Thank you so much. That was really helpful.
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Sent: Monday, August 07, 2017 7:15 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Thalamus ROI

Hi Sara
sure, you can look up the thalamus labels in FreeSurferColorLUT.txt (10
and 49 for lh and rh), then use either mri_extract_labels or mri_binarize
to pull our ROIs.

cheers
Bruce
On Mon, 7 Aug 2017, sarai...@alumni.ubc.ca wrote:

> Hi Freesurfer team,
> Is it possible to extract Thalamus as an ROI from aseg.mgz to be used for
> tractography in FSL.
> If so, what command I have to use to extract it.
> Can I use the LUT table to extract thalamus?
>
> Thanks,
> Sara
>
>
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