Hi Annika,

You are right, there is no easy way to change the colormap (not sure!). So, in conn_displayroi if you replace one of cmap=jet(256); with below script (a customized colormap) and, inactive the rest, and set the 'cmap' variable as global (similar to CONN_gui) you would be able the solve the issue (see the attached fig).

r = [1 0 0]; %# start
w = [1 1 1]; %# middle
b = [0 0 1]; %# end

%# colormap of size 64-by-3, ranging from red -> white -> blue
k = 256/2;
c1 = zeros(k,3); c2 = zeros(k,3);
for i=1:3
c1(:,i) = linspace(b(i), w(i), k);
c2(:,i) = linspace(w(i), r(i), k);
end
cmap = [c1;c2];