Dear Minh,

Maybe user mri_binarize on lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to create a mask, and then use mri_mask to extract the hippocampus?

Cheers,

/E

 

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Hoang Gia Minh <hoanggiaminh1996@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, March 28, 2023 at 9:11 PM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

 

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Dear experts,

I am doing a Hippocampus segmentation task using Freesurfer.

After I run the command:
recon-all -i sub-ADNI002S0295_ses-M00_T1w.nii.gz -s S1 -hippocampal-subfields-T1 -all -openmp 80
in which sub-ADNI002S0295_ses-M00_T1w.nii.gz is my input MRI scan

I received an MRI folder that included "nu.mgz, aseg.mgz, etc." However, file "lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz" is just a mask or label file of the hippocampus. I want to extract the hippocampus from the original scan (nu.mgz or orig.mgz) using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz. Is there any command or step that I can do?
Thank you so much
Best regards
Minh

 

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Hoang Gia Minh, MSc

Research Assistant

Department of Biomedical Science and Engineering

Gwangju Institute of Science and Technology (GIST)

TEL: (+84)-38-521-3040