Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

Dockerhub image missing python3
by Dan Fitch 24 Apr '26

24 Apr '26

External Email - Use Caution Hi folks, In the freesurfer/freesurfer:8.2.0 image from Dockerhub, straightforward `recon-all -all ...` runs have: env: 'python3': No such file or directory in STDERR. I'm running on a HTCondor cluster so I'm getting STDERR and STDOUT in separate files and can't see where this is exactly. It's the first line output to STDERR, followed by a bunch of INFO: using NIfTI-1 sform (sform_code=1) threshold mask volume at 0.001 ... that looks normal. When I converted the Dockerfile to a singularity conf and created my own rockylinux:9 8.2.0 container, I didn't see this issue. I've confirmed that going into the container in writable mode and running `yum install python3` fixes it. (As a side note, recent updates being released as in-place patches with the same version number [instead of using minor version changes] is a bit confusing in places like dockerhub. I'm sure you all have a reason for doing it this way, but there are disadvantages too.) Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging

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7t
by Miriam Taza 23 Apr '26

23 Apr '26

External Email - Use Caution Hello, Im wondering if you know if sclimbic would work well on 7T data? Thanks Miriam

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FS version 8 for 7-T mp2rage UNI
by Huaiyu Liu 23 Apr '26

23 Apr '26

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to preprocess my 7T MP2RAGE UNI image (0.65 mm isotropic resolution, TR = 5000 ms, TE = 2.54 ms) using FreeSurfer 8.2.0 with the following recon-all command: recon-all -all -i sub-01_t1w.nii -s sub-01 According to a discussion thread I found in the FreeSurfer archive<https://secure-web.cisco.com/1LCAbAxlUHY-wISqgMbjgKwSDIJ2615y8K3UxjFEuQ_26m…>, it seems that it is acceptable to run the default recon-all pipeline directly on raw MP2RAGE UNI images without prior skull stripping. 1. May I know that whether this is still the recommended approach for FreeSurfer 8.2.0? 2. Additionally, if I want to use FreeSurfer version 7, would it be preferable to perform skull stripping beforehand, or is it still advisable to use the raw UNI image directly? Thank you very much for your guidance and/or suggestions. Best regards, Huaiyu _________________________________________ Huaiyu Liu (Ted) Postdoctoral Research Fellow Department of Imaging Neuroscience, Functional Imaging Laboratory University College London 12 Queen Square, London WC1N 3AR

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Re: Updates/bug fixes available for the 8.2.0 release
by fsbuild 22 Apr '26

22 Apr '26

External Email - Use Caution As of 04/22/26 there are some new updates for the 8.2.0 release as listed below.  If you previously downloaded the patch script from,https://secure-web.cisco.com/1qCx9Ci-0IiJiQhCxDnRpJLjd0jhRddADqK1i_Bg1… - there is no need to download it again.  Just re-run the script to pick up the latest updates according to the instructions listed here that match your system,https://secure-web.cisco.com/1v_nsy-KSg4QUEFw9AiqUXudF57zbV9lCe77-My… - R. ../bin/mri_histo_atlas_segment_fireantsUpdated citations in mri_histo_atlas_segment_fireants ../bin/mri_glmfitRe-added Logan KM ../bin/segmentHA_T2.shFix typos in segmentHA_T2.sh ../bin/SegmentAAN.shPrint right path of output in SegmentAAN.sh ../bin/mri_tumorsynthFixing the problems with i++ exit status that was incompatible with set -e ../bin/create_nnUNet_v1.7_env.shUpgrade python version to 3.9 to allow nnUnet installation for mri_tumorsynth ../python/packages/SuperSynth/scripts/inference.pyReinstating logic that was unintentionally dropped during refactor On Mar 28, 2026, at 22:49, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         As of 3/28/26 here has been an update to a previously patched file, so please run the update script again; nothing should change if everything is up to date. - R. On 3/25/26 17:55, fsbuild (fsbuild(a)contbay.com) wrote:         External Email - Use Caution        Some updates/bug fixes are available for an existing installation of a Freesurfer 8.2.0 release.   These include fixes for recon-all expert options and an update on Ubuntu24 only for gems bindings.  Please see the instructions at, https://secure-web.cisco.com/1v_nsy-KSg4QUEFw9AiqUXudF57zbV9lCe77-MykJwrZf2… _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1XWi_TGfR4IiDaI_ZYrbuJA_sSMnZbvJJc6pDpYQAi7Wio…

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FreeSurfer virtual course 2026
by Sennott, Liam Ricker 22 Apr '26

22 Apr '26

Come learn about FreeSurfer from the experts! The FreeSurfer team is hosting our next virtual FreeSurfer course on June 2nd, 3rd, and 5th. Registration is now open! 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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SuperSynth
by Pollaro, Jim 21 Apr '26

21 Apr '26

External Email - Use Caution What version is SuperSynth in? I've looked in the archives, the release notes, and the wiki and cannot find when/where its included. Thank you, Jim Pollaro ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: Recon-all error: free(): double free detected in tcache 2; Command terminated by signal 6
by fsbuild 21 Apr '26

