Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30136 discussions

Unable to download from Freesurfer site
by Amnah Eltahir 14 Oct '26

14 Oct '26

External Email - Use Caution Hello, I am attempting to download Freesurfer by going to the Freesurfer site and clicking on the download link up top. However, the page does not load and eventually times out. Is the site down at the moment? Best, Amnah

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Doctoral Research Associate position at the Institute of Psychology, University of Muenster, Germany
by Falko Mecklenbrauck 09 Oct '26

09 Oct '26

External Email - Use Caution The Biological Psychology group at the Institute of Psychology (Fachbereich 07) at the University of Münster, Germany, invites applications for the position of a * Doctoral Research Associate (Salary Level E 13 TV-L)* for the externally funded project “*Updating memories: Computational and neural mechanisms underlying the fate of episodic traces after prediction errors*” commencing on *1 February 2027*. We are offering a *fixed-term part-time position (75%) for 4 years*. The appointment is subject to approval of the requested German Research Foundation (DFG) funding. *Project Description:* We tend to think of memories as records of our past. We know that memories can fade or be forgotten. But more remarkably, memories can change. Our theoretical framework brings together different accounts of memory changes by showing how they can arise from different components of scenario construction. Specifically, we focus on the question of memory updating. When our experiences diverge from what was expected, prediction errors arise that can either modify an existing memory or lead to the formation of a new one. In this project, we combine computational modeling with behavioral and fMRI experiments to study how prediction errors reorganize episodic memories. To this end, we draw on ideas from two frameworks, Latent Cause Theory and cloned Hidden Markov Models, which provide testable computational hypotheses about the balance between integration and separation. The project team consists of neuroinformaticians and cognitive neuroscientists who work closely together to uncover the neurocognitive mechanisms and computational principles that underlie these changes. *Your tasks:* * Participation in a new collaborative project funded by the DFG, involving the Universities of Bochum and Münster, embedded in a large interdisciplinary research consortium spanning psychology, neuroscience, philosophy, and computational modelling * Planning, conducting, analysing, and publishing fMRI experiments. * Application of appropriate, advanced analysis methods for neurocognitive and behavioural data * Close collaboration with the participating research groups at both sites. * Presentation and publication of research findings at national and international conferences and in scientific journals. * The position is intended for the completion of a doctoral research project. *Our expectations:* * An above-average Master’s degree in psychology, cognitive neuroscience, or a related field is required. * Good programming skills, preferably in MATLAB or Python, are required. * Experience with statistical analysis and relevant statistical software is required * Excellent written and spoken English is required. * A strong interest in the research questions outlined above and in interdisciplinary research is desirable * Ability to work independently, reliably, and in a well-organized manner. * Ability and enthusiasm to work collaboratively as part of an interdisciplinary team. *Advantages for you:* * The opportunity to conduct cutting-edge research on episodic memory and complete a PhD in an internationally visible, interdisciplinary research environment. * Access to an exceptional range of cognitive neuroscience methods and facilities on site, including 3T and 7T fMRI, EEG, TMS, eye tracking, peripheral physiological measures, and a computer vision lab. * A supportive and collaborative team, close scientific exchange, dedicated supervision, and support from student research assistants. * Integration into a large interdisciplinary research consortium with regular workshops, talks, and opportunities for national and international networking. * Doctoral researchers may also choose to join and complete a structured PhD Program in Cognitive and Behavioral Neuroscience. * Flexible working arrangements and support in balancing work and family responsibilities. * Tailored professional training and continuing education opportunities, as well as a broad range of sport and health programmes. * Public-sector benefits, including an attractive pension scheme (VBL) and an annual end-of-year bonus The University of Münster strongly supports equal opportunity and diversity. We welcome all applicants regardless of sex, nationality, ethnic or social background, religion or worldview, disability, age, sexual orientation or gender identity. We are committed to creating family-friendly working conditions. https://secure-web.cisco.com/1wSJxahXbIUH6kCyap2mPb9a1MKtxBh_L5KLMIhq9LyPRb… We actively encourage applications by women. Women with equivalent qualifications and academic achievements will be preferentially considered unless these are outweighed by reasons which necessitate the selection of another candidate. If you have any questions, please contact *Prof. Schubotz (rschubotz(a)uni-muenster.de)*. Are you interested? Then we look forward to receiving your application by *2026-11-07* at: *Universität Münster Institut für Psychologie Prof. Dr. Ricarda I. Schubotz Fliednerstr. 21 48149 Münster* Applications should include a letter of motivation, a CV, a current transcript of records, and the Master’s degree certificate. A letter of recommendation or the contact details of one academic referee may be included optionally. Please send us your application electronically in a PDF file to *rschubotz(a)uni-muenster.de*. Note that we cannot consider other file formats. *Reference number: 2026_10_05* For more information: https://secure-web.cisco.com/1zcpQ4_05UUUDgRvH8gs-TCMuBrrabbfCWpL8wQFF2oOnA… -- Falko Mecklenbrauck, Ph.D. University of Münster Institute of Psychology Biological Psychology Fliednerstr. 21 Room 310b Tel.: +49 251 83 34101

