Freesurfer April 2026

freesurfer@nmr.mgh.harvard.edu

33 participants
36 discussions

FreeSurfer Course 2026 Registration LIVE
by Sennott, Liam Ricker 13 Apr '26

13 Apr '26

Hello all, Registration is now OPEN for the next virtual FreeSurfer course happening on June 2nd, 3rd, and 5th! Please visit https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse to sign up and learn more. Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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eTIV underestimation with excessive extracranial tissue
by Pame González 12 Apr '26

12 Apr '26

External Email - Use Caution Dear FreeSurfer experts, I have a subject with good segmentation (aseg appears accurate, with no FOV truncation), but with substantial extracranial tissue, particularly neck tissue. The eTIV is relatively low (~1070 mL), and the MaskVol/eTIV ratio is high (~1.23). This subject also behaves as an outlier, showing artificially increased cortical volumes after normalization by eTIV. What would be the recommended approach to obtain a more reliable eTIV in such a case? Many thanks, P.G.

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Freesurfer on a post contrast MPRAGE.
by Aaron Tanenbaum 10 Apr '26

10 Apr '26

External Email - Use Caution Hello y'all, I have this MRPAGE that looks like it was collected after a contrast injection. It does not do well on FreeSurfer 7.3.2. Is there a flag I can use that can handle the contrast? Also, the FreeSurfer version is not really an issue in this study so I can use other versions if they are more suited for this situation.

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custom ROI in infant_recon_all
by Maarten Naeyaert 10 Apr '26

10 Apr '26

External Email - Use Caution Hi freesurfer developers, We're infant_recon_all (in freesurfer 8.1.0) on a dataset consisting of newborns, but would like to include a custom ROI not yet included in the infant atlas. Is there way to do this? Best regards, Maarten Naeyaert -------------------------------------------------------- Maarten Naeyaert, PhD MR physicist Department of Radiology UZ-Brussel Vrije Universiteit Brussel (VUB) Laarbeeklaan 101 1090 Brussels Belgium Tel: +32 (2) 477 53 88 Maarten.Naeyaert(a)uzbrussel.be Bureau: MRI 1-2 (routenummer: 950)

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Possible recon-all/xopts bug in FreeSurfer 8.1.0: mris_inflate -n 100 becomes bare 100
by Toshiharu Kamishikiryo 10 Apr '26

10 Apr '26

External Email - Use Caution Hello FreeSurfer developers, I would like to report a possible bug in recon-all / expert options handling in FreeSurfer 8.1.0. Environment - FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed - OS: Ubuntu 22.04, Linux 6.8.0-107-generic x86_64 What I am trying to do I am running recon-all on a hi-res dataset and want to increase the number of inflation iterations using an expert options file. expert.opts content mris_inflate -n 100 Command export SUBJECTS_DIR=/mnt/data4/test recon-all -all -subjid sub-01 -i /mnt/data4/Subjects/T1_MPR.nii -T2 /mnt/data4/Subjects/T2_SPC.nii -T2pial -hires -expert /home/kami/expert.opts -xopts-overwrite -openmp 8 Observed behavior The subject-specific scripts/expert-options file is created correctly and contains: mris_inflate -n 100 However, when recon-all reaches Inflation1, the executed command in recon-all.log becomes: mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix So the "-n" appears to be dropped, and "100" is interpreted as an input surface filename. The run then fails with: Reading 100 ** failed to open GIFTI XML file '100.gii' mrisReadGIFTIdanum: ERROR reading gifti 100.gii [INFO] read, cannot find 100, trying 100.gii ... error: No such file or directory error: mris_inflate: could not read surface file 100 Relevant log excerpt #@# Inflation1 lh Fri Apr 10 07:16:38 PM JST 2026 /mnt/data4/test/sub-01/scripts mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading 100 ** failed to open GIFTI XML file '100.gii' mrisReadGIFTIdanum: ERROR reading gifti 100.gii [INFO] read, cannot find 100, trying 100.gii ... error: No such file or directory error: mris_inflate: could not read surface file 100 What I expected I expected recon-all to execute: mris_inflate -no-save-sulc -n 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Additional notes - The expert options file itself is plain text with normal LF line ending. - cat -A /home/kami/expert.opts shows: mris_inflate -n 100$ - od -c /home/kami/expert.opts shows: 0000000 m r i s _ i n f l a t e - n 0000020 1 0 0 \n - mris_inflate itself appears to work normally when run directly. - I also tried -xopts-overwrite, but the same issue occurs. This looks like a recon-all expert-options parsing / argument-passing problem, where the "-n" option is lost before invoking mris_inflate. Please let me know if you would like the full recon-all.log and recon-all.cmd attached. I can also provide a minimal reproducible example. Best regards,Toshiharu ---------------------------------------------------------------------------------------------------- Toshiharu Kamishikiryo M.D.,Ph.D. Department of Psychiatry and Neurosciences. Graduate School of Biomedical & Health Sciences, Hiroshima University. -----------------------------------------------------------------------------------------------------

