and you can use mri_binarize --i aseg.mgz --match index1 index2 --o yourmask.mgz
On 8/3/2021 10:07 AM, Fischl, Bruce wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer