Freesurfer November 2025

freesurfer@nmr.mgh.harvard.edu

32 participants
40 discussions

Next brain atlas on ex vivo MRI
by Yasmine Salman 17 Nov '25

17 Nov '25

External Email - Use Caution Dear FreeSurfer developers, I am trying to run the command mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS MODE SIDE from NexBrain atlas on my ex vivo left hemisphere scan called EX_VIVO_18. I therefore use the following command : mri_histo_atlas_segment_fireants T2.nii EX_VIVO_18 1 -1 hemi left And I get this answer back : "Incorrect number of arguments. Usage: mri_histo_atlas_segment_fireants INPUT_SCAN OUTPUT_DIRECTORY GPU THREADS [BF_MODE] Or, for help mri_histo_atlas_segment_fireants --help" which corresponds to the SynthMorph version, which is designed for in vivo MRI. I therefore do not know how to run the "real" ex vivo MRI command. Thanks in advance, Yasmine

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Re: QDEC license error
by fsbuild 15 Nov '25

15 Nov '25

External Email - Use Caution The system libraries have changed on newer versions of Linux such that the freesurfer 6 binaries can no longer read the license file.  Freesurfer 6 was released in 2017 at the time when CentOS6 (RedHat 6) and MacOS 10..7 were still relatively current.  Some 8 years later, the encryption, etc., libraries have changed on current Linux OS’s.  Also, qdec has been deprecated (no longer supported) in the subsequent 7.X and 8.X freesurfer releases where the alternative is to use freeview and commands like mris_surf2surf mri_glmfit, mri_glmfit-sim, etc., for stream processing.  Any license you download now should work with the 7.X and 8.X releases. If you already have experience using a version of a Linux OS where you were able to run the 6.0 release using your own personal or perhaps your institutions license file, then I would try and duplicate that setup.  That may mean you need to use a container or VM to host that older version of the Linux OS where FS6 could read the license file on top of a newer version of Linux OS, i.e., if the original system where FS6 ran is no longer available. - R. On Nov 15, 2025, at 21:02, Henry Do <minhhiep.do(a)sydney.edu.au> wrote:        External Email - Use Caution        Hi Freesurfer expert, I am having an error with the QDEC. I am using Freesurfer v6.0 stable and it keeps giving me error when I do the analyze. I can load the qdec table and all other commands still run fine but when I did the analyze, it gave this error. I have converted the license.txt to $FREESURFER_HOME/.license like previous suggestion but doesn't work. Writing to /home/henrydo/subjects/qdec/Untitled/contrasts.sig.mgh--------------------------------------------------------------------------ERROR: Invalid FreeSurfer license key found in license file /home/henrydo/software/freesurfer/.license  If you are outside the NMR-Martinos Center,  go to http://secure-web.cisco.com/1ZlyBXRvfJ4TIBTtdtGuv0qPMrQ2CslRKxOtpCD… get a valid license file (it's free).  If you are inside the NMR-Martinos Center,  make sure to source the standard environment.--------------------------------------------------------------------------  I want to use QDEC to see which subjects will have impacts on different regions. If possible, I would like to have instruction how to do visualize it without qdec.  Many thanks,Henry_______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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QDEC license error
by Henry Do 15 Nov '25

15 Nov '25

External Email - Use Caution Hi Freesurfer expert, I am having an error with the QDEC. I am using Freesurfer v6.0 stable and it keeps giving me error when I do the analyze. I can load the qdec table and all other commands still run fine but when I did the analyze, it gave this error. I have converted the license.txt to $FREESURFER_HOME/.license like previous suggestion but doesn't work. Writing to /home/henrydo/subjects/qdec/Untitled/contrasts.sig.mgh -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /home/henrydo/software/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1ZMUb3rLIKtbUCpTz2aOiKX5ZTHQDVKbpcuykvo5CNFCnYX… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- I want to use QDEC to see which subjects will have impacts on different regions. If possible, I would like to have instruction how to do visualize it without qdec. Many thanks, Henry

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sbTIV SAMSEG error
by Chelsea Hennessy 14 Nov '25

