Dear Qi,
You can try:
mri_threshold -U
[lr]h.hippoAmygLabels-T1.v21.mgz 300
[lr]h.hippoLabelsNoAmyg-T1.v21.mgz
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 5, 2020 at 11:54
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz
External Email - Use Caution
Hi,
I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ?
Best,
Qi
--
Ph.D. candidate
Icahn School of Medicine at Mount Sinai