Luckily, it works beautifully on my iPad, even though it's an iPhone app. It's really cool. By making the brain a little bit transparent it's possible to see half way through the brain. The stereo aspect does make it easier to realise how deep inside the brain the activations are (or whatever you are observing).
This technique is not limited to the 3D glasses. If you own an LCD-TV with support for 3D stereo, it will hopefully support the side-by-side stereo format that the app is using. Then you can connect your iPad to your TV and watch the 3D brain coming out of your screen.
The image below shows what it looks like. The side-by-side technique means the left part of the screen goes to your left eye and the right part goes to your right eye. You can actually see the effect yourself by looking at the picture below if you are good at crossing your eyes. Try look behind the screen to overlap the two brains and you should get a third brain image in the middle in stereo.