Heinrich Kulver and Paul Bucy guide Angie and Nicky through the structure of the brain. They then explain that the Amygdala is the part of the brain that processes emotional reactions.
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Joel has decided to have his ex-girlfriend, Clementine, erased from his memory because she had erased him from her memory. At the start of the procedure, the "doctors" put items that remind Joel of Clementine in front of him as they monitor his brain activity. Parts of his brain light up on the machine as he thinks about Clementine. Joel's thoughts are illustrated as incoherent events as the procedure progresses.