Is the brain merely shown "sideways" in FSLview?  What matters is that the A/P/S/I/L/R labels are correct in FSLview, in which case the orientation info is read just fine, and it is solely a matter of how FSLview choses to display data that doesn't have an RAS/LAS orientation.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: "stdp82@virgilio.it" <stdp82@virgilio.it>
Reply-To: "stdp82@virgilio.it" <stdp82@virgilio.it>, Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, April 29, 2014 1:19 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] R: Re: R: Re: thalami mask (nii.gz) to import in FSL

Hi Bruce,

in tkmedit the orientation is ok. Is wrong in fslview. Now, I'm running probtrackx. I'll update you on results.

Thanks,


Stefano


----Messaggio originale----
Da: greve@nmr.mgh.harvard.edu
Data: 29-apr-2014 17.52
A: <freesurfer@nmr.mgh.harvard.edu>
Ogg: Re: [Freesurfer] R: Re:  thalami mask (nii.gz) to import in FSL


How do you know the orientation is wrong? Is it right in tkmedit?

On 04/29/2014 10:23 AM, stdp82@virgilio.it wrote:
> 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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