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30084 discussions

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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ventricle edits
by Alexopoulos, Dimitrios 07 May '26

07 May '26

External Email - Use Caution I need to make some edits to a segmentation for underestimating of vernicles. As shown below, the right ventricle needs to be re-labeled from WM-hypointensities to lateral ventricle. What segmentation need to be edited in Freeview before re-running recon-all -all? [cid:image001.png@01DCDE2B.D94FD500] ________________________________ 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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Question about merging two volumetric atlases on fsaverage
by Zoe Cheng 06 May '26

06 May '26

External Email - Use Caution Dear FreeSurfer Developers, I am trying to merge two atlases on the fsaverage brain for my project: aparc+aseg.mgz and brainstemSsLabels.v13.mgz. My goal is for brainstemSsLabels.v13.mgz to serve as a subdivision of the single brainstem label in aparc+aseg.mgz, so that I can obtain a more fine-grained brainstem parcellation. Could anyone suggest a recommended way to merge these two label volumes and save the resulting atlas either through Freeview or via the command line? Thank you very much for your help. Best, Zoe

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Postdoc position: the noradrenergic system in Alzheimer’s disease using cognitive computational modeling and multimodal neuroimaging
by Jacobs, Heidi I.,PHD 06 May '26

06 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 / Harvard Medical School 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 to investigate the neural mechanisms underlying how the noradrenergic locus coeruleus system contributes to tau progression and cognitive decline. This position is intended for candidates with demonstrated experience in cognitive computational, and/or biophysical modeling of neural dynamics, and linking these models to in vivo human neuroimaging. The project will involve integrating multimodal imaging (e.g., sMRI, fMRI, 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 and advanced computational modeling. The lab also evaluates specific monoaminergic PET tracers to characterize age- and Alzheimer's disease-related changes in the noradrenergic and serotonergic systems from multiple perspectives. The successful candidate will also have the opportunity to contribute to these ongoing projects, depending on their 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. This position is funded by NIH and foundation grants. 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. Requirements: Candidates should hold a Ph.D. in Cognitive Neuroscience, Computational Modeling, Bio/medical Physics, Biomedical Engineering, Neuroimaging, or a related discipline. A strong publication record, including at least three first-author peer-reviewed publications with demonstrated research experience in neuroimaging combined with computational modeling approaches 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, and an ability to relate neuroimaging findings within a pathobiological framework of neurodegenerative diseases. The candidate should be highly motivated, a strong communicator (both 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 or aging research would be beneficial. 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> ___________________________________________ 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 [A blue and black logo Description automatically generated] [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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recon-all segmentation with motion artifacts
by Villagran Asiares, Alberto Gaston 05 May '26

05 May '26

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Finishing LeftHemi LGI and Not Starting RightHemi on Linux HPC
by Toms, Robert 04 May '26

04 May '26

External Email - Use Caution Dear FreeSurfer Team, I'm currently testing an LGI pipeline using FreeSurfer 8.0.0's -localGI recon-all command on our university's Linux-based computing cluster, aiming to get LGI statistics from 12,000ish subjects. We've got it successfully working for the most part, but we've run into the following issue: We currently run 50 subjects at a time in parallel (using TAC Launcher) across 4 nodes. In each batch of 50, 4 subjects (1 on each node) finish the left hemisphere of the -localGI command, and never start the right hemisphere process. They maintain the IsRunning.lh+rh file in their scripts directory, where it stays after the computation times out and is ended by the SLURM system. The other 46 complete both the lh and rh with no problems, apart from the occasional failure due to an MRI artifact. We've tried shrinking the batch sizes, looking for missing files, and checking matlab dependencies, and haven't been able to figure out the problem, though we've ruled out it being a memory issue. We've also separated these one-hemisphere-run folks out and tried running just the right hemisphere -localGI command on them. Few if any of these go through. I've checked the mailing list and haven't found anything relevant—any ideas? I've attached recon-all logs and IsRunning files from one of these groups of 4, as well as an additional recon-all log from an attempted right hemisphere rerun. Thank you for your time and attention, Robert Toms --------------------------------- Lab Manager, DAMMI Lab School of Brain & Behavioral Sciences University of Texas at Dallas ---------------------------------

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claustrum segmentation
by Vittorio Rispoli 03 May '26

03 May '26

External Email - Use Caution Dear FreeSurfer Developers, I am interested in a tool for automated claustrum segmentation for a dataset of 1x1x1mm in-vivo T1. Does the command "mri_claustrum_seg" provide an analysis with identical performance of what "mri_histo_atlas_segment_fireants" does in term of claustrum volumetric analysis and segmentation? Thanks in advance Best Vittorio

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