Freesurfer October 2026

freesurfer@nmr.mgh.harvard.edu

10 participants
12 discussions

Question about aseg.auto_noCCseg.label_intensities.txt
by Yanez-Ramos, Lupita, Ph.D., M.S. 21 Oct '26

21 Oct '26

External Email - Use Caution Hello, I’m reaching out for some help to identify the equivalent of a FreeSurfer output text file in version 8 or newer. When using FreeSurfer version 7.3.2, our workflow relies on the following file located in the subject’s mri directory: aseg.auto_noCCseg.label_intensities.txt We recently began transitioning to FreeSurfer 8.1.0 and noticed that this file is no longer generated. Could you please let us know whether there is an equivalent output file in FreeSurfer 8.1.0 or newer that contains the intensity labels and corresponding values for an individual subject? Any guidance on where to locate this information in the newer versions would be greatly appreciated. Thank you for your assistance. Lupita

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Re: Trouble searching freesurfer list archives
by fsbuild 21 Oct '26

21 Oct '26

External Email - Use Caution It worked for me to run a search from the page,https://secure-web.cisco.com/1b0MWTWlF2Dz6wSZ71FWeVeDbazjE_suxqA0vMlWB… e.g., on mri_synthmorph,https://secure-web.cisco.com/1YH3H3KpItvQPrI-4S4Mj5trk-9uzgd… Perhaps your internet connection is behind a firewall and/or going thru a VPN causing some connections to fail.  In the case of using a VPN, changing your connection to a different VPN server can sometimes fix blocked access. - R. On Oct 20, 2026, at 15:14, Dierker, Donna <donna(a)wustl.edu> wrote:        External Email - Use Caution        I'm having trouble searching the archives -- similar to what was described here: https://secure-web.cisco.com/1xMYjnD6If15eYbYGRdPfmcn0-S1kjgRUY5ns5WoV82HSA… Except I can find recent posts here: https://secure-web.cisco.com/1oCxAaaBe_0v893uhD-ZU2bjc60biwkPU-KA9vLvNxP0Mc… But when I try to sign in or search the archives, I get: ForbiddenYou don't have permission to access this resource. The freesurfer wiki (https://secure-web.cisco.com/14Achg4W2BMEF1UV1kvwbLNLDIJL7QMB5wNwRAwzWJjhRA…) links to the old mail-archive address in two places: Search the archives: It is highly likely that someone else has run into the same problem before you. The fastest way to get answers is therefore to search the archives of our mailing list. .... and here: FreeSurfer mailing list (<freesurfer AT nmr DOT mgh DOT harvard DOT edu>): This is the list to email for general support on installing and using FreeSurfer. You need to subscribe to the list before you can send messages to it, and you need to send your messages from the email address with which you subscribed. (This prevents spam.) Messages sent to this list are read by the FreeSurfer developers and user community. All questions and responses are archived. These mail-archive posts are searchable, and they do now include more recent posts than they did a couple of months ago, but there seems to be a gap between March and September 2026, for example. 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._______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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Re: Matlab runtime and freesurfer 8
by fsbuild 21 Oct '26

21 Oct '26

External Email - Use Caution The Wiki Page you referenced shows the install of R2014b and R2012b for older Freesurfer releases. The most recent install information is available from the main Freesurfer release page for 8.X (and 7.X) releases.https://secure-web.cisco.com/1WVlXtdE4g7hfznXulPO9d433DTVOpKZZHIiD… Follow the link there under the 8.2.0 release for 8.X setup and patch updates, and you will load the page,https://secure-web.cisco.com/1NXUBe4oUZxu3lMDHfpZbc0u3FEgZB5zxfx1sOQjR… Then scroll down to the section for SETUP A MATLAB DISTRIBUTION and you will see the example install for the R2019b (MCRv97) runtime. I’m not aware of issues with Fresurfer 8.2.0 binaries using R2019b, but even if that is the case, I  don’t think the Mathworks supports overriding the included libc with a different one. - R. On Oct 20, 2026, at 08:04, Michael Firbank <michael.firbank(a)newcastle.ac.uk> wrote:        External Email - Use Caution        Below, an issue, and solution to matlab runtime libraries with freesurfer8 on Ubuntu 24. I was trying to use the AANSegment tool: https://secure-web.cisco.com/1PkARILS7Gu-lAiyUyRV0scVChP6Y8FVlzo7FGdFaYluaM… And came across some problems (now solved). 1) The utility uses the Matlab runtime. I have freesurfer 8 installed, but the instructions on that page (and also theMatlabRuntime page) only refer to version 6 and 7. Could this be updated? 2) Having got the right matlab version, I ran into problems with missing libraries.Discussing this with our IT team, they said: "The problem is that the MCR runtime is supplying its own version of libstdc++ (the GLIBC C++ standard library) which is conflicting with other software/libraries which are loaded at the same time, namely /lib/x86_64-linux-gnu/libitkvnl_algo-5.3.so.1 (probably some other code/application which is part of freesurfer is wanting that library). So the MCR runtime is adjusting the library path to load its own libstdc++ library (an older version), but other code which is running wants libitkvnl_algo-5.3.so.1 which in turn wants the (later) version of libstdc++ which is included as part of the Ubuntu 24 OS." Their solution was to replace the library in the MCR directory with a symbolic link to the ubuntu system one.ie that/usr/local/freesurfer/8.2.0/MCRv97/sys/os/glnxa64/libstdc++.so.6is now a symbolic link to/lib/x86_64-linux-gnu/libstdc++.so.6 which seemed to solve the problem. Best wishes Michael Michael Firbank       #mynameis   [my-kel fur-bank]                                                                 Newcastle UniversityHealth Innovation Neighbourhood (formerly Campus for Ageing and Vitality)Newcastle upon Tyne, NE4 5PL                                                        _______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/

