Freesurfer January 2026

freesurfer@nmr.mgh.harvard.edu

29 participants
31 discussions

Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 05 Mar '26

05 Mar '26

External Email - Use Caution [A close up of a logo Description automatically generated][cid:91EF027C-9846-4FE1-B2F9-8AA9ABA8FEE6] 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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Query on use of FreeSurfer with Clinical Epilepsy MRI Protocols (Anisotropic Voxel Size)
by Uttara Bakshi 02 Mar '26

02 Mar '26

External Email - Use Caution Dear FreeSurfer Support Team, Season's Greetings! I hope this email finds you well. May I take this opportunity to seek your support regarding the use of FreeSurfer for structural MRI data acquired using clinical epilepsy imaging protocols with non-isotropic voxel sizes in our hospital setting. To date, I have processed MRI data from over 90 epilepsy patients using *FreeSurfer v 6.0* (3T scanner 64-channel head coil, TA: 3:49 min; Voxel Size: 1.0 × 1.0 × 0.5 mm³; Acceleration factor: 2; Relative SNR: 1.00). The complete recon-all pipeline ran successfully for all subjects, generating cortical and subcortical segmentations as well as quantitative statistics files without any processing errors. However, I learnt that 1 mm³ isotropic resolution is recommended for optimal performance, although voxel sizes up to *1.3 × 1 × 1.3 mm³* are considered acceptable to reduce scan time or improve signal-to-noise ratio, as per FreeSurfer Wiki. Therefore recently, I have acquired one additional patient data using an isotropic protocol (1.0 × 1.0 × 1.0 mm³) and compared to epilepsy protocol mentioned above. To conclude , I got two different quantitative values. For example, in Left Hippocampus - Anisotropic : 3640.2 mm³ vs Isotropic : 3876.2 mm³ , Total intracranial volume- Anisotropic : 1504943.411530 mm³ vs Isotropic : 1529703.225834 mm3 , Mean cortical thickness – Anisotropic : 2.18512 mm vs Isotropic: 2.28844 mm. In this context, I would greatly appreciate your guidance on the following: 1. Would you recommend resampling 1 × 1 × 0.5 mm³ images to 1 mm³ isotropic resolution prior to running recon-all, or is it fine to process the native anisotropic resolution data? 2. Are there any appropriate FreeSurfer steps or commands to convert my already acquired 1 × 1 × 0.5 mm³ MRI data to isotropic resolution before running the FreeSurfer recon-all pipeline? 3. Are there any known limitations, biases, or segmentation inaccuracies, particularly affecting hippocampal volumetry or cortical thickness estimates, when FreeSurfer is applied to anisotropic voxel data in epilepsy research like I did? I am attaching the recon-all log files of both the protocols here. Thank you very much for your time and guidance. I would greatly appreciate your recommendations. -- Warm regards, *Uttara Bakshi* *Doctoral Fellow* *Institute Of Neurosciences Kolkata, India.*

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Query on use of FreeSurfer with Clinical Epilepsy MRI Protocols (Anisotropic Voxel Size)
by Uttara Bakshi 23 Feb '26

23 Feb '26

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Regarding Collaboration and Partnerships
by Ozgur Akbulut 31 Jan '26

31 Jan '26

External Email - Use Caution Dear Sir or Madam, We are a company established in Turkey under the names beyinverimerkezi.com and braindatacenter.com, dedicated to providing measurement and reporting of brain volumetric values to MR Imaging Centers, private hospitals, and the Turkish Ministry of Health. Our primary objective is to deliver the data we obtain to neurologists, psychiatrists, and neurosurgeons prior to diagnosis, thereby guiding early detection and treatment strategies, as well as evaluating the efficacy of implemented treatments through controlled measurements. In pursuit of this goal, we would like to request an online meeting to explore opportunities for collaboration, integration to your ecosystem, and assuming roles that will contribute to the development processes. The meeting will include participation from our Turkish team: Prof. Dr. Niyazi Acer, who received his training at Johns Hopkins University; our software partner, Özgür Akbulut; and Turgay Şahin, the brain researcher and originator of the core concept. We eagerly anticipate discussing a suitable date and time, taking into account the time difference between our locations. We extend our profound gratitude to every FreeSurfer volunteer for their invaluable contributions to the field. Özgür Akbulut CTO - Brain Data Center ozgurakbulut(a)braindatacenter.com http://secure-web.cisco.com/1Nv6cgLfVYARoj7aVwFaISaxYAGpnS9POwcvMOuJue_MIHT… +90 533 541 19 00

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Regarding Collaboration and Partnerships
by info＠braindatacenter.com 31 Jan '26

