Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30050 discussions

Question on FreeSurfer recon-all workflow for brain tumor MRI
by nooshin Safari 01 Jun '26

01 Jun '26

External Email - Use Caution Hello, We are processing T1-weighted MRI from brain tumor patients and aim to run high-quality FreeSurfer recon-all for morphometric analysis. We are considering this workflow: TumorSynth tumor mask → VBG/virtual-brain correction → recon-all. Could you advise whether this is methodologically sound? Should tumor cases be handled with VBG/lesion filling before recon-all, by passing a mask directly, or another approach? Any recommended flags, QC steps, manual edits, example commands, or references would be appreciated. Best, Nooshin

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Recon-all for multiple subjects on parallel
by Huaiyu Liu 28 May '26

28 May '26

External Email - Use Caution Dear FreeSurfer Developers, I am using the following code on my department's HPC to (1) reconstruct a single participant’s T1w image and (2) perform brainstem segmentation. The code works well, but I have 40 participants in total. Hence, I wonder how I can run recon-all and brainstem segmentation for multiple subjects in parallel. Could you tell me the code? 1) FreeSurfer version: --freesurfer-linux 8.2.0-1 on my department's HPC (high-performance cluster) 2) My shell script for recon-all and brainstem segmentation for single subject: #!/bin/bash #$ -cwd #$ -o /data/holly-host/UserName/logs/ #$ -j y #$ -S /bin/bash #$ -N reconall export FREESURFER_HOME=/usr/local/freesurfer/8.2.0-1 export FS_LICENSE=/usr/local/freesurfer/8.2.0-1/license.txt export SUBJECTS_DIR=/data/holly-host/hliu/freesurfer_subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh mkdir -p $SUBJECTS_DIR env | grep -E "FREESURFER|FS_LICENSE|SUBJECTS_DIR" recon-all -all -i /data/holly-host/UserName/anat/sub-01_t1w.nii -s sub-01 SegmentAAN.sh sub-01 3) My command for submit the jobs to the cluster with 32 GB of RAM request qsub -l vf=32G -l h_vmem=32G reconall Thank you very much for your time and consideration, I look forward to hearing from you. Best, Huaiyu _________________________________________ Huaiyu Liu (Ted) Postdoctoral Research Fellow Department of Imaging Neuroscience, Functional Imaging Laboratory University College London 12 Queen Square, London WC1N 3AR

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Re: Singularity/Apptainer Image for FreeSurfer 8.2.0 on RHEL 8 HPC
by fsbuild 25 May '26

25 May '26

External Email - Use Caution We support Rocky8 Linux now instead of CentOS8/RHEL 8.  The Rocky8 installer may however work on RHEL 8.   There is also a CentOS7 installer for Freesurfer 8.2.0 which could also work on RHEL 8,https://secure-web.cisco.com/1vmYDp5mv23tqWzQ6UYVDN6np38kpfPQa_nY4_VDIYVD… but we no longer support the CentOS7 installer. There is a 8.2.0 docker file and an 8.0.0 singularity file for use with Rocky8 linux listed under,https://secure-web.cisco.com/1otR-Nsj7mSUktWs9KYtmVJiwIwW_YtvtnKZ2IcR… If you want to use something newer than 8.0.0 with that singularity file, you could try editing that exiting 8.0.0 singularity file to instead use the 8.2.0 Rocky8 installer freesurfer-CentOS7-8.2.0-1.x86_64.rpm and likewise change all 8.0.0 entries to 8.2.0 in that file.   You can download the Rocky8 8.2.0 installer from,https://secure-web.cisco.com/14IoQ-fNJng0Jj1BRFCbUBdge8u1ckTL1UZp8lV_w… Alternately if you search for "use dockerfile to create singularity image” you will find various ways to create a docker image from a  docker container and and subsequently use the docker image to create a singularity image. - R On May 17, 2026, at 16:04, nooshin Safari <noonoosh91(a)gmail.com> wrote:

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Postdoc position (MGH): the noradrenergic system in Alzheimer’s disease using cognitive computational modeling and multimodal neuroimaging
by Jacobs, Heidi I.,PHD 22 May '26

