Its a special kind of technology that makes it possible to keep a brain or other organs preserved even though they clearly are in a state that would normally cause them to deteroriate and in case of the brain, in a hovering container with three screens showing the persons or ponys eyes and mouth and making it possible for it to speak to other people/ponys. Oh and it is because the scientists used a widerange teleportation spell as a form of evacuation, but there was a major mistake, that caused most of the organs to be teleported away from Canterlot before the balefire strike, therefore leaving the skin, tails, manes and other external tissue behind as a empty husk just lying in the streets and houses, waiting to be fried by the heat from the explosion.