Freesurfer September 2025

freesurfer@nmr.mgh.harvard.edu

36 participants
42 discussions

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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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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Intra cranial volume as a covariate
by Alan Francis 07 Oct '25

07 Oct '25

External Email - Use Caution Hi Freesurfer group: I have been using ICV as a covariate in all my analyses. Can CORTEX VOLUME be a better measure of covariance? If not, why? Thanks, Alan -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* Dr. Alan N. Francis Assistant Professor of Neuroscience Director: Neuroimaging & Neuromodulation Research Lab Institute of Neuroscience University of Texas, School of Medicine Rio Grande Valley, Texas.

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Freesurfer 7.4.1 memory usage differences between Ubuntu 20 and Ubuntu 22
by Suzanne Witt 03 Oct '25

03 Oct '25

External Email - Use Caution Hello, I have previously been running Freesurfer 7.4.1 Ubuntu 20 from a Docker container on a GCP n1-highmem-4 machine (4 CPUs, 26GB RAM, 207GB Disk, 32GB Swap) with no issues. I recently updated the Docker image to install Freesurfer 7.4.1 Ubuntu 22 from the official distribution, and now “recon-all” is getting stuck after mri_nu_correct.mni completes and at the very start of “mri_add_xform_to_header -c /usr/local/freesurfer/subjects/05/mri/transforms/talairach.xfm nu.mgz nu.mgz”. Currently, in order to get Freesurfer 7.4.1 Ubuntu 22 to run to completion, I am having to launch the jobs on a GCP n1-highmem-8 machine (8 CPUs, 52GB RAM, 207GB Disk, 32GB Swap). I am not seeing anything in either the release notes or the message boards to suggest that the Ubuntu 22 version of Freesurfer 7.4.1 has additional memory requirements compared with the Ubuntu 20 version. I have tested reducing both of the omp threads and itk threads from 4 to 2. I am also not running with the “parallel” flag. Are there any other options that can be used to reduce the memory usage of the Ubuntu 22 version of Freesurfer 7.4.1? I’ve attached a typical log file showing the recon-all workflow getting stuck at the “mri_add_xform_to_header” step. cheers. Suzanne T. Witt, PhD Scientific Solutions Engineer suzannewitt(a)flywheel.io<mailto:suzannewitt@flywheel.io> she/her flywheel.io<https://secure-web.cisco.com/1lauWKjXr4_chpBjaaXEv16-WgEUjyLdWrrdE7rj4CoASO…> [A close-up of a logo Description automatically generated] Sign up to receive our monthly updates<https://secure-web.cisco.com/1yipTZHLgLQzEDOTwlegpN9Mp4brS1wWsbahzxQ9yRI6Gu…>

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Waiting for PID error.
by Sambamoorthy, Sowmya 30 Sep '25

30 Sep '25

External Email - Use Caution Dear Experts, One of my recon-all seems to be in a hung state. Started the recon at 10AM and its still going on - we have other brains that typically finish within 4 hrs. These are the last few entries from the recon-all log. Should I kill this process? What could be the root cause for this state? Any help appreciated. TIA! -Sowmya 280/300: dt: 0.9000, rms radial error=124.996, avgs=0 285/300: dt: 0.9000, rms radial error=124.336, avgs=0 290/300: dt: 0.9000, rms radial error=123.681, avgs=0 295/300: dt: 0.9000, rms radial error=123.030, avgs=0 300/300: dt: 0.9000, rms radial error=122.383, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 152036.29 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00112 epoch 2 (K=40.0), pass 1, starting sse = 54086.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/13 = 0.00388 epoch 3 (K=160.0), pass 1, starting sse = 32919.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00615 epoch 4 (K=640.0), pass 1, starting sse = 27218.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00710 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.1488 hours FSRUNTIME@ mris_sphere 0.1488 hours 4 threads #VMPC# mris_sphere VmPeak 2099556 mris_sphere done PIDs (2329613 2329616) completed and logs appended. #@# Fix Topology lh Tue Sep 30 11:59:56 CDT 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 lh #@# Fix Topology rh Tue Sep 30 11:59:56 CDT 2025 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 rh Waiting for PID 2398610 of (2398610 2398617) to complete...

