you can define the colormap used. here is a quick example
point3d = imread('pears.png');
value = rgb2gray(point3d);
BIN = value>124;
cmap = [ 0 0 0;0 1 0];
so since i have a binary i know the green area is the logical 1 and black 0. if it is not logical then you'll have to scale the colormap to the values of white and black.