21 Apr '26

External Email - Use Caution The "double free" notification may be from data corruption in memory, e.g.,  memory management in the Ubuntu Linux virtual machine running on top of the Windows host via WSL2 has gone wrong from trying to free the same location in memory 2X.  So the Linux OS kills the process (signal 6).  This might be from mri_synthseg running tensorflow and running out of memory.  I would check on how much memory WSL2 has been given to run the guest Linux OS, Ubuntu 22.   My guess is at least 4G of physical RAM needs to be reserved to run the Windows OS on the machine, and subsequently you could try allocating the rest to WSL2.  I would try to give Ubuntu22 at least 16G of RAM, but for a full recon-all 32G ay be needed. - R.. On Apr 20, 2026, at 11:14, Huaiyu Liu <huaiyu.liu(a)ucl.ac.uk> wrote:

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[WARNING: ATTACHMENT UNSCANNED][WARNING: UNSCANNABLE EXTRACTION FAILED]Brainstem substructure ROIs in fsaverage
by Zoe Cheng 20 Apr '26

20 Apr '26

External Email - Use Caution Dear list, I have a question and wanted to share an updated solution in case it’s helpful to others. I was wondering whether there are recommended approaches to obtain brainstem substructures for the fsaverage template brain. In the aparc+aseg atlas, the brainstem is defined as a single ROI. I’m interested in using a more fine-grained parcellation of the brainstem. I just received a solution from Eugenio, the original author of the brainstem substructure atlas. I’m sharing the atlas here in case others have a similar need. Many thanks to Eugenio for the generous help! Best Regards, Zoe

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Recon-all error: free(): double free detected in tcache 2; Command terminated by signal 6
by Huaiyu Liu 20 Apr '26

20 Apr '26

External Email - Use Caution Dear FreeSurfer Developers, I'm attempting to use the recon-all command to reconstruct my participants’ T1w image. However, for my first subject I got the ERROR message as shown below, highlighted in yellow text SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://secure-web.cisco.com/10_kcPN3k0kfptURbnOBpXPLalN06CN9jiSyVxZ_4dUhl9… Website: https://secure-web.cisco.com/1O4alEhXXfpduXDK8u0gWl94GE3VCnVsRFU5Pzm78c5SxB… @#@FSTIME 2026:04:20:15:14:17 mri_synthstrip N 6 e 37.26 S 12.60 U 22.37 P 93% M 5936164 F 1480 R 6260625 W 0 c 73 w 5135 I 394368 O 0 L 0.87 0.56 0.28 @#@FSLOADPOST 2026:04:20:15:14:55 mri_synthstrip N 6 1.01 0.63 0.32 mri_synthseg --i /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/mri/orig.mgz --o /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/mri/synthseg.rca.mgz --threads 1 --vol /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/stats/synthseg.vol.csv --keepgeom --addctab --cpu free(): double free detected in tcache 2 Command terminated by signal 6 @#@FSTIME 2026:04:20:15:14:55 mri_synthseg N 11 e 9.72 S 1.43 U 3.04 P 46% M 456024 F 3608 R 61055 W 0 c 11 w 34031 I 704560 O 8 L 1.01 0.63 0.32 @#@FSLOADPOST 2026:04:20:15:15:04 mri_synthseg N 11 1.17 0.68 0.34 Linux gangoffour 6.6.87.2-microsoft-standard-WSL2 #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-02 exited with ERRORS at Mon Apr 20 15:15:05 BST 2026 I've searched the list and found one same issue on github, however that issue was closed and no answers provided? Also, I’ve attached the recon-all.log for your information . 1) FreeSurfer version: --freesurfer-linux-ubuntu22_x86_64-8.2.0-20260314-d932c45 – 2) My command: -bash: /usr/local/freesurfer/7.3.2/SetUpFreeSurfer.sh: No such file or directory -------- freesurfer-linux-ubuntu22_x86_64-8.2.0-20260314-d932c45 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/8.2.0 FSFAST_HOME /usr/local/freesurfer/8.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/8.2.0/subjects MNI_DIR /usr/local/freesurfer/8.2.0/mni FSL_DIR /usr/local/fsl hliu@gangoffour:/mnt/c/Program Files/WSL$ freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ export SUBJECTS_DIR=/mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ echo $SUBJECTS_DIR /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ cd /mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ ls sub-02_t1w.json sub-02_t1w.nii hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ sudo chmod -R a+w $SUBJECTS_DIR hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ recon-all -all -i sub-02_t1w.nii -s sub-02 3) Platform: Windows 11 Enterprise, WSL2, Ubuntu 22 4) uname -a: Linux gangoffour 6.6.87.2-microsoft-standard-WSL2 #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux 5) recon-all.log: see attached

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Freesurfer license request - gateway http:504 timeout
by John Snowdon 17 Apr '26

17 Apr '26

External Email - Use Caution Hi, I am applying for a license.txt for the use of Freesurfer on our new institutional HPC facility and the license request page submits (the Cloudflare captcha loads correctly) but responds with a HTTP:504 Gateway timeout. No content is displayed on https://secure-web.cisco.com/1_GLfjGC6pStqhd3q2FmaTuWfeF3RJQAslaHrjXQXMwfVc…<https://secure-web.cisco.com/1YfL38c6Fk32S6IUVhw6LTkvpE7YE8ImJlKozEt6ORxQx2…> Is anyone from the Freesurfer team able to resolve this with their local IT colleagues? John Snowdon Senior Research Infrastructure Engineer (HPC) Research Software Engineering Catalyst Building, Room 2.01 Newcastle University 3 Science Square Newcastle Helix Newcastle upon Tyne NE4 5TG https://secure-web.cisco.com/1VA3bk7k4IMKSUQQ-PvZCdkh-R4dWX6tc4uPkDJBTH8cEI…

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