The larger map representing the neural areas in the brain for the lower limb are the joints, knee, ankle and the great toe. These are the phantom images most commonly identified by the patient, but as the brain adapts to the loss of the limb, recognition occurs and there is perception of a fore shortening of the phantom towards the stump, rather than just fading away. Before it fades away completely the foot may image on the end of the stump.
If a history of severe chronic and unrelenting pain has been elicited before the amputation of the limb, rather than just a phantom image, phantom pain will also sometimes ensue. The brain we know has a self-adjusting capacity to add or delete mapped areas of itself that serve the body parts as need be and it is increasingly understood, but change is slower and less deliberate than we may wish. Despite the impatience we may have this capacity is wonderful adaptation in time. Where chronic pain has been present the cortical representation is larger and adaptation slower.
Given this problem of pain perceived in our parts generally, there is something to learn from the phenomenon of phantom limb. Given the mystery of pain where the physical source no longer exists; it could follow that, that pain in other parts of the human vessel we call our own, might also be "remembered" when the part is removed or no residual pathology remains. Phantom pain in the low back or empty gall bladder bed or a legion of other painful conditions, corrected, but still slow to be deleted by the cerebral cortex.
When they say it's all in your head, it would have a different meaning if the analogy to phantom limb is a viable theory. It just might mean that it's still on your cerebral cortical spot in it's usual place for a while until that three pounds of grey matter remaps itself. It may be my simpleton's theory to a high powered neurophysiologist. but I am long in the tooth and have too little time left to shut up!