22 May '26

Postdoctoral fellow position: Understanding how the noradrenergic system contributes to Alzheimer’s disease using cognitive computational modeling and multimodal neuroimaging at Massachusetts General Hospital The Athinoula A. Martinos Center for Biomedical Imaging, located within the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for a highly qualified postdoctoral individual to work with Dr. Heidi Jacobs. The Jacobs lab is focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 3T MRI, 7T MRI, PET imaging, pupil measurements, physiological recordings, blood-based markers, cognitive assessments and perturbational approaches, such as pharmacological manipulations and non-invasive vagus nerve stimulation. We are seeking a postdoctoral fellow with a background in cognitive computational, and/or biophysical modeling, including frameworks such as predictive coding and reinforcement learning, to investigate the neural mechanisms underlying how the noradrenergic locus coeruleus system contributes to tau progression and cognitive decline. Although these approaches have a strong tradition in psychiatry, they are increasingly recognized as promising tools for understanding Alzheimer's disease: the noradrenergic system has been computationally linked to the regulation of belief updating and exploration/exploitation balance, and given that the noradrenergic locus coeruleus is one of the first systems to undergo neurodegenerative and functional changes in Alzheimer's disease, these frameworks offer a principled and largely untapped lens through which we can study cognitive decline and disease progression. The Jacobs Lab is actively expanding in this direction and is looking for candidates who are eager to bring this expertise, help shape this line of work, and forge collaborations that bridge the computational and clinical neuroscience communities. This position is particularly suited to candidates with demonstrated experience linking such models to in vivo human neuroimaging and who are excited by the opportunity to apply these methods in a neurodegenerative disease context. The project will involve integrating multimodal imaging (e.g., sMRI, fMRI, (f)MRS, PET) with pupillometry and advanced modeling approaches, including dynamic causal modeling (DCM) and reinforcement learning, in observational and pharmacological manipulation studies. In parallel, the lab develops approaches to characterize heterogeneity and temporal trajectories of disease progression using large-scale, well-characterized longitudinal datasets. The lab also evaluates specific monoaminergic PET tracers to characterize age- and Alzheimer's disease-related molecular changes in the noradrenergic and serotonergic systems. The successful candidate will have the opportunity to contribute to these ongoing projects depending on expertise and interests. The Jacobs Lab consists of a multidisciplinary team of two instructors, three postdocs, two PhD students, two clinical research coordinators, and one project manager. The work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and work in a stimulating and inspiring environment. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference), collaborations with partners within and outside MGH, and manuscript preparation for publication in high-impact journals. Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Her trainees have a strong publication record, obtained competitive awards/grants, and many have secured faculty or senior positions. Requirements: Candidates should hold a Ph.D. in Cognitive Neuroscience, Computational Modeling, Bio/medical Physics, Biomedical Engineering, Neuroimaging, or related disciplines. A strong publication record, including at least three first-author peer-reviewed publications with demonstrated research experience in neuroimaging combined with computational modeling is required. Essential qualifications include: strong expertise in fMRI analyses and other neuroimaging methods (e.g. MRS, PET), advanced programming skills (e.g., Python, MATLAB), experience with computational modeling (e.g. cognitive computational modeling), a solid background in signal processing. Candidates must be able or willing to learn to relate neuroimaging findings within a pathobiological framework for neurodegenerative diseases. The candidate should be highly motivated, a strong communicator (verbally and in scientific writing), have an internal drive to learn independently, and be comfortable working as part of a larger collaborative team. A real necessity is a passion for science and a positive attitude. Experience in Alzheimer’s disease/aging/memory-related research would be beneficial. Start date is negotiable. Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Associate Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> (www.heidijacobs.org) ___________________________________________ Heidi Jacobs, PhD Associate Professor of Radiology Massachusetts General Hospital | Harvard Medical School Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu www.heidijacobs.org<http://www.heidijacobs.org> Learn about what we do and why: https://shorturl.at/fEFa8 [Image removed by sender. A blue and black logo Description automatically generated] [Image removed by sender. signature_3581815700] Social media: Linkedin: https://www.linkedin.com/in/heidijacobs/ Bluesky: https://bsky.app/profile/heidijacobslab.bsky.social [Please note: I might send an email out of office hours, at weekends or during holidays. This suits me – but doesn’t mean I expect you to do the same]

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Singularity/Apptainer Image for FreeSurfer 8.2.0 on RHEL 8 HPC
by nooshin Safari 18 May '26

18 May '26

External Email - Use Caution Dear FreeSurfer team, We need a Singularity/Apptainer image for the latest stable version of FreeSurfer to be run on RHEL 8 HPC. We would like to work with a Singularity/Apptainer image for FreeSurfer 8.2.0. We will be running it on the institutional machine at MD Anderson Cancer Center. The operating system is Red Hat Enterprise Linux 8.7 (Ootpa). Given that the Apptainer image for FreeSurfer 8.2.0 does not appear to be available online, could you please let us know how long it would take to create one? We have a grant deadline in 45 days, and having this image available would significantly help us meet that deadline. Thank you for your guidance. Best regards, Nooshin

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Singularity/Apptainer Image for FreeSurfer 8.2.0 on RHEL 8 HPC
by nooshin Safari 18 May '26

18 May '26

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When is a pial surface edit required
by Bronwyn Overs 17 May '26

17 May '26

External Email - Use Caution Dear FS mailing list, I am currently reviewing and editing a large set of sMRI scans in FS version 8.1. I've noticed that while the pial surface sometimes includes dura and non-brain that can be edited away, the aparc accurately aligns to the surface of the brain and doesn't need editing. If the aparc is accurate, do I still need to edit the pial surface when non-brain is included? Kind regards, Bronwyn.

