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:
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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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