Thank you so much. That was really helpful. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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, saraizad@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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