Hi Minh,

 

I think you can first use mri_binarize to obtain the mask, then apply the mask to nu.mgz using mri_mask.

 

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize

https://surfer.nmr.mgh.harvard.edu/fswiki/mri_mask

 

Best,

 

Yujing

 

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Hoang Gia Minh
Sent: Tuesday, March 28, 2023 9:10 PM
To: 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

 

--

Hoang Gia Minh, MSc

Research Assistant

Department of Biomedical Science and Engineering

Gwangju Institute of Science and Technology (GIST)

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