.d2.d1  = connections.d2.all((connections.d2.all(:, 2) <= max(list.d1(:, 1))), :);
    connections.d2.d2  = connections.d2.all((connections.d2.all(:, 2) >  max(list.d1(:, 1))), :);

    connections.fsi.d1 = connections.fsimsn((connections.fsimsn(:, 2) <= max(list.d1(:, 1))), :);
    connections.fsi.d2 = connections.fsimsn((connections.fsimsn(:, 2) >  max(list.d1(:, 1))), :);
end