Revert "Major revision: Add non-cortex labels; replace FreeSurfer gray matter fill; remove protocol directory; fix transforms, clean up nipype workflow and directory tree, improve documentation,…"

This reverts commit 218c690aea024ac9b55676a3f6556964c5b64c62.
Major revision: Add non-cortex labels; replace FreeSurfer gray matter fill; remove protocol directory; fix transforms, clean up nipype workflow and directory tree, improve documentation,…