sorry, not sure what you mean. do you mean you want to extract, say, two labels (amygdala and hippocampus) into a single volume file? If so, you can run something like
mri_binarize --i aseg.mgz --match 17 18 --o amyg-hippo.lh.mask.mgz
mri_mask aseg.mgz amyg-hippo.lh.mask.mgz amyg-hippo.lh.mgz
where 17 = left hippo and 18 = left amyg (see $FREESURFER_HOME/FreeSurferColorLUT.txt)

On 12/5/2023 7:44 AM, Aurora Orazi wrote:

External Email - Use Caution

Hello Freesurfer Developers,

I'm attempting to save more than one label in as a single volume file from the aseg.mgz file obtained with the infant FreeSurfer pipeline.

However, given the lack of tutorials I'm finding it difficult to do so.

I hope you can help me with this problem.

Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460

Platform: Ubuntu 22.04

Hoping to hear from you soon,

Best regards,

Aurora
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