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
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