Hi All,

I find the following content on the wikipage of freesurfer:

Q. I have already skull-stripped data. Can I submit it to recon-all?

A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit differently.

First you must run only -autorecon1 like this:
recon-all -autorecon1 -noskullstrip -s <subjid>

Then you will have to make a symbolic link or copy T1.mgz to brainmask.auto.mgz and a link from brainmask.auto.mgz to brainmask.mgz. Finally, open this brainmask.mgz file and check that it looks okay (there is no skull, cerebellum is intact; use the sample subject bert that comes with your FreeSurfer installation to make sure it looks comparable). From there you can run the final stages of recon-all:
recon-all -autrecon1 -autorecon3 -s <subjid>


I am a little confused: should the final stages be "recon-all -autorecon2 -autorecon3 -s <subjid>" since we have already run the -autorecon1 via "recon-all -autorecon1 -noskullstrip -s <subjid>"?

Thanks a lot for your answering.

Best,
Xiaoying Tang