Hi Wei-Ta

if the remaining skull and dura don't affect the pial surface then it doesn't matter. Run it all the way through recon-all and you'll probably find it doesn't matter.

cheers Bruce

On Fri, 19 Aug 2011, Wei-Ta Chen wrote:

Hi   I did autorecon1 on T1 structural brain images acquired by GE magnet. However, a small piece of skull with dura  still remained on brainmask.mgz (around the occiput), even after adjustment of watershed threshold to 10. (Some brain would loss  when threshold was lowered to 7 or 5). I wondered if I can use the brush to erase these pieces then click Save Volume from the File menu before continuing autorecon2 and autorecon 3? Do I have to do this?   If I can use the brush to edit brainmask.mgz, do you recommend that instead of watershed adjustment because it is more intuitive and I don't have to find the optimal threshold value of watershed. Is there any difference between their effects?   Thanks for your time and patience answering these.   Best,   Wei-Ta