Stereopsis is one of the processes of the human visual system that extracts depth information from a viewed scene and builds a three dimensional understanding of that scene. It makes use of the slight difference in perspective of one eye relative to the other. It is stereopsis that is exploited by those 3D glasses used at Disneyland/Disneyworld and the IMAX theaters. You can certainly exploit stereopsis yourself through use of similar technology. Turns out though that stereopsis is only of use within the immediate proximity of the viewer, say on the order of < 30 feet. The distance to objects farther away is judged by an assortment of other cues. For example, if one object partially obscures another, the obscuring object must be closer. If an object of known large size appears to be small, it must be far away. If the air is hazy, increasingly distant objects will appear increasingly hazy and bluish. There are a number of such depth cues, but the important point is that beyond roughly 30 feet, those depth cues are monocular and do not depend on stereoscopic vision at all. With rare exceptions, external view images that the flight sim software generates represent objects that are considerably farther than 30 feet away. So even though we are generating images representing a 3D world, stereopsis doesn't (and shouldn't) come into play. If visual perspective in a computer generated image is amplified to force stereopsis into play for images beyond 30 feet, an enhanced 3D effect will result that will make the display look like a totally unrealistic amusement park ride. The cleverly crafted sim software generates scenery that incorporates monocular depth clues. The farther object is occluded by the nearer object, distant objects recede into a bluish haze, and so on. The problem is that our eyes are not quite tricked into believing that the glass surface of the monitor is a window into a 3D world. The images obstinately remain flat.
The problem is that even though stereopsis is not needed, the stereopsis corner of our brains steadfastly refuses to go on holiday. Perceiving the flat nature of the image it continues to scream "FLAT, FLAT, FLAT", even as the monocular depth corner whispers, "of course there's depth out there, can't you see the Microsoft blimp moving in front of those buildings"? "LIES! DECEPTION! WE'RE BEING TRICKED!" replies stereopsis central. Understanding how to get stereopsis to quiet down requires a brief look at physiology.
The drawing above reduces the human visual system to the bare essentials: two lenses, two retinas. This is a view from above, so the lower lens represents the left eye while the upper lens represents the right eye. These "eyes" see two objects. Although each eye sees the same two objects, the (admittedly exaggerated) different perspectives result in very different images being focused onto each retina. The images of the two objects projected on the left retina are widely separated, while the images on the right retina are right next to each other. It is this difference in perspective that the human visual system uses in stereopsis to deduce the three dimensional nature of a scene.
Here's another view of perspective at work. The images of a near object projected onto the retinas will be more to the outside than will be the images of an object that is farther away. Another way to say this is that as an object moves away, the images of it on the retinas will move toward the center of each retina.
(Now you may be thinking that when you look at something close up, you go slightly cross eyed, and that doing so cancels this image-moving trick. Well, somewhat it does, but it does not eliminate it, nor remove its importance in stereopsis. Just take my word for this. We're seriously in danger of being too technical as it is.)
There are two very important points to take away from this.
First, an object, or a whole scene, which is close to the eyes will result in images being projected onto the retinas more to the outside, than if that object or scene were farther away. This, my friends, is the reason that stereopsis central cries foul when you view a supposedly 3D image on a close up monitor. No matter how dark you make the room, no matter how you mask around the monitor to obscure potential distractions, your stereoptic vision knows the image is flat. The retinal images are too far to the outside, too close to your ears.
Take another look at the drawings. Notice the angle between the two light paths from the object to each of the two eyes. As the object moves farther away, the angle gets smaller. In fact, if the object is farther than, oh, say, 30 feet or so, the angle is so close to zero, and the light paths are so close to parallel, that the human eye can't tell the difference. This is how to silence stereopsis central. Keeping S. C. quiet requires that the light path from an image representing a distant object to one eye be essentially parallel to the light path from that same image to the other eye.
(Short vocabulary note: An optical system that causes a light source to have parallel light paths (okay, "light rays" if you want to call them that) emitting from it is called a collimator. A graphical display system incorporating an optical system that makes the light paths from the display to each eye of the viewer be parallel is termed a "collimated display".)
Actually, there is an incredibly cheap (which is to say free) way to get stereopsis out of the picture. Close one eye. Honest! Stereopsis is a two-eye process. Because it functions by exploiting the difference in perspective between two eyes, closing one shuts it down. For those of you who are into hardware solutions, get an eye patch. It will look cool and go well with your leather bomber jacket. For those of you who are not into that particular retro look, read on. There are other options.