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license
by 宗信达 08 Oct '26

08 Oct '26

External Email - Use Caution license

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Temporal Interference (TI) Brain Stimulation Workshop | SfN Satellite Event | Register now
by Melanie Boly 07 Oct '26

07 Oct '26

External Email - Use Caution <2.png> SfN 2026 · Satellite Event TI Brain Stimulation Workshop Society for Neuroscience Annual Conference · Washington, D.C. This event is not sponsored by the Society for Neuroscience 📅 Friday 13 November 2026 | Washington, D.C., USA Satellite event at the Society for Neuroscience (SfN) Annual Conference Temporal interference (TI) is a novel brain-stimulation technology that enables precise, noninvasive modulation of deep brain structures — a capability previously achievable only through invasive neurosurgery. TI has also catalysed significant engineering advances and provided new fundamental insights into neuromodulation. We are delighted to invite participants to the TI Brain Stimulation Workshop, held on Friday 13 November 2026, in Washington, D.C., as a satellite event of the Society for Neuroscience (SfN) annual conference. The workshop aims to equip participants with key knowledge and capabilities critical to the highest-standard implementation of TI stimulation in human brain research and clinical therapy development, thereby facilitating the translational impact of this rapidly growing field. The workshop will be led by Professor Nir Grossman (Imperial College London) and leading TI researchers from the US, Europe, and China.See the workshop website for the complete list →<https://secure-web.cisco.com/1bgDwtFe5UUJkYJgNNI3g8FVRs8fH9ty8Oc6PzMf0NMlc4…> Topics The workshop will be divided into thematic sessions addressing: ⚡ Fundamentals The concept of TI brain stimulation and the underpinning neuromodulation mechanism. 🔧 Equipment The principal requirements of TI brain stimulation hardware, solution strategies, and performance testing approach. 🧠 Deployment The principles governing the deployment of TI electrical stimulation to modulate human brain activity, and best practices for maximal safety, precision, and efficiency. 💊 Applications The challenges and prospective strategies in developing TI stimulation into brain therapy applications. It will include interactive lectures, hands-on practice and open discussions to maximise knowledge transfer and synergy. Target Audience The workshop is designed to provide essential in-depth knowledge and hands-on practice for a broad range of research professionals who integrate, or are interested in integrating, TI stimulation into translational brain research. Registration & Further Information For further information and registration, please see the workshop website<https://secure-web.cisco.com/1bgDwtFe5UUJkYJgNNI3g8FVRs8fH9ty8Oc6PzMf0NMlc4…>. There are limited spaces. Don't hesitate to get in touch with us at UKDRI(a)imperial.ac.uk<mailto:UKDRI@imperial.ac.uk> for registration inquiries. 👉<https://secure-web.cisco.com/1O97JJBwl4DLuuCta83GhXUsSxZolbQaEhhxPrS4fp70Vq…> Register Now<https://secure-web.cisco.com/1O97JJBwl4DLuuCta83GhXUsSxZolbQaEhhxPrS4fp70Vq…> TI Brain Stimulation Workshop · SfN 2026 Satellite Event Washington, D.C., USA · Friday 13 November 2026

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PhD positions in computational neuroscience at the University of South Carolina
by Z S 28 Sep '26

28 Sep '26

External Email - Use Caution Dear all, Dr. Sha’s lab (https://secure-web.cisco.com/1zZvkpEMU-2uxy_jpyQYDQwnfzCYLwW9h9_ymm0uoRbXBd…) at the University of South Carolina is seeking *PhD students in computational neuroscience *in the Department of Psychology. Our lab is affiliated with the Carolina Autism & Neurodevelopment Center, the Institute for Mind & Brain, and working closely with the McCausland Center for Brain Imaging in Columbia, center of SC Metropolitan Statistical Area. Our lab explores the mechanisms of atypical brain development and neurodevelopmental disorders (e.g., autism spectrum disorders) by leveraging computational modeling (e.g., deep learning models) to bridge neural circuitry, exposure (e.g., early life adversity) and psychopathological phenotypes, and treatment outcomes. These innovative projects will leverage state-of-the-art machine learning models and neuroimaging, supported by the brand-new Brain Imaging Center (with 3T and 7T MRI scanners) and the Biobehavioral Research Center at the University of South Carolina. This position provides an excellent opportunity for a self-motivated student to gain hands-on experience with neuroimaging (e.g., MRI) and biomedical research techniques. The candidate will have full access to rich in-house and public datasets, and advanced neuroimaging platforms. Our lab fosters a collaborative and productive environment, and we fully support PhD students in generating high-quality research publications, applying for fellowships and securing their future career paths. Requirements: · Bachelor’s or Master’s degree in a relevant field (e.g., neuroscience, math, data science, biostatistics, biomedical engineering) · Experience with neuroimaging MRI data analysis is preferred. · Candidates with coding experience are preferred. How to apply: Please submit your CV to Dr. Sha (zsha(a)mailbox.sc.edu) Best, Zhiqiang

