A mask is an image in black and white where each pixel actually represents a depth marker. The whiter the points, the closest the points are to you. So, black represents the background, and the different shades of white represent points floating above the background.
Just select a mask and a pattern of your choice and then you are ready to generate your own stereogram. It's that easy! You can also use custom patterns or custom masks created by your self (this is for advanced users).