14 Nov '25

External Email - Use Caution Hello, I am trying to run sbTIV following on my SAMSEG output through Freesurfer, but am running into issues. My SAMSEG code: #!/bin/bash # script to run SAMSEG on all participants # define directories DATA_DIR=“XYZ" OUTPUT_BASE_DIR=“XYZ" LOG_DIR=“XYZ" # create directories if they don't exist mkdir -p "${OUTPUT_BASE_DIR}" mkdir -p "${LOG_DIR}" # log file LOG_FILE="${OUTPUT_BASE_DIR}/samseg_log.txt" echo "SAMSEG processing started: $(date)" > "${LOG_FILE}" # loop through all participant directories for SUB_DIR in "${DATA_DIR}"/sub-*/; do # extract participant ID from directory name SUB_ID=$(basename "${SUB_DIR}") # define directory paths T1_FILE="${SUB_DIR}ses-01/anat/${SUB_ID}_ses-01_T1w.nii.gz" OUTPUT_DIR="${OUTPUT_BASE_DIR}/${SUB_ID}" INDIVIDUAL_LOG="${LOG_DIR}/${SUB_ID}_samseg_log.txt" # check if T1w image file exists if [ -f "${T1_FILE}" ]; then echo "Processing ${SUB_ID}..." | tee -a "${LOG_FILE}" echo "Input: ${T1_FILE}" | tee -a "${LOG_FILE}" echo "Output: ${OUTPUT_DIR}" | tee -a "${LOG_FILE}" # run SAMSEG run_samseg --input "${T1_FILE}" --output "${OUTPUT_DIR}" --threads 8 2>&1 | tee "${INDIVIDUAL_LOG}" # check if analysis completed successfully if [ $? -eq 0 ]; then echo "SUCCESS: ${SUB_ID} completed at $(date)" | tee -a "${LOG_FILE}" else echo "ERROR: ${SUB_ID} failed at $(date)" | tee -a "${LOG_FILE}" fi echo "-----------------------------------" | tee -a "${LOG_FILE}" else echo "WARNING: T1 file not found for ${SUB_ID}" | tee -a "${LOG_FILE}" echo "Expected: ${T1_FILE}" | tee -a "${LOG_FILE}" echo "-----------------------------------" | tee -a "${LOG_FILE}" fi done echo "SAMSEG analysis completed: $(date)" | tee -a "${LOG_FILE}" echo "Log file saved to: ${LOG_FILE}" When trying to run sbTIV for one participant as an example: sbtiv <path>/samseg.stats -o <path>/sbtiv.stats Error: Traceback (most recent call last): File "/Applications/freesurfer/8.1.0/python/scripts/sbtiv", line 8, in <module> sys.exit(main()) File "/Applications/freesurfer/8.1.0/python/packages/samseg/cli/sbtiv.py", line 23, in main with open(args.input) as fid: AttributeError: 'Namespace' object has no attribute 'input' Am I correct in understanding that the value provided in the sbtiv.stats is the sbTIV value? Even when it is the same as the intra-cranial measure from the samseg.stats file? I have very limited coding/neuroimaging analysis knowledge, so any help you can provide here is greatly appreciated! Cheers, Chelsea

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Freeview crashing
by Scanga, Joey 12 Nov '25

12 Nov '25

External Email - Use Caution Hello, I’m trying to run Freeview over VNC on our server. The application will open, I'll try to open a file, the progress bar will begin to fill up, then the application crashes. Has this error been encountered before? I tried both versions 7.3.2 and 8.0.0, but both had the same issue. We’re running this on Ubuntu 22.04.5 LTS. Thanks! -Joey ________________________________ 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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reply
by 顾梦凯 11 Nov '25

11 Nov '25

External Email - Use Caution reply

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freesurfer license error: qdec not recognize license
by Henry Do 11 Nov '25

11 Nov '25

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to use Qdec to perform group comparisons and use the interactive UI to identify which subjects have a significant influence on my clusters. I’m currently running the stable version 6.0 of FreeSurfer. However, Qdec returns an error indicating that my license is invalid. Other FreeSurfer commands run without any issues — it seems that only Qdec reports this error when I run the analysis. Could you please advise on how to resolve this issue? Thank you very much for your time and help. I have attached the terminal screen and the license below. Regards, Henry. [cid:image001.png@01DC5326.B7453120] 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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confirm
by Matteo Galassi 10 Nov '25