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Re: FS 8.2.0 on Rocky 9 / RHEL 9
by fsbuild 25 Sep '26

25 Sep '26

External Email - Use Caution I would not say “ignore” the rocky9 installer. The rocky9 binaries should run more efficiently on rocky9 than the rocky8 binaries.   If you don’t need to run what you listed, then I would default to using the rocky9 installer, e.g., what you listed is not necessary to run recon-all or freeview on rocky9.  You will eventually need to abandon the rocky8 binaries as they are not expected to work going forward on newer OS’s like rocky10 (which is the current release). You can install only 1 instance of the freesurfer package using the .rpm installers.   So I would install the rocky9 .rpm on rocky9 and make that the default for users.  You could then manually unpack the rocky8 rpm, and copy the contents somewhere such that you can access it as a fallback on the rocky9 machine in case someone needs to try and run those older binaries. - R. On Sep 3, 2026, at 02:54, Anderson Winkler <anderson.winkler(a)utrgv.edu> wrote:

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Question about holes in the FreeSurfer 8 ICC mask
by Cajgfinger, Thomas 25 Sep '26

25 Sep '26

External Email - Use Caution Hello, I am using FreeSurfer 8.2.0 and noticed some enclosed holes in the intracranial cavity (ICC) mask produced by recon-all. The holes appear in several slices, and they account for approximately 3% of voxels in one subject. Could you let me know: 1. Is this expected behavior for the ICC mask? 2. Is there a FreeSurfer option or recommended command to avoid or fill these holes? I have attached an anonymized screenshot showing an example. [cid:0c624e69-4e2b-463c-a0cc-5181c59362b3] Thanks, Thomas Cajgfinger --Confidentiality Notice: This e-mail transmission may contain restricted, confidential, and/or legally privileged information that is intended only for the individual(s) or entity(ies) named in the e-mail address(es), or the individual(s) or entity(ies) reasonably understood to be the intended recipient(s) via the content or context of the transmission. If you are not the intended recipient, any disclosure, copying, distribution, or reliance upon the contents of this e-mail is by you is prohibited. If you have received this transmission in error, please reply directly to the sender to notify them of their error then immediately delete the message.

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Repost: mri_gtmpvc error - segmentation ROIs disappear in PET space
by Qassim Alkassir 23 Sep '26

