Freesurfer February 2026

freesurfer@nmr.mgh.harvard.edu

32 participants
33 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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Truncated T1.mgz after recon-all
by Kim, Minhae 04 Mar '26

04 Mar '26

Hello FreeSurfer team, I encountered an error while running recon-all where T1.mgz files for two subjects appear to be cropped posteriorly along the Y dimension (RAS). The cortex is preserved, but portions of the skull and the scalp are removed. The input file ($subj/mri/orig/001.mgz) is intact, suggesting a possible issue during conversion (e.g., mri_convert). I didn’t find similar reports in the archive, and the problem reproduces identically across both versions of FreeSurfer below. recon-all.log files are attached. * FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 AND freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 * OS: Rocky 8.10 * uname -a: Linux r440-05.nmr.mgh.harvard.edu 4.18.0-553.79.1.el8_10.x86_64 #1 SMP Wed Oct 15 12:48:32 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Any insight would be greatly appreciated. Thank you! Kindly, Ellie Ellie Minhae Kim (she/her/hers) Program Director | Pain and Neuroinflammation Imaging Lab Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 Thirteenth St, Suite 2316 Charlestown, MA 02129 Phone: (617) 643-0569 https://loggialab.mgh.harvard.edu/

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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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Trouble finding recent archives
by Dierker, Donna 26 Feb '26

26 Feb '26

External Email - Use Caution I'm having trouble finding the mailing list archives. This exists, but I can't find more recent messages: https://secure-web.cisco.com/1_AzCMVLSYPWXrEp1K-AJyCtXx9QQ9JDRC8EUf3bu9E09G… The archives link here says Forbidden: https://secure-web.cisco.com/1t7pgqdKCNN4T1zl63JGJU0ZpokAYt_RliqFTp2CWPt9AG… Thanks, Donna ________________________________ 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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recon-all in severe atrophy
by Andrea Müller 25 Feb '26

25 Feb '26

External Email - Use Caution Hello, I am running both longitudinal and cross-sectional FreeSurfer (version 7.4.1) on a dataset which includes participants with significant levels of atrophy.If I run the 'default' versions, I see many errors in segmentation and cortical surfaces during QC afterwards (mostly related to undersegmentation of gyri). We want to avoid having to add manual corrections. Therefore, I wanted to ask what the recommended settings are for running FreeSurfer on these populations (eg adding the -bigventricles or -seg-wlo flags?) Thanks!

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glm, longitudnal analysis
by Eszter Boros 24 Feb '26

24 Feb '26

External Email - Use Caution Dear FreeSurfer Team, We are trying to run some longitudinal data using FreeSurfer 7.4.1. We have one group and 3 scans. We would like to see the changes between these timepoints. I am not sure how to proceed with the GLM because I found two tutorials. One here is saying I should create a longitudinal qdec table including fsid-base column and years/timepoints then run mri_glmfit --osgm https://secure-web.cisco.com/12qS0acHTgwXhZDIytchwCnsXkPJ57shyJ2uQEuf0WkwB9… The other one is saying to do a paired analysis. This one does not include the base and years data. https://secure-web.cisco.com/1voT6D0EOLTXJrVgGSmPK-onn8JIxg74dwxqLG9An8DuCh… How should I proceed? Thank you! Best regards, Eszter

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FreeSurfer Longitudinal Pipeline Exits with Errors - Prior to Sphere registration?
by Peter Najdzionek 24 Feb '26

24 Feb '26

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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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Instensity normalisation issues - how to fix bias field correction?
by Chanelle Hendrikse 23 Feb '26

23 Feb '26

External Email - Use Caution Dear FreeSurfer developers I am processing longitudinal 3T T1-weighted data (Freesurfer 7.1.1) from the same scanner and protocol at 3 timepoints across childhood. The first two waves processed without major issues, but in the current pre-adolescent wave I am seeing consistent segmentation failures, mainly in occipital regions (sometimes frontal/parietal). Recon-all “misses” these regions, which were also excluded from the brain mask. I managed to correct the brain masks by fixing skull stripping (using ms_watershed) and rerunning recon-all, but the segmentation issues persisted. Inspection of norm.mgz suggests residual intensity inhomogeneity as posterior white matter intensity is substantially higher than expected (up to ~140–150). The brain mask also appears brighter here. Could this be causing recon-all to “miss” these regions? From what I’ve read, a potential solution is running N4BiasFieldCorrection on the raw T1 prior to recon-all (then processing from scratch), and only using control points if needed afterward. Would this be an acceptable approach, particularly in a longitudinal developmental dataset? Any alternative suggestions are also welcome! Many thanks in advance for your advice. Kind regards, Chanelle Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at https://secure-web.cisco.com/1xGpoPcjPQtqGoQemnEYmTxxk01Cml8DAbleqc_se8czt_… or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://secure-web.cisco.com/12QWH4f3q4K3n4d15-z-1Z4Ye2973t6xEKRh2n4qKT28F1…

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Clarification on FreeSurfer recon-all Output and Preprocessing Steps
by Akanksha Upadhyay 23 Feb '26

23 Feb '26

External Email - Use Caution Hello FreeSurfer Developers, Greetings of the day. I am attempting to replicate a previously published work and have applied the recon-all pipeline on our structural MRI data (T1w.nii) using FreeSurfer. After segmentation and normalization, the output we are obtaining appears unusual to us. I would like to confirm whether these results are expected or if additional preprocessing steps are required prior to running recon-all . I have also attempted reorientation of the input image; however, I was only able to find GUI-based orientation options. I would appreciate your guidance on the following points: 1. Whether the observed segmentation and normalization outputs are expected, or if further preprocessing steps (such as reorientation, intensity correction, or format conversion) should be performed before running recon-all. 2. If manual reorientation is recommended, how should the orientation be determined (e.g., reference axes, alignment criteria, or specific angles)? 3. Any best practices for preparing T1w.nii files to ensure optimal processing with FreeSurfer. I am attaching screenshots of the normalization and segmentation results (aseg output) for your reference. Kindly guide me on how to proceed further. Thank you very much for your time and support. [image: Normalisation_results.jpg] [image: Segmentation_output_aseg.jpeg] -- *Regards* *Akanksha Upadhyay* *Department of Computer Science* *University of Delhi*

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Freesurfer February 2026