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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
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
External Email - Use Caution 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 EMAIL: hoanggiaminh1996@gmail.commailto:hoanggiaminh1996@gmail.com
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
External Email - Use Caution 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 EMAIL: hoanggiaminh1996@gmail.commailto:hoanggiaminh1996@gmail.com
freesurfer@nmr.mgh.harvard.edu
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Hoang Gia Minh -
Huang, Yujing -
Iglesias Gonzalez, Juan E.