Hi Chris, I believe if you do not include the -clean-bm flag then it should have an effect when run multiple times. You should make a copy of the brainmask.mgz and brainmask.gcuts.mgz to compare before/after to verify if there are any differences. -Louis

On Tue, 30 Jul 2013, Chris Watson wrote:

Hello, Is there any value in running recon-all with "-gcut" multiple times? e.g. in a case where skull/dura continues to be left on brainmask.mgz?

Thanks, Chris