Hi Arman

You can use mri_extract_labels or mri_binarize – match. The labels are in $FREESUFER_HOME/FreeSurferColorLUT.txt

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Arman Avesta
Sent: Tuesday, March 23, 2021 9:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] extracting brainstem / lentiform nucleus / hippocampus binary masks from aparc+aseg.mgz

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Hi,

Thank you so much for helping me with my previous question!

I have downloaded from LONI's ADNI study the aparc+aseg.mgz files of ~3K subjects. Now I want to extract binary masks for the brainstem, lentiform nucleus (putamen + GP), and hippocampus from aparc+aseg.mgz files. What command should I use to do that? 

Thank you,

Arman

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Arman Avesta, MD
Radiology Resident & PhD Student
Yale School of Medicine & Yale Graduate School of Arts and Sciences

Email: arman.avesta@yale.edu