I have used:

recon-all -s -subcortseg

which runs through step 11 (-calabel), with the understanding re: accuracy that Bruce pointed out.

-Julie

On 7/7/10 8:07 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Salem,

yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up.

cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote:

...

Hi,

I am a new user of freesurfer. Is it possible to do just the volumetric processing stages without the surface processing stages?

In fact what I want is to segment the subcortical structures.

Is there a command line for this purpose only or should we run all the recon-all steps?

Thank you for your help

Salem

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