It is tricky but possible, but not might be worth it. You need to have a whole brain segmentation, so you could superimpose the subfields onto the aparc+aseg. You will need to create a color table for it (see gtmseg.ctab after running gtmseg). You can then specify the new seg with --seg to mri_gtmpvc. How well it works is another question. The smaller the ROI, the harder it is to do the PVC. It will give you an answer, probably without complaining, but it might not be an accurate one.

On 9/18/2024 10:40 PM, Sneha Pandya wrote:

External Email - Use Caution

Dear team,

I wanted to follow up on the following question. Thank you.

Regards,

Sneha

From: Sneha Pandya
Sent: Tuesday, August 27, 2024 12:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: petsurfer using brainstem subfields

Dear team,

We need to use PVC brainstem subfield which we intend to use as high binding region for MRTM based kinetic analysis. Can we run mri_gtmpvc using brainstemSsLabels.v12.mgz as input segmentation? Or is to possible to combine gtmseg and brainstem subfields and use this combined segmentation for mri_gtmpvc (will be using GTM or RBV for PVC).

Thank you,

Sneha
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