The best replacement for cortex is medulla.

The best alternatives to cortex are rated as following:
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★★★★  flashpaq
★★★  cerebrum
★★★  neocortex
★★  snapdragon
★★  lobe
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★★  nume
★  bellezza
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★  motor cortex
★  sensory cortex
★  amygdala
★  prefrontal cortex
★  eggman
★  renal medulla
★  occipital lobe
  limbic system
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  gyrus
  corioliss

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Speaking about cortex, one probably shouldn't forget about insight.

Other search terms related to cortex and their ratings are:
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