Freesurfer

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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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PAG and VTA delineation
by Huaiyu Liu 15 Apr '26

15 Apr '26

External Email - Use Caution Dear Freesurfer developers, I am using this tutorial (https://secure-web.cisco.com/1XD9LLQnRJF77R_wsTSJMenKzi1tmGnEXcYl0tRY2Xeca6…) to segment my brainstem AAN nuclei. My freesurfer version is 7.3.2. However, I couldn't find this segmentation shell script in my freesurfer. SegmentAAN.sh I wonder do I need to install it from somewhere else? Or do I need to install a recent freesurfer version? Best, 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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Volumetry of 3 T scans and longitudnal study
by Ajay Sharma 15 Apr '26

15 Apr '26

External Email - Use Caution Dear FreeSurfer Team, I am looking for brain parcellation tool for 3 T T1w images. Could you please suggest the DL tool in freesurfer that is more relevant for brain parcellation of 3 T scans. The study is based on high-field images only. Best, Ajay

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Automatic delineation of PAG and VTA using FreeSurfer
by Huaiyu Liu 15 Apr '26

15 Apr '26

External Email - Use Caution Dear FreeSurfer Team, I hope you are well. My name is Ted and I am a postdoc working at the UCL, faculty of brain science I am working with high-resolution T1-weighted MRI data and would like to identify an automated approach to delineate the periaqueductal gray (PAG) and ventral tegmental area (VTA) at the individual participant level. I was wondering whether FreeSurfer provides: 1) Automated segmentation or masks for PAG and/or VTA 2) If so, how precise these segmentations are (e.g., spatial resolution, validation), and 3) Whether these delineations are available at the single-subject level, rather than only in standard space If FreeSurfer does not support this directly, I would also appreciate any recommendations for alternative tools or workflows. Many thanks for your time and help in advance. Best regards, Huaiyu Liu (Ted)

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Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 13 Apr '26

13 Apr '26

External Email - Use Caution [A close up of a logo Description automatically generated] Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The IMPACT Mental Health Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing proton magnetic resonance spectroscopy (MRS) data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Experience with MRS data acquisition (e.g. MEGA-PRESS) and processing (e.g. LCModel) techniques as well as Unix/Linux scientific computing environments is expected. Familiarity with MATLAB, Python, or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and adult populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The position is funded by five ongoing NIH R01 neuroimaging projects (R01MH120601, R01DA054885, R01MH128878, R01MH131207, and R01DA059527), providing unparalleled resources for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge sequences licensed from the University of Minnesota Center for Magnetic Resonance Research (CMRR), high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PIs' proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. All qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by the University of Miami. Andrea Otero, M.D. IMPACT Lab Research Supervisor Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu Phone: 305-243-7086 [Image][cid:image002.png@01DC085F.16143290]

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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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