do you mean you want a binary mask? If so you can run something like
mri_binarize --i aseg.mgz --match 17 --o left.hippocampus.mgz
where 17 is the index for left hippo as found in $FREESURFER_HOME/FreeSurferColorLUT.txt

On 8/3/2021 4:18 AM, Ammar Shujaa wrote:

External Email - Use Caution

Hello FreeSurfur Developers,

A have completed the segmentation of T1 MRI image using recon all.

I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later.

Looking forward to hearing from you.

Best regards,

Ammar Shujaa Addin
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