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Error with segmentHA_T2.sh on FreeSurfer 7.4.1
by Rashid, Shams 29 Sep '25

29 Sep '25

External Email - Use Caution Dear FreeSurfer experts, I am running into a problem with hippocampal subfield segmentation with T2 input on a newly installed FreeSurfer 7.4.1 and I really need help. On this subject, recon-all and segmentHA_T1.sh completed successfully, but when I ran segmentHA_T2.sh, I get the following error after a few minutes of processing: ------ writing to T2corrected.mgz... set final LTA type to 1 ERROR: tried to read 51314688, actually read 0 Index in position 1 exceeds array bounds. Error in applyCropping (line 15) Error in segmentSubjectT1T2_autoEstimateAlveusML (line 935) MATLAB:badsubscript Command exited with non-zero status 249 ------ This instance of FreeSurfer 7.4.1 is running on Ubuntu 22.04.5 running on VirtualBox 7.1.8 on a Windows 11 Pro for Workstations. I have tried segmentHA_T2 with two different T2 input images (axial and coronal), and get the same error both times. The images open OK on Matlab. Not sure if this is a problem with the Matlab runtime. I have installed (and re-installed) Matlab runtime R2019b using fs_install_mcr 2019b. I have attached the log files for segmentHA_T2 (and also recon-all, which worked OK). I would greatly appreciate your help. Thank you very much! Best regards, Shams -- Shams Rashid, PhD Instructor Diagnostic, Molecular and Interventional Radiology BioMedical Engineering & Imaging Institute (BMEII) Icahn School of Medicine at Mount Sinai 1470 Madison Ave 1st floor, S1-116 New York, NY 10029

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Large discrepancies between FreeSurfer v7.2.0 and v8.0.0 outputs
by Hana McMahon 26 Sep '25

26 Sep '25

External Email - Use Caution Hi, I’ve processed the same set of T1‐weighted scans with both FreeSurfer v7.2.0 and the newer v8.0.0. When I compare the regional stats (aseg + subfield tables), the absolute proportional differences are surprisingly large (anywhere from ~1 % up to nearly 200 %, depending on the structure). I first noticed the issue while running ANCOVAs: with the v8 outputs, estimated total intracranial volume (eTIV) is highly significant in every model, whereas the v7 results (using identical R code and covariates) show a very different pattern. I am wondering: * Are these version‐to‐version shifts expected, given the changes in v8? * Have others reported similar magnitude differences, particularly for eTIV and subcortical/hippocampal measures? * Are large shifts expected from run-to-run as well? * Any insight would be greatly appreciated, as I am concerned by the magnitude of the differences I am seeing between versions, which are significantly changing my results. Thanks for your time. Kindest, Hana Confidential communication - This email and any files transmitted with it are confidential and are intended solely for the addressee. If you are not the intended recipient, please be advised that you have received this email in error and that any use, dissemination, forwarding, printing, or copying of this email and any file attachments is strictly prohibited. If you have received this email in error, please notify me immediately by return email and destroy this email.

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Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 25 Sep '25

25 Sep '25

External Email - Use Caution [A close up of a logo Description automatically generated][UGWqtuoMAAAAASUVORK5CYII=] Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay 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 fMRI and proton MR spectroscopydata 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. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/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 high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding 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 accelerated and multi-echo fMRI sequences, 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 PI’s 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 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][signature_4161372267]

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Question about using FreeSurfer license on another computer
by Andy Junghyun Kim 23 Sep '25

23 Sep '25

External Email - Use Caution Hi, I am currently using FreeSurfer on my local laptop and have a license.txt file. I will also need to run FreeSurfer on our lab server. Can I simply copy my existing license.txt file to the lab server, or do I need to request a new license for each computer? Kind regards, Andy Kim

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Freeview questions
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 22 Sep '25

22 Sep '25

External Email - Use Caution Hi freeview developers - Still trying to make a rough transition from tkmedit to freeview. I have two questions: *I want to the recon brush to paint the main volume voxels from a secondary volume. Is there a possible way to do that in freeview without doing it one voxel at a time? Ex. I want to draw back voxels from the brainmask.mgz from the T1.mgz. *What are waypoints? I don't see any instructions on the wiki on how to take advantage of them - are they designed to supersede control points? Thanks. Victor Zeng Beth Israel Deaconess Medical Center Vial of Victory LLC -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1an1yVo6v6mmRxVNWBlv4yPHWVxCUoCso9_-8NIHwNomwWY… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Freesurfer September 2025