2011/4/25 Bruce Fischl <fischl@nmr.mgh.harvard.edu>

yes, I think that's a typo and should be autorecon2. Perhaps Nick can confirm?

On Mon, 25 Apr 2011, Xiaoying Tang wrote:

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*

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