Hi Dear Emma,

Here's the command :

"mri_watershed -LABEL 001.mgz out.mgz"

and the output file is attached.

Thank you in advance

Fereshte

On Mon, Oct 16, 2017 at 6:45 PM Boyd, Emma <EBOYD2@mgh.harvard.edu> wrote:

Interesting.. would you mind sending me the command you ran and file drop the input and output volumes to me?: https://gate.nmr.mgh.harvard.edu/filedrop2/

Emma

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fereshte <fereshte.ramezani@gmail.com>
Sent: Sunday, October 15, 2017 6:43:08 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Extracting labels using mri_watershed

Hi Emma,

I've tried this before but surprisingly not such labels in the output volume.

On Wed, Oct 11, 2017 at 9:03 PM Boyd, Emma <EBOYD2@mgh.harvard.edu> wrote:

Hi Fereshte,

mri_watershed -LABEL inputvolume.mgz outputvolume.mgz

The output volume will contain 6 labels:
0 = exterior
1 = scalp
2 = skull
3 = csf
4 = gray
5 = white
6 = fat tissue

Emma

> On Oct 11, 2017, at 3:38 AM, Fereshte <fereshte.ramezani@gmail.com> wrote:
>
> Dear Experts,
> How is it possible to extract labels like scalp and skull using -LABEL flag in mri_watershed ?
> Thanks for your attention.
>
>
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