Hi,

We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the “cloning to T1 method”, using the Recon Edit tool in Freeview for adding brain back to the brainmask.mgz.

Once the revised brainmask.mgz is re-saved with the same file name, what command needs to be run to regenerated the entire pipeline?

We originally ran: recon-all -s -i -hires –all

Do we run the same command again or should we use: recon-all –s –make –hires all

Thanks.

Jim

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