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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