Hi Ammar

In the mri dir there are segmented volumed called aseg.mgz and aparc+aseg.mgz where every voxel has an index into the FreeSurferColorLUT.txt lookup file

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Ammar Shujaa
Sent: Tuesday, August 3, 2021 4:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] How to extract individual structures after recon-all

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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