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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