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Registration for next FreeSurfer course opening soon
by Sennott, Liam Ricker 09 Apr '26

09 Apr '26

Hello all, The next virtual FreeSurfer course will be held on June 2nd, 3rd, and 5th, 2026. Registration for this virtual FreeSurfer course is opening on Monday, April 13th at 10am EDT. Visit our course website to find out more information: https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse Specific questions about the course can be sent to fscourse(a)mgb.org<mailto:fscourse@mgb.org>

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Re: use of a custom annot for mri_segstats
by Simone Cauzzo 09 Apr '26

09 Apr '26

External Email - Use Caution Thank you for your reply. Anyway, I think that the option "--excludeid" would only exclude from the stats report some parcel ids. What I would like to do is not to exclude some parcel ids, but to exclude from the computation of the stats some nodes of the --i input surface, i.e., those that are exactly zero. Maybe I should create a surface mask first? Do you have any suggestions? Thanks Simone Cauzzo

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options for extensive atrophy
by Amelie Metz 09 Apr '26

09 Apr '26

External Email - Use Caution Hi, I wanted to ask for suggestions on how segmentations and surface reconstruction for CT could be improved in individuals with extensive atrophy. I noticed that with my data, FreeSurfer outputs (version 7.4.1) have significant errors especially in areas affected by atrophy in that GM is undersegmented. On the other hand, in controls I sometimes see the opposite issue, where parts of the skull are included as GM. I have been exploring options like -seg-wlo and -bigventricles to improve the output but wanted to see if anyone has encountered similar issues and had other ideas. Thanks, Amelie

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Re: Freesurfer recon-all longitudinal fails: "cp: preserving permissions for '/subjects/sub-X_ses-Y.long.sub-X/mri/filled.mgz': Invalid argument"
by fsbuild 09 Apr '26

09 Apr '26

External Email - Use Caution You could make sure every directory is writeable under subjects, e.g.,$ find /subjects -type d -exec chmod u+w {} +    If /subjects is located outside of the container, then this might help,https://secure-web.cisco.com/1SLN7bBYjZu-bnafE0XmYBKp4_8pWxmQpnG8QIjVG… - R. On Apr 1, 2026, at 16:04, Camacho, Paul <pcamach2(a)illinois.edu> wrote:        External Email - Use Caution        cp -p /subjects/sub-SAY118/mri/filled.mgz /subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgzcp: preserving permissions for '/subjects/sub-SAY118_ses-B.long.sub-SAY118/mri/filled.mgz': Invalid argumentLinux ccc0425.campuscluster.illinois.edu 5.14.0-570.76.1.el9_6.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Dec 17 04:36:29 EST 2025 x86_64 x86_64 x86_64 GNU/Linux

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FLAIR Normalization Error in FreeSurfer (v.7.4.1)
by Boa Sorte Silva, Narlon 09 Apr '26

09 Apr '26

External Email - Use Caution Hi there, I am running recon-all (freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460) on a number of participants with both T1w and FLAIR images. For some participants, we noticed that the pial segmentation does not improve as a result of using the FLAIR (screenshot #1 attached, lh.pial.FLAIR in red). In checking the mri subfolder files, I notice that the was some type of error with the FLAIR.prenorm.mgz —> FLAIR.norm.mgz conversion (screenshot #2 and #3). The log is also attached. I wanted to ask if there’s a way to prevent this from happening or should I just go with the T1w-only recon-all in these cases? For context, I have tested FLAIR with preprocessing (biasfield correction, denoising, registration to T1w space) and without preprocessing, same outcome. Thanks for your help! Best regards Nárlon [cid:d02c9cb3-6cad-410f-9374-43a351d386ca@CANPRD01.PROD.OUTLOOK.COM] [cid:1322927a-21fa-4c30-a0ca-5943d71fd483@CANPRD01.PROD.OUTLOOK.COM] [cid:9a18d9a3-360a-4dff-b9c7-88431f032e12@CANPRD01.PROD.OUTLOOK.COM]

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Freesurfer April 2026