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From LiveScience.com:
Everything changes after the surgeons open your skull.
Your brain, and the tumor inside it, no longer fully float in their protective bath of cerebrospinal fluid. Gravity comes into play, as does the atmospheric pressure of the operating theater. The brain responds to these foreign forces, the cerebral tissue sagging, rebounding and changing shape. The tumor that the neurosurgeons want to remove also has changed position.
The preoperative MRI image is no longer accurate enough for brain surgery.
Thus, the brain the surgeon operates on is a different shape from the one depicted in the preoperative MRI. Of course, once the surgeon begins work, the shape of the brain changes even more.
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