Freesurfer October 2025

freesurfer@nmr.mgh.harvard.edu

36 participants
33 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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GLM on runs with different conditions
by Xu, Yaoda 23 Dec '25

23 Dec '25

External Email - Use Caution Hi there, I have a large number of conditions to include in a study, like 60. So I split the conditions into multiple runs, with 40 conditions per run, say run 1 with conditions 1 to 40, run 2 with conditions 21 to 60, and run 3 with conditions 1 to 20 and 41 to 60. Can I put all three runs in a run list and run a single GLM with 60 conditions? Normally, I would have the same number of conditions in each run when I put a bunch of runs together in a single GLM to increase SNR. In this case, different runs would share some of the conditions, but not all conditions appear in each run. I just want to make sure that it is OK to run a GLM like this and get a valid beta estimate for each of the 60 conditions. Thanks a lot. Yaoda Xu

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make_average_subject
by Don Hagler 23 Dec '25

23 Dec '25

External Email - Use Caution We have used make_average_subject to resample the white and pial surfaces of an individual subject to ico 7 to produce surface coordinates in the standard tessellation, allowing for group analyses of cortical shape. It may be worth noting that we temporarily replace the talairach.xfm in the subject’s mri/transforms directory with an identify matrix so that the resampled surfaces have the same position and shape as the native surfaces but with the standard ico 7 tesselation. This resampling procedure works great with FreeSurfer version 5.3, but as of version 6.0 or 7.1.1, when a single subject is supplied to make_average_subject, it runs for a while but then eventually produces an error like this: nframes = 1 Computing std/var across frames ERROR: cannot compute std from one frame ERROR: make_average_surface While we can continue doing this resampling step using FS 5.3 (e.g., after running the initial recon with 7.1.1), we would like to stop relying on this very old version. Is there an alternative approach to re-tesellation of an individual subject’s surfaces into ico? Or could a future release of FreeSurfer include a modification to make_average_surface to allow it to once again handle a single subject as input?

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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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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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Research Scientist within the Center for Cognitive and Behavioral Brain Imaging at The Ohio State University
by Adam Gorka 30 Oct '25

30 Oct '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/1G9Pu1E13gCtz_U_gZNIi-R3JIQ6BVAMgg6aRV_k4OQ2nehr468lg0M02pOzlAga9jNx1CLqfyNYcmi7cFEOQSJxKx5MGtYRZmWXvRwFUCv3IyKMJzKHyLWrlnkwebJKM-SHvz_cs42pVqgNOSkEnp34_hNPB6io-at5LjL_TqnOtNn0ybcCB3iWjn5Jp4YTYpYSlSX0_eIKzqPj6ocj_jM-5-BooSd8TP7J2d9y_8NAzAxhIKeU_Tm5mvwyH7eSb7ML6l167AkUNqXpQGhbc5ClUIozYprjcToNVkvoXi6VxQUbzUD2Zql0o-Cyp8ZsJwCFY1cMy6QO6YhQ-rH1mBw/https%3A%2F%2Fosu.wd1.myworkdayjobs.com%2FOSUCareers%2Fjob%2FColumbus-Campus%2FResearch-Scientist_R137913-1 <https://secure-web.cisco.com/1G9Pu1E13gCtz_U_gZNIi-R3JIQ6BVAMgg6aRV_k4OQ2ne…>* 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 30 Oct '25

30 Oct '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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Will there be a docker image for freesurfer 8.1 on dockerhub?
by Enrico Glerean 30 Oct '25

30 Oct '25

External Email - Use Caution Hello we are installing FreeSurfer 8.1 on our HPC cluster. We can create our own container/module but I was wondering if there is any plan in adding FS8.1 to the official dockerhub list? https://secure-web.cisco.com/10SK8DgtsfSQtHTS3aXkR1pDqh6-xaoFVKDe_WG4W32gQX… Cheers Enrico

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AABC Release 1 of HCP-Aging & AABC Data on BALSA
by Jennifer Elam 27 Oct '25

