Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

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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Postdoctoral fellowship program 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 (CCBBI) at the Ohio State University is pleased to announce its Postdoctoral fellowship program. CCBBI is an interdisciplinary research facility located in the Department of Psychology at The Ohio State University. In alignment with its mission to advance neuroimaging research and train the next generation of scientists, CCBBI is pleased to announce the inaugural cohort of its Postdoctoral Fellows Program. This competitive two-year fellowship provides salary and benefits (including health insurance) to outstanding early-career scientists. The program is designed as a collaborative investment between CCBBI and participating faculty mentors. Year 1 salary and benefits are fully supported by CCBBI. For Year 2, fellows are expected to continue under the sponsorship of a CCBBI Faculty Fellow. Priority will be given to applicants whose faculty mentors can provide matching funds for Year 2, though applicants without confirmed cost-match support will also be considered based on scientific merit, sponsor fit, and alignment with CCBBI’s mission. The fellowship supports scholars who wish to pursue independent research at CCBBI while contributing to the center’s dynamic and interdisciplinary scientific community at The Ohio State University. *Eligibility Criteria* - Doctoral degree in Psychology, Neuroscience, or a closely related field, earned within the past two years. For candidates who received their degree before this period, please contact CCBBI to discuss the specifics of your circumstances (ccbbi.service(a)osu.edu) - As the goal of this program is to recruit new talent to Ohio State, current graduate students or postdoctoral scholars already working at Ohio State are not eligible. - Sponsorship from CCBBI faculty who will serve as the primary mentor. CCBBI Faculty Affiliates are strongly encouraged to consider a CCBBI Faculty Fellow as a co-mentor. - Faculty cost-match for Year 2 is preferred but not required; priority will be given to mentors who can provide matching funds. - Evidence of superior academic achievement (such as honors or other academic designation, peer-reviewed publications, invited presentations). - Dedication to a research-focused career, with preference given to individuals aiming to pursue academic pathways. *Fellowship Details* The fellowship offers a competitive annual salary of $61,008 plus benefits, with funding available to begin before *August 1, 2026*. Fellows will dedicate 90% of their time to pursuing independent research within a CCBBI-affiliated lab. The remaining 10% of their time will be devoted to professional development through CCBBI activities, including engaging in community outreach, hosting distinguished invited speakers, and contributing to the center’s signature Research Day conference. Fellows will also be encouraged to attend the annual meeting for the Organization for Human Brain Mapping, and all travel costs will be covered by CCBBI. This is a two-year position, structured as follows: - Year 1: Fully funded by CCBBI - Year 2: Continued support anticipated through the sponsoring faculty mentor (cost-match preferred but not required). A progress report will be required at the end of Year 1 to evaluate research progress and confirm Year 2 funding arrangements. *Application Guidelines* Applicants should submit all required materials as a single PDF file to ccbbi.service(a)osu.edu. Letters of recommendation, including one from the faculty mentor, must be sent directly by the recommenders to ccbbi.service(a)osu.edu. All application materials, including letters of recommendation, must be received by *December 15, 2025*. Final decisions will be announced by the end of *January 2026*. 1. *Cover Letter* 2. *Curriculum Vita* 3. *Personal Statement (2-page limit)* Describe your research interests, career goals, and how the CCBBI Postdoctoral Fellowship will support your professional development. The statement should include a summary of your prior training and research experiences, your motivation for pursuing postdoctoral work at CCBBI and the sponsor’s lab, and the ways in which your research aligns with the mission of the center. 4. *Research Plan (3-page limit, with the following sections) * Applicants must submit a research statement that is no more than 3 pages (excluding references) and formatted in 11-point Arial font, single-spaced, with 0.5-inch margins. References should be included at the end and do not count toward the page limit. The research plan should include the following sections: • Aims, Significance, and Innovation (1 page) • Approach and Feasibility (2 pages) • References (no page limit) 5. *Two letters of recommendation* 6. *Nomination letter from CCBBI Faculty Mentor (and co-mentor, if applicable)* Letter should describe the expected impact of the applicant on the sponsor’s scholarly program and the likely impact on scholarship in the discipline. Please also confirm the mentor’s intent to provide matching funds for Year 2. 7. *Up to three peer-reviewed publications* Best, Adam Gorka Ph.D. Research Assistant Professor CCBBI/Psychology Department The Ohio State University

