Freesurfer December 2025

freesurfer@nmr.mgh.harvard.edu

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Implementing the Glasser Atlas on Processed Participants
by Carly McIntyre-Wood 23 Dec '25

23 Dec '25

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Recon failing: normal vector of length zero at vertex NNNNN with N faces
by Sambamoorthy, Sowmya 23 Dec '25

23 Dec '25

External Email - Use Caution Hello! Need help getting past these errors (attached recon log) for reference. Many of my brains are throwing errors like below: "normal vector of length zero at vertex 101440 with 6 faces first tangent vector of length zero at vertex 101440" Last few lines of recon.log below: [cid:image001.png@01DC27E0.966D3810] Any help appreciated! Thank you in advance for your support. --Sowmya

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GLM on runs with different conditions
by Xu, Yaoda 23 Dec '25

23 Dec '25

External Email - Use Caution Hi there, I have a large number of conditions to include in a study, like 60. So I split the conditions into multiple runs, with 40 conditions per run, say run 1 with conditions 1 to 40, run 2 with conditions 21 to 60, and run 3 with conditions 1 to 20 and 41 to 60. Can I put all three runs in a run list and run a single GLM with 60 conditions? Normally, I would have the same number of conditions in each run when I put a bunch of runs together in a single GLM to increase SNR. In this case, different runs would share some of the conditions, but not all conditions appear in each run. I just want to make sure that it is OK to run a GLM like this and get a valid beta estimate for each of the 60 conditions. Thanks a lot. Yaoda Xu

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make_average_subject
by Don Hagler 23 Dec '25

23 Dec '25

External Email - Use Caution We have used make_average_subject to resample the white and pial surfaces of an individual subject to ico 7 to produce surface coordinates in the standard tessellation, allowing for group analyses of cortical shape. It may be worth noting that we temporarily replace the talairach.xfm in the subject’s mri/transforms directory with an identify matrix so that the resampled surfaces have the same position and shape as the native surfaces but with the standard ico 7 tesselation. This resampling procedure works great with FreeSurfer version 5.3, but as of version 6.0 or 7.1.1, when a single subject is supplied to make_average_subject, it runs for a while but then eventually produces an error like this: nframes = 1 Computing std/var across frames ERROR: cannot compute std from one frame ERROR: make_average_surface While we can continue doing this resampling step using FS 5.3 (e.g., after running the initial recon with 7.1.1), we would like to stop relying on this very old version. Is there an alternative approach to re-tesellation of an individual subject’s surfaces into ico? Or could a future release of FreeSurfer include a modification to make_average_surface to allow it to once again handle a single subject as input?

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PETSurfer v8.1.0 vs 7.x.x — missing pons in gtmseg.ctab and rescale issue in mri_gtmpvc
by Carme Uribe 23 Dec '25

23 Dec '25

External Email - Use Caution 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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Re: freesurfer license error: qdec not recognize license
by fsbuild 23 Dec '25

23 Dec '25

External Email - Use Caution   Freesurfer 6  does not use the FS_LICENSE environment variable to find the license, e.g., by setting it to the path of the license.txt file in your home directory.  You can try making a copy of license.txt to be read as $FREESURFER_HOME/.license You should NEVER post the contents of a license file to a public online forum. - R.

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expert.opts is not parsed correctly in FS 8
by Billah, Tashrif 23 Dec '25

23 Dec '25

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences-1 Did you guys change how parameters from expert.opts is ingested by recon-all in FS 8.1.0? We have successfully been using the following line in expert.opts file with FS 7: mris_inflate -n 30 (https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate) But now, FS 8.1.0 recon-all gives an error: ``` mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 ``` This almost certainly means FS 8.1.0 is not parsing expert.opts line correctly. The "-n 30" is bein parsed as just "30". Best, Tashrif

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Support regarding QDEC
by Henry Do 23 Dec '25

23 Dec '25

External Email - Use Caution Hi freesurfer experts, I am working on a project, and I have used mri_glmfit to compare the cortical thickness of the patient cohort with that of the control. When I examined the results, I noticed some unexpected clusters of atrophy and wanted to investigate which subjects contributed to each cluster. In the previous version, I could do this easily with QDEC, but unfortunately, my current computer can’t set up QDEC because the Windows version is not compatible with FreeSurfer 6.0. I hope you can help me with an alternative method for performing this analysis, as it would be greatly beneficial for my project. Sincerely, Henry Hiệp ĐỖ (Henry DO) Tran Minh Hiep DO (Henry DO) PhD Candidate | B.Biomed.Eng Faculty of Science, School of Psychology THE UNIVERSITY OF SYDNEY FRONTIER Frontotemporal Dementia Research Group | Brain and Mind Centre | M02G | Level 1, 94 Mallet Street | Camperdown | NSW | 2050 Contact: +61 451 973 339 Email: trdo0838(a)sydney.edu.au<mailto:trdo0838@sydney.edu.au>

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7.2.0 -notal-check talairach.xfm relevant beyond eTIV?
by Dr. Cornelius Kronlage 23 Dec '25

23 Dec '25

External Email - Use Caution Dear freesurfer team, using freesurfer 7.2.0, recon-all fails for some subjects in a certain dataset (denoised MP2RAGEs) for me at this stage: #@# Talairach Failure Detection Wed Dec 10 11:30:01 GMT 2025 /data/output/fs_outputs/sub-007/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0056, pval=0.0000 < threshold=0.0050) Command exited with non-zero status 1 The talairach.xfm registration indeed looks completely off. However, if I use "-notal-check", recon-all runs through with outputs (surfaces etc.) that look fine. It seems like the talairach.lta created by mri_em_register a couple of steps later is correct and downstream steps use this. The incorrect talairach.xfm only appears to have have an impact on the eTIV estimation (not so relevant for me). Is it appropriate to run recon-all with -notal-check with an incorrect talairach.xfm but an accurate talairach.lta - or are there other issues this might cause? Thank you and best wishes, Cornelius

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mri_gtmpvc error in version 8.1 - missing segmentation ids
by Daniel Gutstein 23 Dec '25

23 Dec '25

External Email - Use Caution 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(a)northwestern.edu<mailto:daniel.gutstein@northwestern.edu> | (312) 503 - 8150

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Freesurfer December 2025