31 Jan '26

External Email - Use Caution Dear Sir or Madam, We are a company established in Turkey under the names beyinverimerkezi.com and braindatacenter.com, dedicated to providing measurement and reporting of brain volumetric values to MR Imaging Centers, private hospitals, and the Turkish Ministry of Health. Our primary objective is to deliver the data we obtain to neurologists, psychiatrists, and neurosurgeons prior to diagnosis, thereby guiding early detection and treatment strategies, as well as evaluating the efficacy of implemented treatments through controlled measurements. In pursuit of this goal, we would like to request an online meeting to explore opportunities for collaboration, integration to your ecosystem, and assuming roles that will contribute to the development processes. The meeting will include participation from our Turkish team: Prof. Dr. Niyazi Acer, who received his training at Johns Hopkins University; our software partner, Özgür Akbulut; and Turgay Şahin, the brain researcher and originator of the core concept. We eagerly anticipate discussing a suitable date and time, taking into account the time difference between our locations. We extend our profound gratitude to every FreeSurfer volunteer for their invaluable contributions to the field. Özgür Akbulut CTO - Brain Data Center ozgurakbulut(a)braindatacenter.com http://secure-web.cisco.com/1ADYhfrm1D5yD7eBi9ik3wPlCDLf0aUJ937KGbH28CBHRzW… [1] +90 533 541 19 00 Links: ------ [1] http://secure-web.cisco.com/1ADYhfrm1D5yD7eBi9ik3wPlCDLf0aUJ937KGbH28CBHRzW…

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Fwd: recon-all doesn't find 001.mgz in mri/orig
by Angelika Wolman 30 Jan '26

30 Jan '26

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute recon-all on my nii files. It seems it doesn't find 001.mgz in mri/orig *Subject does not have a bstampfile, copying /opt/fox_cloud/share/app/imaging/freesurfer/7.3.2-1/build-stamp.txt* I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 Platform: Linux PlatformVersion: 3.10.0-1160.119.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 2) Platform: *CentOS Linux release 7.9.2009 (Core)* 3) uname -a: *Linux fox-c18 3.10.0-1160.119.1.el7.x86_64 #1 SMP Tue Jun 4 14:43:51 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux* 4) recon-all.log: see attached 5) script used: attached (T1_recon_all2.sh) Thank you ! Angelika

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AABC Release 2 of more longitudinal HCP-Aging & AABC Data
by Jennifer Elam 28 Jan '26

28 Jan '26

External Email - Use Caution *AABC Release 2 of more longitudinal HCP-Aging & AABC Data * The Aging Adult Brain Connectome (AABC) consortium is pleased to announce its second release of imaging and non-imaging phenotypic data on the *ConnectomeDB powered by BALSA <https://secure-web.cisco.com/1XxcWoohRobuw1WSCh6edBdaGxyD_rp1GlemcFbF_8jlSX…>* platform. AABC Release 2 includes 632 additional sessions collected on participants from targeted groups newly recruited for AABC and more longitudinal visit data and followups (up to visit 4) from HCP-Aging (HCA) participants. It is inclusive of the previous AABC 1 Release. AABC is a longitudinal follow-on study to the HCA study of typically aging participants ages 36-90+. AABC has recruited ~950 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 2 includes cross-sectional (V1) and longitudinal (V2, V3, V4) 3T MR scans and non-imaging phenotypic data from 1396 typically aging adults (ages 36-90+) in the *HCP-Aging* and *AABC* projects. This includes data for 1396 V1, 915 V2, 471 V3, and 96 V4 sessions (total = 2878). It includes preprocessed and unprocessed imaging data for all included modalities (structural, high-res hippocampal T2 [unprocessed only], resting state fMRI, task fMRI, diffusion, and ASL) from 1390 participants in 2789 imaging visits. It also contains non-imaging data collected over a broad range of domains at imaging visits and in remote follow up surveys (non-imaging events). See *session breakdowns by study and visit/event <https://secure-web.cisco.com/1Ofguj5c8lU0m74FZoyTK636BZvRWBKivB_ywzv82i4vra…>* . *Release 2 Highlights:* - Preprocessed and unprocessed structural MRI, resting state fMRI, task fMRI, diffusion MRI, ASL, and high-res hippocampal T2 [unprocessed only] 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) using HCP pipelines <https://secure-web.cisco.com/1aacJvW1mdHImrMoNlsjQrehkTIWQkvMzctNAfsV9nqCzE…> that have been developed specifically for HCP-style data. - 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 282 participant visits. - 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 all Core Variables or selected subset). - >3,000 Extended (XL) variables, including item-level and follow up event variables, for all participant events available in a comprehensive spreadsheet. See Data Dictionary <https://secure-web.cisco.com/1w4WLQASL7dgUjowrLA8VjSQ7qcqVF_OOAecYbXSr4cxpd…> for descriptions of included variables. - 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/1ABz6nrHeh7ZY5Ld4JgxvDpDxuqcrXwViuNH3SssZ7jJh8…>*, 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/1p324dA-654tn2LU5RMwFk65I2EC6rLjVBaKSkVvXw-xBH…>* (*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. Use the Column Selector and Export CSV to view, filter on, and download all or subsets of Core Variables for selected subjects. To download the full non-imaging data, click the Files tab and Download under AABC_Release2_Non-imaging_Data-XL.csv. *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/1j4HC4mBHaSeH8_MLgylhkjZx2ucjxd5dcQPzIN-bPYM-6…>*, 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 <hcp-users(a)humanconnectome.org>*. *Share your Analyses.* As you work with AABC data and prepare your work for publication, we encourage you to use *Connectome Workbench <https://secure-web.cisco.com/1UksVOQxCxXN1PSTD8_iZe0FH8nhqNyabpAFfqrgZIUGzw…>* to prepare your figures as scenes and *upload your scenes as a BALSA dataset <https://secure-web.cisco.com/188H9BkiEI_P6I5P_y380WASXc34AB_Sd3NhkG0D6zxkkD…>* that can be linked from your publication. Don’t forget to cite the *HCA and AABC grants <https://secure-web.cisco.com/1RaBEYH46916aUctXV_85CuHdH1TMaqlcjbKYOvFi8x2ZQ…>* and *BALSA <https://secure-web.cisco.com/1Kt_PfcOWm9-dzMelOgh3-pR4S8ZnTQqKtnFPm3gsk8EMQ…>* in your manuscript! *Stay Tuned!* In coming months, we will be working on improvements to ConnectomeDB powered by BALSA to enable additional ways to transfer data via command line and other transfer services we are exploring. We will announce updates on the HCP-Users group! Best, AABC Consortium -- Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience 660 South Euclid Avenue St. Louis, MO 63110 elam(a)wustl.edu http://secure-web.cisco.com/1bLLYhhcdC_J57LMgAzFLkNi-KlCY6dxwIXHFcQbEgJ-ydM…