27 Oct '25

External Email - Use Caution *AABC Release 1 of HCP-Aging & AABC Data * The Aging Adult Brain Connectome (AABC) consortium is pleased to announce its initial release of imaging and non-imaging phenotypic data on the ConnectomeDB powered by BALSA <https://secure-web.cisco.com/1E3sA1hpgb9eIUb1EkJtSztyGN1osO5SHdKLoHmILD8z7p…> platform. This includes data for all HCP-Aging (HCA) participants and visits, plus an initial set of AABC visits. AABC is a longitudinal follow-on study to the HCA study of healthy participants ages 36-90+. AABC is recruiting 1000 participants (legacy HCA and new) for two additional longitudinal visits, collecting up to four timepoints per participant to generate within-participant brain trajectories over spans of up to 10 years, enabling examination of vulnerability and resilience factors related to cognitive decline. AABC Release 1 includes cross-sectional (V1) and longitudinal (V2, V3) 3T MR scans and non-imaging data from 1248 healthy older adults (ages 36-90+) in the *HCP-Aging* and *AABC* projects. It includes multi-modal preprocessed (including with FreeSurfer) and unprocessed imaging data from 1248 participants across 2214 imaging visits (many subjects have data from more than one visit). It also contains non-imaging data collected over a broad range of domains for 1248 V1, 762 V2, and 236 V3 (2246 total) in-person visits and remote follow up surveys (non-imaging events). See session breakdowns by study and visit/event <https://secure-web.cisco.com/1e5aBoX5ZR8ehhwVS1IbFviFaTUSuBv-_3C81m6beQNcfR…> . 7 T Magnetic Resonance Spectroscopy (MRS) data are available for 138 participants. Multi-modal Imaging Derived Phenotypes (IDPs) are available for participants with imaging data. *Release 1 Highlights:* - Preprocessed and unprocessed structural MRI, resting state fMRI, task fMRI, diffusion MRI, and ASL data in modality-specific "HCP package" datasets downloadable from BALSA (see below). Most users should access Preprocessed Recommended fMRI data that have been cleaned of spatially and temporally specific structured noise and precisely aligned across subjects by multimodal cortical surface registration (MSMAll). - 3T Multi-modal Imaging Derived Phenotypes (IDPs) for released participant sessions available in CSV (zip archives in IDPs tab) and Connectome Workbench-compatible CIFTI imaging package formats. - 7 T Magnetic Resonance Spectroscopy (MRS) brain metabolite data are available for 138 participants. - Non-imaging behavioral and biomeasure data available for released participant sessions and follow up events. - Core Variables, high interest primary variables and summary scores, including MRS brain metabolites, can be viewed and filtered in the BALSA UI (use Column Selector to add, Export CSV to download). - >3,000 Extended variables, including item-level and follow up event variables, for all participant events available in a comprehensive spreadsheet. - NIH Toolbox raw and score data for in-person visits are available as spreadsheets/zip archive. - Visualization instructions and HCA1798 group average template data for visualizing HCP pipelines output, including IDPs, in Connectome Workbench wb_view. *Get Access and Download the data: *Get started by Registering for BALSA <https://secure-web.cisco.com/1zlKesUDMp29RSUVbSD292xuZape2LcLiWdzVpZBVGzNz0…>, click on the “ConnectomeDB” tab, and agree to the AABC Data Use Terms. An academic, non-profit, or government email address is required to agree to the AABC Data Use Terms and access the data. To download imaging data, you must 1) install Aspera Connect <https://secure-web.cisco.com/1Xr8Q6C27qOK7Ae_kDB0rxbRWJ0oJaa_RR7QfLJCsb5syo…> (*scroll down to “IBM Aspera client-deployed software” to find Aspera Connect download links*) and 2) an Aspera Connect plugin for your browser (available from Firefox, Chrome, Safari, etc.). Set Preferences>Transfers in Aspera Connect to a directory with sufficient space for large downloads. To download the full non-imaging data, click the Files tab and Download under AABC_Release1_Non-imaging_Data-XL.csv <https://secure-web.cisco.com/1W0PF5h5DPNy4MZqxW2xvdWhizhWq2M12bMNdiCs4f-eEO…>. Use the Column Selector and Export CSV to view, filter on, and download all or subsets of Core Variables for selected subjects. *Join the Community.* If you are actively using HCP data and tools, we encourage you to join and be active in the HCP-Users Google group <https://secure-web.cisco.com/16VYRKxOjfiaFENy_kteTyNOu85xi0i-u0aDPu_RVOuL5_…>, so that you can tune in to technical discussions on issues that may be of interest. Once you have joined (posts from nonmembers are moderated to control spam), post questions to hcp-users(a)humanconnectome.org. *Stay Tuned!* In addition to this release, we are actively preparing AABC Release 2 to be made public soon. It will include 600+ more participant session data and other minor updates. We will announce Release 2 on the HCP-Users group, so yet another reason to join! Best, AABC Consortium -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 elam(a)wustl.edu http://secure-web.cisco.com/1FBuEJLFK1AdhzuTMoWgpdt_f3pYUtjnskrijVK6TU3ZRe_…

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Research Alliance Ruhr invites applications for a W3 Professorship in Computational Psychiatry at Ruhr University Bochum
by Caspar M. Schwiedrzik 25 Oct '25

25 Oct '25

External Email - Use Caution The Research Alliance Ruhr invites applications for a W3 Professorship in Computational Psychiatry at Ruhr University Bochum (Faculty of Medicine). 🔗 https://secure-web.cisco.com/1KcfglGyEXhDSldV3wDT4tlyyNLIFLdFLUm96KlHn10wZ2… We're looking for someone who can build bridges between machine learning, neuroscience, and mental health, using computational approaches to uncover how the brain, body, and environment give rise to resilience—or vulnerability. The position is exceptionally well-funded and part of the One Health Center, an interdisciplinary cluster of 15 professors across three universities in Bochum, linking AI, medicine, systems biology, and environmental science. The Ruhr area also hosts multiple SFBs and research centers, making this a perfect ecosystem for collaborative computational science. 📅 Deadline: November 12, 2025 Please share this with researchers who think in code, models, and mechanisms—and who want their work to make a societal impact. Warm regards, Caspar M. Schwiedrzik

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Freesurfer October 2025