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