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.
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 (almost
> nothing) with mri_watershed –atlas in images converted from DICOM to .mgz
> with mri_convert. I lowered the threshold but did not improved considerably.
> I have tried with a subject from the tutorial dataset and it’s OK. What can
> be the problem?
>
> Thank you very much!
>
>
> Úrsula
>
>
>
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