It might just work to give recon-all skull stripped brains. I've done it before

On 10/19/15 8:38 AM, Bruce Fischl wrote:

Hi John

I guess you could run recon-all through to the skull stripping, then copy your skull-stripped volume to brainmask.mgz in the subject's mri dir, then restart recon-all from there.

cheers
Bruce

On Fri, 16 Oct 2015, John Anderson wrote:

Dear experts,
I want to run recon-all on a stripped brains ( T1 images after applying bet
tool).
Do I need to add any flags to the command recon -all -all subjid <subj>

Bests,
John
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