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Re: T1 + DTI for thalamus segmentation
by fsbuild 06 Nov '25

06 Nov '25

External Email - Use Caution You need to install the Matlab R2019b (inside the freesurfer distribution) using the fs_install_mcr script we provide in order for freesurfer commands to reference the Matlab libmwm* libraries.  See the section SETUP A MATLAB DISTRIBUTION under the URL,https://secure-web.cisco.com/1MwJU4ffnWRIUhCWZFkXCcFIUb9Rtul3l-BDi7QFgT… R. On Nov 6, 2025, at 05:23, Antonio Di Renzo <antoniomp777(a)hotmail.it> wrote:

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T1 + DTI for thalamus segmentation
by Antonio Di Renzo 06 Nov '25

06 Nov '25

External Email - Use Caution Messers Freesurfer developers, I am using the joint segmentation of thalamic nuclei from T1 scan and DTI, but unfortunately I did not achieve results. I installed: Freesurfer 7.4.1, OS Ubuntu 22.04.5 jammy and VM Oracle 7.0.6 r155176. - Bayesian Tool Bash: export TUTORIAL_DATA=/home/vboxuser/SIEMENS export SUBJECTS_DIR=$TUTORIAL_DATA/GRUPPO_1_6 cd $SUBJECTS_DIR # Subject's data are stored in subj_01 folder source $FREESURFER_HOME/SetUpFreeSurfer.sh export MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/v97 export LD_LIBRARY_PATH=$MCRROOT/runtime/glnxa64:$MCRROOT/bin/glnxa64:$MCRROOT/sys/os/glnxa64:$MCRROOT/sys/opengl/lib/glnxa64:$LD_LIBRARY_PATH # Run segmentation for subj_01 using the simplified -s option /home/vboxuser/freesurfer/ThalamicNucleiDTI/linux_x86_64/run_SegmentThalamicNuclei_DTI.sh $MCRROOT -s subj_01 Answer: /home/vboxuser/freesurfer/ThalamicNucleiDTI/linux_x86_64/run_SegmentThalamicNuclei_DTI.sh $MCRROOT -s subj_01 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v97/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 THIS IS THE NEW COMPILED VERSION 2====================================================== subj_01, DTI model DSWbeta. ====================================================== ====================================================== Error while running segmentation. Saving error struct. ====================================================== Error using TS_fnc_thalamus_seg_gem_joint (line 250) The value of 'ASEGsharedParamsPath' is invalid. It must satisfy the function: @(x)exist(x,'file'). Error in TS_fnc_jointSegmentationWrapper (line 64) MATLAB:InputParser:ArgumentFailedValidation -CNN tool Bash: CNN segmentation does work, previous steps were performed accurately and without errors. mri_segment_thalamic_nuclei_dti_cnn --t1 $SUBJECTS_DIR/subj_01/mri/norm.dwispace.mgz --aseg $SUBJECTS_DIR/subj_01/mri/aseg.dwispace.mgz --fa $SUBJECTS_DIR/subj_01/dmri/dtifit_FA.nii.gz --v1 $SUBJECTS_DIR/subj_01/dmri/dtifit_V1.nii.gz --o $SUBJECTS_DIR/subj_01/dmri/segthal.nii.gz --vol $SUBJECTS_DIR/subj_01/dmri/segthal_vol.csv --threads 1 Answer: Illegal instruction (core dumped) How can I do to solve these issues? Thank you in advance, Antonio

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