es, this is just an error that I discovered. Unfortunately, it will have to wait for a new version. You can download and run the dev version for the purposes of running gtmseg only (make sure to delete the mri/xcerebral.samseg folder).

On 11/5/2025 6:46 AM, Carme Uribe wrote:

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Hi all,

I’m running into an issue after upgrading from FreeSurfer 7.1.2 to 8.1.0 when using PETSurfer.

In v7.1.2, the |gtmseg.ctab| included the *pons (Id 174)*, which allowed the subsequent |mri_gtmpvc| step to perform the default *rescale normalization based on pons intensity*.

However, in v8.1.0, the pons no longer appears in the |gtmseg.ctab|. Since the rescale step still expects that region by default, the pipeline fails when trying to normalize by the pons.

From the release notes I see that |gtmseg| now uses SAMSEG by default, and I suspect that this change may have modified how subcortical or brainstem structures are handled.

Also, any chance the gtmseg step could add other regions typically used as reference (e.g., wm/whole cerebellum, centrum semiovale) maintaining the aseg and aparc parcellations from FS?

Thanks very much in advance for your help,

Carme

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