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Move mri_super_synth output in MNI space
by Maurilio Genovese 12 May '26

12 May '26

External Email - Use Caution Hi FreeSurfer Experts, I have successfully run mri_super_synth and obtained the following outputs: mni_deformation.mgz, mni_affine.txt, and segmentation.mgz. I am now trying to warp the segmentation to MNI space. I converted the .txt affine matrix to .lta format, but when I run mri_vol2vol, the output is not in the correct mni space: mri_vol2vol --mov ribbon.mgz \ --targ $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz \ --m3z /path/to/mni_deformation.mgz \ --lta ./mni_affine.lta \ --o seg_mni.nii.gz \ --interp trilinear \ --noDefM3zPath Thanks, Maurilio Genovese

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Segment AAN
by David, Michael C B 11 May '26

11 May '26

External Email - Use Caution Hello, I would be grateful for your help in trying to run segmentAAN. I’ve tried running segementAAN but cannot find the function in the freesurfer version installed which is 7.3.2 to be able to run it as the command on their website SegmentAAN.sh<http://secure-web.cisco.com/1jyjVmYiR_9gjCSQh6QtCc1HU5rWJkKVLmgv493Ak6LyDdJ…> <SUBJECT_ID> <SUBJECT_DIR> Can you advise on if it should be currently available and how to go about finding it if so? Many thanks, Mike Dr Michael David Academic Clinical Fellow UK Dementia Research Institute – Care Research & Technology Imperial College London Email | md2012(a)ic.ac.uk<mailto:md2012@ic.ac.uk> Phone | 07914658195 Twitter | @michaelcbdavid Web | http://secure-web.cisco.com/1ewUvxJmXgeVy0ERHWAN30_iThKQ6768wjmIw1y3VTAPqC2…<http://secure-web.cisco.com/128tVPRpNKlBmHdqCtzJsQvORrmsQ4bvgQ2MaebBMAoAeqh…> Address | Sir Michael Uren Hub, Imperial College, 86 Wood Lane, London W12 0BZ [cidimage001.gif(a)01D75E0C.55347A40]

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Neuroimaging Learning & Research Initiative
by Sahil Bajaj 11 May '26

11 May '26

External Email - Use Caution For students interested in learning basic to advanced concepts and techniques in neuroimaging, I am excited to share the Launch of BRAIN: Bajaj Research Academy in Neuroimaging https://secure-web.cisco.com/1Xnd4fv-wEiRr0v-PO--c7pD5xMuReh3rfoWc7ivUvU738… <https://secure-web.cisco.com/1NX-yK3HmTQRoKII211VMRk2sZIVYIEnLJE9KyDffNYR6T…> Neuroimaging has transformed how we understand the human brain—from structure to behavior to disease. It has been central to my work, and over time, a space I feel deeply committed to teaching and mentoring in. At the same time, the research landscape is becoming increasingly competitive, with tighter funding and fewer structured opportunities for early-stage trainees. This makes it harder for many students to gain meaningful, hands-on exposure early in their journey. Globally, the gap is even wider. In many regions/countries, access to neuroimaging training, infrastructure, and mentorship remains limited. With this in mind, I am excited to launch BRAIN (Bajaj Research Academy in Neuroimaging)—an independent initiative (registered as a DBA), not affiliated with any institution, focused on introducing students to how modern brain imaging research actually works. The goal is simple: 👉 Help students move beyond textbooks and understand real-world neuroimaging research Through BRAIN, students gain exposure to: • How the human brain is studied using imaging approaches and techniques • Links between brain structure, function, and behavior • Research thinking and analytical approaches • Early pathways into neuroimaging, medicine, and scientific careers This is especially relevant for students interested in: • Medicine and brain health • Neuroimaging and human behavior • Data-driven, research-oriented careers More broadly, I hope this initiative contributes (however modestly) to building a stronger, more prepared pipeline of future "neuro-imagers". I would be happy to connect with: • Students seeking research exposure • Schools and academic programs • Colleagues interested in mentoring/training • Organizations or companies exploring research consulting or academic–industry collaboration Join : https://secure-web.cisco.com/1vNxk4eo-1t1auksvJb4_7axZRyui_6WCRP-_3-qmJ2ItJ… 🌐 Learn more: https://secure-web.cisco.com/1Xnd4fv-wEiRr0v-PO--c7pD5xMuReh3rfoWc7ivUvU738… <https://secure-web.cisco.com/1NX-yK3HmTQRoKII211VMRk2sZIVYIEnLJE9KyDffNYR6T…> If this resonates, feel free to share or reach out.

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