10 Nov '25

External Email - Use Caution confirm d2cbad9ab01119a669fb325a2966a2e6d283dc7d -- ------------------------ Indirizzo istituzionale di posta elettronica degli studenti e dei laureati dell'Università di TorinoOfficial University of Turin email address for students and graduates

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Recon-all-clinical/SynthSeg Concerns w/ Atrophy
by Rudolph, Marc D 07 Nov '25

07 Nov '25

External Email - Use Caution Our group is trying to decide on whether we should move to FS8/clinical recon all indefinitely, however we note some inconsistencies. In some instances, SynthSeg seems to completely ignore the underlying structure and “imputes” tissue. Cortical thickness estimates are overall most different from FS7, as may be expected, however, in some cases volumes (e.g., hippocampus) may also be overestimated. We have 1mm isotropic T1s, which I see that recon-all may be "generally more accurate than recon-all-clinical.” We’re looking to take advantage of SynthSeg’s ability to overcome poor data quality/dropout/complex folding etc., but do not want to necessarily “in-paint normal looking tissue.” Can you provide any additional information or guidance on the best path forward? Thank you very much for your time and any guidance! ________________________________ This electronic message is intended only for the use of the individual(s) and entity named as recipients in the message. If you are not an intended recipient of this message, please notify the sender immediately and delete the material from any computer. Do not deliver, distribute or copy this message, and do not disclose its contents or take any action in reliance on the information it contains. Thank you.

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Research Scientist within the Center for Cognitive and Behavioral Brain Imaging at The Ohio State University
by Adam Gorka 06 Nov '25

06 Nov '25

External Email - Use Caution Dear Colleagues, The Center for Cognitive and Behavioral Brain Imaging (CCBB) at The Ohio State University is currently accepting applications for the following position. *Research Scientist* The Center for Cognitive and Behavioral Brain Imaging (CCBBI) at The Ohio State University is seeking a highly motivated Research Scientist to join our team. This one-year appointment (renewable based on performance and funding) supports an active research program aligned with CCBBI’s mission. Responsibilities include: - Conducting and disseminating human neuroscience research - Pursuing extramural funding - Presenting at national and international conferences - Supporting CCBBI’s scientific and training initiatives, including scanner operations, TMS facility management, workshops, and innovation in neuroimaging *Minimum Education Required:* Ph.D. in Neuroscience, Psychology, or a related field. *Required Qualifications* - At least three years of postdoctoral experience. - Extensive experience with functional MRI approaches for studying human brain function. - Thorough familiarity with programming and analysis in MATLAB and/or Python. - Strong record of peer-reviewed publications and productivity beyond the postdoctoral level. - Demonstrated ability to conduct independent research. - Excellent written and verbal communication skills. *Apply here:* *External Applicants*: *https://secure-web.cisco.com/1EAShsmOgZ3bGyHB5pzbcnf3VW1fI2AzSK8BQ1GpTkgaoaGviRbM18XV7uYDpHBSDr9YPGdkjnV8R0HreDjSXuU27nxtMDK7zWIyKi2uQlJI-QFF00Bab8shbKipeLmIlNJwkDRK5bsfJAeDHOmLeVZamkvoeS-ZV51O_vJpC2TD7qKr59Blesuk9U6biK1Ohaw1aXQkgsWUnSEur4Ba8rINYzW98uC1F0oV6sAObZOcKFT8796J-6CLq4D1tDc_BYKFigwkajC_MBe2KX1crMVk-8hs4ixm1JDTIgkeRBAMKa0pzvpZkOBfn0dBVGvcXjdbPaaztS3NOD5HaV7h_Cw/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2FOSUCareers%2Fjob%2FColumbus-Campus%2FResearch-Scientist_R137913-1 <https://secure-web.cisco.com/1EAShsmOgZ3bGyHB5pzbcnf3VW1fI2AzSK8BQ1GpTkgaoa…>* Best regards, Adam Gorka Ph.D. Research Assistant Professor CCBBI/Psychology Department The Ohio State University

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Freesurfer November 2025