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) http://www.jeiglesias.com
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
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Ph.D. candidate Icahn School of Medicine at Mount Sinai