23 Sep '26

External Email - Use Caution Just reposting this to gently bump it since I did not see it on the forum: Hello, I am using PETSurfer/mri_gtmpvc for PET quantification in the WRAP Alzheimer's cohort. I am encountering a reproducible error when regions present in gtmseg.mgz have no voxels after the segmentation is mapped into PET space. I searched the mailing-list archives and found a previous discussion of the same error message involving segid 29. In our data, however, the affected labels differ between subjects, so I wanted to ask what the recommended general approach is. What I am trying to accomplish ------------------------------ We are processing motion-corrected, frame-averaged 11C-PiB PET images with PETSurfer. Our PET images are approximately: Matrix: 128 x 128 x 63 Voxel size: 2.574 x 2.574 x 2.425 mm Voxel volume: 16.07 mm^3 The corresponding gtmseg.mgz images have: Voxel size: 0.5 x 0.5 x 0.5 mm Voxel volume: 0.125 mm^3 Command ------- The relevant mri_gtmpvc options generated by our PETSurfer workflow are: mri_gtmpvc \ --psf 0 \ --no-tfe \ --seg gtmseg.mgz \ --default-seg-merge \ --auto-mask 10 0.01 \ --mgx 0.01 \ --no-reduce-fov \ --no-rescale \ --save-input \ ... I have attached the full PETSurfer log from a representative failed subject. It contains the complete generated command and output. Exact error ----------- For example: ERROR: creating region for nthseg=22, segid=78, Left-WM-hypointensities It may be that there are no voxels for this seg when mapped into the input space. I initially encountered this problem in another subject for segid 79 (Right-WM-hypointensities). Before changing the segmentation or adding replacement rules, I tested four additional independent PiB subjects using the same unmodified workflow. gtmseg completed successfully for all four subjects. PETSurfer completed successfully for one subject and failed during mri_gtmpvc for three subjects. Results ------- The regions producing mri_gtmpvc errors were: Subject SegID Region GTM vol PET vox ---------------------------------------------------------------- WRAP1 78 Left-WM-hypointensities 6 mm^3 0 WRAP1 79 Right-WM-hypointensities 5 mm^3 0 WRAP2 31 Left-choroid-plexus 6 mm^3 0 WRAP2 78 Left-WM-hypointensities 21 mm^3 0 WRAP2 79 Right-WM-hypointensities 1 mm^3 0 WRAP3 78 Left-WM-hypointensities 2 mm^3 0 We also have an informative within-subject comparison in WRAP3: segid 78: GTM volume = 2 mm^3 PET-space representation = 0 voxels mri_gtmpvc reports an error for segid 78 segid 79: GTM volume = 46 mm^3 PET-space representation = 1 voxel mri_gtmpvc does not report an error for segid 79 For the failing labels, we directly counted the voxels in both gtmseg.mgz and the PET-space segmentation at: no_pvc_6.0fwhm/aux/seg.nii.gz In every case listed above, the label is present in gtmseg.mgz but has zero voxels in the PET-space segmentation. This makes us suspect that the immediate failure occurs when a region retained in the GTM definition receives no voxel representation after mapping the segmentation onto the much coarser PET grid. One detail that of note was that total region volume alone does not determine whether a label survives. For example, segid 78 in WRAP2 occupies 21 mm^3 in gtmseg.mgz, which is greater than the volume of one PET voxel (16.07 mm^3), but it still maps to zero PET voxels. Questions --------- 1. What is the recommended PETSurfer/mri_gtmpvc approach when a valid region in gtmseg.mgz has zero voxels after mapping into PET space? 2. For segids 78 and 79 (Left/Right-WM-hypointensities), is --merge-hypos intended for this situation? 3. We also see the same problem for segid 31 (Left-choroid-plexus). Should choroid plexus be merged/replaced for GTM analysis, or should this be handled differently? 4. More generally, should very small regions be merged before GTM construction, or is there another recommended way to handle regions that disappear at PET resolution? Additional FreeSurfer context ----------------------------- The anatomical FreeSurfer reconstructions were originally generated with FreeSurfer 8. The PETSurfer/gtmseg environment currently uses FreeSurfer 7.4.0. Because the FreeSurfer 8 reconstructions did not contain the classical talairach.m3z expected by the FreeSurfer 7.4 gtmseg, we generated talairach.m3z using FreeSurfer 7.4 mri_ca_register. gtmseg subsequently completes successfully for all subjects tested. The error described above occurs later during mri_gtmpvc. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.0-20230510-e558e6e 2) Platform: Ubuntu Linux, x86_64 3) uname -a: Linux hpclogin.sri.utoronto.ca 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) PETSurfer log: See attached. I have attached the PETSurfer log from WRAP2, which demonstrates the failure for three different labels (31, 78, and 79). Thank you, Qassim Alkassir

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Update/fix for freesurfer license registration page
by fsbuild 22 Sep '26

22 Sep '26

External Email - Use Caution The freesurfer license registration form,https://secure-web.cisco.com/1eH4NN8hGQ-iq5ACClrSdWb_RLJ7QvNokZX4eXy95… - has been updated to try and prevent gateway timeout and other related errors.  Please try the form again if you have been unable to obtain a license.  As always, if you are accessing the web from behind an institutional, corporate or government firewall (and/or using a VPN), then your connection times may take longer or be interrupted and so may still fail.   But the response times seem improved from what we can see. - R.

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Failed talarach
by El_Duderino_422 22 Sep '26

22 Sep '26

External Email - Use Caution Hello All, I have got an issue with the procedure for dealing with a fail talairach registration. Failed talairach happen quite often for us. I go through the whole procedure of manually registering. I follow the procedure outlined in the URL. https://secure-web.cisco.com/13NWWpMXxUVWAfIn9KlHlBzoCyjMJjY8qB8jWk4-Z8YLCN… This never seems to work. Yesterday, I did some digging and I am a bit confused on the procedure and how it even works.. In the step where we run tkregisterfv --s tal_before --fstal When saving the transform it saves in the lta format. The file that need to be replaced is talairach.xfm. There is no way to save in a xfm format; if there is I could not figure it out. The talairach.lta is generated in the beginning of the autorecon2 step and is also a transform to register to a different target. After running the recon-all transform.xfm does not update. I followed the direction. Furthermore, the part were your check the registration with the command freeview -v tal_before/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm T1.mgz and brainmask.mgz are always registration. should the command be freeview -v fsaverage/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm Please correct me. I know I am completely misunderstanding things.

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