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Editing segmentation output from SuperSynth
by Paine, Isabel 28 Jan '26

28 Jan '26

External Email - Use Caution Hi, I am new to FreeSurfer and have been testing the new SuperSynth tool on ex vivo chimpanzee scans. The segmentation output is generally good, but the cerebellum white/gray matter is often mistaken as cerebral white/gray matter. How can I manually edit the segmentations and recalculate volumes? Thanks! Isabel -- *Isabel Paine *(she/her) Neuroscience PhD Candidate Hof Lab <https://secure-web.cisco.com/12vWcbyCY5P0ckWnU8cN-d7Qo7iUhB7t-1PwYJ7s4zFUK9…> Icahn School of Medicine at Mount Sinai

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Talairach transformation
by Serena Tang 27 Jan '26

27 Jan '26

External Email - Use Caution Hi there, I just had a question about the Talairach matrix calculated during the recon-all processing. Is that matrix calculated with an affine transformation? And how many DOF is default? I couldn't find information on it in talairach_avi or the other pages on the Talairach function. Also just to clarify, the talairach function doesn't convert to Talairach coordinates or some average of MNI and Talairach, but rather MNI specifically, is that correct? Thank you, Serena *---* *Serena Tang* *UC Berkeley / UCSF joint Bioengineering PhD Program* *serenatang(a)berkeley.edu <serenatang(a)berkeley.edu> | (201)-238-9861*

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Re: Bug Report: Typo in surfreg script (FreeSurfer 7.4.1)
by fsbuild 26 Jan '26

26 Jan '26

External Email - Use Caution A fix was made in 09/2024 and was subsequently in the Freesurfer 8.0.0 (02/2025) and 8.1.0 (07/2025) releases which you can download from,https://secure-web.cisco.com/1a_cLCaihbBr4j3zAtLN867XJeh4MYOVKCUkQ-FlY… R. On 1/23/26 03:34, Ben Sinclair (ben.sinclair(a)monash.edu) wrote:         External Email - Use Caution         Dear FreeSurfer Development Team, I'm reporting a typo in the surfreg command that causes registration operations to fail with an error, though the actual registration completes successfully. **Bug Details:** - File: /apps/freesurfer/7.4.1/freesurfer/bin/surfreg - Line: 107 - Current: set fsaorig = $FREESURFER/subjets/fsaverage/mri/orig.mgz - Should be: set fsaorig = $FREESURFER/subjects/fsaverage/mri/orig.mgz **Impact:** When running surfreg with the --no-annot flag (as recommended in the error messages for FreeSurfer 7.4.1), the command completes the registration successfully but then fails on the post-processing mris_convert step with: "error: mghRead(/apps/freesurfer/7.4.1/freesurfer/subjets/fsaverage/mri/orig.mgz, -1): could not open file" This causes the command to return a non-zero exit code even though the primary registration file (e.g., lh.fsaverage_sym.sphere.reg) is created correctly. **Reproduction:** surfreg --s <subject_id> --t fsaverage_sym --lh --no-annot **Version:** FreeSurfer 7.4.1 Thank you for your work on FreeSurfer. Please let me know if you need any additional information. Cheers Ben

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Freesurfer January 2026