Dear All,
I plan starting running the -FLAIRpial flag for pial refinement, after recently upgrading freesurfer to dev (12/19/2013), centos6 86X64 build. I installed the new fs according to the wiki guidelines.
I read on the forum that FSL_DIR has to be set up, and FSL has to be installed for bbregister to work. The default wiki installation does not set FSL_DIR.
I found a bbregister file dated 12/17/2013 by Doug in freesurfer/bin, so it could be that the above issue has been solved, please confirm.