Freesurfer

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30128 discussions

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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wm edits, fs8.0.0: rerunning leaves wm-surfs unchanged
by Zahnert, Felix 23 Dec '25

23 Dec '25

Dear experts, I have run recon-all using Freesurfer 8.0.0 and corrected wm.mgz in some subjects (deleting voxels where ?h.white grossly extended into gm by assigning them values of 1; adding voxels where juxtacortical hypointensities were misclassified as gm by assigning them 255). After these edits (and saving wm.mgz), I ran recon-all -s <subject> -autorecon2-wm -autorecon3. However, this left the reconstructed surfaces virtually unchanged. Even areas of larger edits are left unchanged. I did check for small areas of stray voxels that could have led to such misclassification. In the documentation, it is recommended to run recon-all with the -make flag in such cases, which no longer seem to be supported. Do you have any recommendations? Thank you so much, Best, Felix

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(无主题)
by m15178125606 22 Dec '25

22 Dec '25

External Email - Use Caution confirm8ab604b7c10759a86abf9caa297c113d800ff2d7

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Fw:Welcome to the "Freesurfer" mailing list
by 杜文杰 21 Dec '25

21 Dec '25

External Email - Use Caution 杜文杰 251300255(a)st.usst.edu.cn Forwarded message: From：freesurfer-request<freesurfer-request(a)nmr.mgh.harvard.edu>Date：2025-12-22 12:25:17(中国 (GMT+08:00))To：251300255<251300255(a)st.usst.edu.cn>Cc：Subject：Welcome to the "Freesurfer" mailing listWelcome to the "Freesurfer" mailing list! To post to this list, send your message to: freesurfer(a)nmr.mgh.harvard.edu You can unsubscribe or make adjustments to your options via email by sending a message to: freesurfer-request(a)nmr.mgh.harvard.edu with the word 'help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You will need your password to change your options, but for security purposes, this password is not included here. If you have forgotten your password you will need to reset it via the web UI. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1nbhTglPHEWpxskmpl1j9uJdZLKzEP0NJ39X1S2NTtNvDK… <https://secure-web.cisco.com/1nbhTglPHEWpxskmpl1j9uJdZLKzEP0NJ39X1S2NTtNvDK…> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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skull-stripped images in longitudinal pipeline
by Marco Ganzetti 16 Dec '25

16 Dec '25

External Email - Use Caution Hello, I would like to ask whether providing skull-stripped images as input to the FreeSurfer longitudinal pipeline is appropriate for estimating regional atrophy rates. In particular, are there any drawbacks or limitations when generating the within-subject template if skull-stripped images are used instead of the original T1-weighted images? Best regards, Marco

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Dimension mismatch in bvec & bval
by Ramesh Babu 15 Dec '25

15 Dec '25

External Email - Use Caution Hello, I am frequently facing this issue in the dt-recon process. I used dcm2niix to convert the dicom files. Now I facing an issue Loading BValues from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2 Found 99 bvalues Loading BVectors from /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2 Found 11 bvectors Detected BVec file as FSL formatted ERROR: DTIstructFromBFiles(): dimension mismatch /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bvec.fixed2 has 99 rows, /mnt/conn_analysis/sr_projects_dti/subjects/subj001/dti/subj001_dti.bval.fixed2 has 11 rows $ awk '{print NF; exit}' subj001_dti.bval 33 $ awk '{print NF; exit}' subj001_dti.bvec 33 Could you please provide some suggestions? Regards Ramesh

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