My apologies, how can I visualize mri_binarize output? I tried in fslview but orientation is wrong. Different orientation is a file's feature or swapdim is request?

Thanks,

Stefano

----Messaggio originale----
Da: fischl@nmr.mgh.harvard.edu
Data: 29-apr-2014 16.01
A: <stdp82@virgilio.it>, "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] thalami mask (nii.gz) to import in FSL

Hi Stefano

you can use either mri_binarize --match or mri_extract_label with labels
10 and 49 (which I got from FreeSurferColorLUT.txt)

cheers
Bruce
On Tue, 29 Apr 2014,
stdp82@virgilio.it wrote:

> Hi list,
> I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed
> mask in probtrackx.
>
> Thanks,
>
>
> Stefano
>
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