Actually, if all you want to do is skullstrip on a raw volume, then you'll have to use mri_watershed by itself. Running with recon-all -skullstrip will assume that you've run the previous steps. mri_watershed can take a lot of parameters. You can look inside recon-all to see which ones we use by default.

doug




Durastanti, Valentina (NIH/NINDS) [F] wrote: 
Dear Nick,
I tried to run
 recon-all -s <subjname> -skullstrip 
but always came out an error: read error
I tried to run 
recon-all -subjid <subjname> -autorecon1 
on the same subjects and it looks good
have you any suggestion?
Thanks
 Valentina


-----Original Message-----
From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] 
Sent: Saturday, April 08, 2006 7:23 PM
To: Durastanti, Valentina (NIH/NINDS) [F]
Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List
Subject: Re: [Freesurfer] (no subject)

Use:

  recon-all -s <subj> -skullstrip

Also, recon-all -help will list-out most of the steps which can be run
individually (see section titled STEP-WISE DIRECTIVES).

On Sat, 2006-04-08 at 19:47 -0400, Durastanti, Valentina (NIH/NINDS) [F]
wrote:
  
Hi,
I'm using Freesurfer and I'd like to run the autorecon1 just for the
skull stripping (without intensity and spatial normalization). Is there
a command just to do that? 

Thanks
valentina

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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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