I'm glad to hear it improved.
cheers
Bruce
On Sat, 30 Aug 2014, Úrsula Pérez Ramírez wrote:
Hi all,
Thanks Bruce for your recommendation, with recon-all I obtain a much better
skull stripping. Now I'm going to change thresholds because at the top and
bottom slices the segmentation is inadequate: central segmentation is
missing.
Cheers,
Úrsula
Date: Fri, 29 Aug 2014 11:48:51 -0400
From: [email protected]
To: [email protected]
Subject: Re: [Freesurfer] mri_watershed: really bad skull stripping
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 fo
r
> recon-all if I have already the .mgz file?, I'm getting errors, appart fro
m
> the warning for updating tcsh.
>
> Cheers,
> Ursula
>
> Date: Fri, 29 Aug 2014 11:23:06 -0400
> From: [email protected]
> To: [email protected]
> 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 (al
mo
> st
> > nothing) with mri_watershed –atlas in images converted from DICOM to .mg
z
> > with mri_convert. I lowered the threshold but did not improved considera
bl
> 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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