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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Durastanti, Valentina (NIH/NINDS) [F]