Yes, 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 12/8/2025 4:21 PM, Daniel Gutstein wrote:

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Hello,

I am encountering an issue when running mri_gtmpvc in Freesurfer 8.1.0. It fails with the following "ERROR: scale reference id 174 cannot be found in seg id list". Upon inspecting gtmseg.ctab, seg id 174 (pons) is missing in version 8.1 while this was present in version 7.x. Several other segmentation ids are also inconsistent between version 7 and 8. 
Could you please clarify whether mri_gtmpvc is fully compatible with the updated segmentation FreeSurfer 8.1, and whether there is a recommended workflow?

Below is the full command and output:

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mri_gtmpvc --i pet/S09/PET.nii.gz  --o pet/S09/gtmpvc --reg-identity --mask S09/mri/brainmask.mgz --psf 3.0 --mg 0.20 2 41 --seg S09/mri/gtmseg.mgz
Loading input pet/S09/PET.nii.gz
  done loading input 1 frames
Using identity registration

8.1.0
mri_gtmpvc --i pet/S09/PET.nii.gz --o pet/S09/gtmpvc --reg-identity --mask S09/mri/brainmask.mgz --psf 3.0 --mg 0.20 2 41 --seg S09/mri/gtmseg.mgz
vgthresh   0.001000
nReplace   0
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 
256 avail.processors, using 1
Creating output directory pet/S09/gtmpvc
Loading seg for gtm S09/mri/gtmseg.mgz
Loading seg ctab S09/mri/gtmseg.ctab
Reading S09/mri/gtmseg.lta
Pruning ctab
tissue type schema 
Checking tissue type
done with seg vol
maxFWHM = 3 (voxels), PadThresh=0.0001, nPad=10
Loading mask S09/mri/brainmask.mgz
Automask, reducing FOV 1
region 256 256 256 reduced to 56 25 23  140 149 180
Data load time 10.2 sec
nmask = 1646176, nsegs = 101, excluding segid=0
FWHM: 3 3 3
Std:  1.27398 1.27398 1.27398
nPad 10, PadThresh 0.0001
Checking Ref Ids
ERROR: scale reference id 174 cannot be found in seg id list
----------


Thank you.


Daniel Gutstein

Research Data Analyst Senior

Northwestern University | Mesulam Institute for Cognitive Neurology & Alzheimer's Disease

300 E. Superior Street | Tarry 8-734 | Chicago, IL 60611

daniel.gutstein@northwestern.edu | (312) 503 - 8150


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