you can give any format we support to recon-all as the input, including 
.mgz
 
cheers
Bruce
On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
 
> Hi Bruce,
> 
> thank you very much for your fast answer. I'm running outside recon-all,
> only with mri_watershed. Thanks, that could help. Which are the options for
> recon-all if I have already the .mgz file?, I'm getting errors, appart from
> the warning for updating tcsh.
> 
> Cheers,
> Ursula
> 
> Date: Fri, 29 Aug 2014 11:23:06 -0400
> From: fischl@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
> 
> Hi Arsula
> 
> are you running this through recon-all or outside of it? The skull 
> stripping works better after the intensity normalization  that is part of 
> recon-all
> 
> cheers
> Bruce
>
> 
> On Fri, 29 Aug 2014, Úrsula Pérez Ramírez wrote:
> 
> > 
> > Hello,
> > 
> > 
> > I’m new with FreeSurfer and I’m getting a really bad skull stripping (almo
> st
> > nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
> > with mri_convert. I lowered the threshold but did not improved considerabl
> y.
> > I have tried with a subject from the tutorial dataset and it’s OK. What ca
> n
> > be the problem?
> > 
> > Thank you very much!
> > 
> > 
> > Úrsula
> > 
> > 
> >
> 
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