Hi Zeno,

We recommend using the output of gtmseg for the segmentaion.

See: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer

To change the reference region, change the `--km-ref` values when running mri_gtmpvc. You can use freeview to open gtmseg.mgz to find the values visually, or use the lookup table here: https://github.com/freesurfer/freesurfer/blob/dev/distribution/FreeSurferCol...

For the whole whole cerebellum, the values would be `--km-ref 7 8 46 47`

-Paul

________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of zeno Zeng zeno3175@gmail.com Sent: Tuesday, October 1, 2024 12:05 PM To: Freesurfer support list Subject: [Freesurfer] PetSurfer, PVC uptake of ROI relative to Pons

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Hi Freesurfer experts,

Instead of adjusting the 'PVC uptake of ROI relative to the Pons,' I want to adjust it to the 'whole cerebellum.' Are there any parameters I should modify in the command for this? Also, which parcellation or segmentation method would you recommend for this adjustment? Thank you!