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) 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 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.edumailto: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) http://www.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Zeng, Qi" <qi.zeng@icahn.mssm.edumailto:qi.zeng@icahn.mssm.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, June 5, 2020 at 11:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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