Hi Arman
You can use mri_extract_labels or mri_binarize – match. The labels are in
$FREESUFER_HOME/FreeSurferColorLUT.txt
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
External Email - Use Caution
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
________________________________
Arman Avesta, MD
Radiology Resident & PhD Student
Yale School of Medicine & Yale Graduate School of Arts and Sciences
Email: arman.ave...@yale.edu<mailto:arman.ave...@yale.edu>
[Inline image][Inline image]
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