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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