Yes 😊 the amydala labels are in the 7000 range and the hippocampal in the 200s. Feel free to use eg 4129 next time!
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 14:42
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz
External Email - Use Caution
Thanks, it works. Does the code mean that it only allows labels under 300 to pass through?
Best,
Qi
On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:
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
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Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Ph.D. candidate
Icahn School of Medicine at Mount Sinai