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Trouble searching freesurfer list archives
by Dierker, Donna 20 Oct '26

20 Oct '26

External Email - Use Caution I'm having trouble searching the archives -- similar to what was described here: https://secure-web.cisco.com/1vx8uZ6LU3vk7AT_G6Zh5-8b6Vf-q1O1EHR2mZXTeCNFW6… Except I can find recent posts here: https://secure-web.cisco.com/1kdqWytfhePnZnlnDUX6hDac87ndijCRK5-GQLnGgxTZl4… But when I try to sign in or search the archives, I get: Forbidden You don't have permission to access this resource. The freesurfer wiki (https://secure-web.cisco.com/1KgOZvMQhNCdWsP8FjV4szIi4kgJxo4PL4cfkLQXkZ-upt…) links to the old mail-archive address in two places: Search the archives: It is highly likely that someone else has run into the same problem before you. The fastest way to get answers is therefore to search the archives of our mailing list. ... and here: FreeSurfer mailing list (<freesurfer AT nmr DOT mgh DOT harvard DOT edu>): This is the list to email for general support on installing and using FreeSurfer. You need to subscribe to the list before you can send messages to it, and you need to send your messages from the email address with which you subscribed. (This prevents spam.) Messages sent to this list are read by the FreeSurfer developers and user community. All questions and responses are archived. These mail-archive posts are searchable, and they do now include more recent posts than they did a couple of months ago, but there seems to be a gap between March and September 2026, for example. ________________________________ 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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Matlab runtime and freesurfer 8
by Michael Firbank 20 Oct '26

20 Oct '26

External Email - Use Caution Below, an issue, and solution to matlab runtime libraries with freesurfer8 on Ubuntu 24. I was trying to use the AANSegment tool: https://secure-web.cisco.com/1H4cbEXrxSNts7sQntuDLTelBVbN0CKybPNrkpsA2FJAKH… And came across some problems (now solved). 1) The utility uses the Matlab runtime. I have freesurfer 8 installed, but the instructions on that page (and also the MatlabRuntime<https://secure-web.cisco.com/1_scv-lDtfw8ziHNttN1aI2gULzNJVSX5styh_neviSU-H…> page) only refer to version 6 and 7. Could this be updated? 2) Having got the right matlab version, I ran into problems with missing libraries. Discussing this with our IT team, they said: "The problem is that the MCR runtime is supplying its own version of libstdc++ (the GLIBC C++ standard library) which is conflicting with other software/libraries which are loaded at the same time, namely /lib/x86_64-linux-gnu/libitkvnl_algo-5.3.so.1 (probably some other code/application which is part of freesurfer is wanting that library). So the MCR runtime is adjusting the library path to load its own libstdc++ library (an older version), but other code which is running wants libitkvnl_algo-5.3.so.1 which in turn wants the (later) version of libstdc++ which is included as part of the Ubuntu 24 OS." Their solution was to replace the library in the MCR directory with a symbolic link to the ubuntu system one. ie that /usr/local/freesurfer/8.2.0/MCRv97/sys/os/glnxa64/libstdc++.so.6 is now a symbolic link to /lib/x86_64-linux-gnu/libstdc++.so.6 which seemed to solve the problem. Best wishes Michael Michael Firbank #mynameis [my-kel fur-bank] Newcastle University Health Innovation Neighbourhood (formerly Campus for Ageing and Vitality) Newcastle upon Tyne, NE4 5PL

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aseg.auto_noCCseg.label_intensities.txt
by Yanez-Ramos, Lupita, Ph.D., M.S. 15 Oct '26

15 Oct '26

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Re: [RE] Publishing a docker container with Freesurfer inside
by fsbuild 15 Oct '26

15 Oct '26

External Email - Use Caution Re-distribution of Freesurfer source or binaries is subject to the license terms,https://secure-web.cisco.com/1cTrvpXdBk4S3JOl5ZD84kFuWYszh74F9Tx8ojcs… The license states that Freesurfer is for research purposes only and not intended for clinical use, 4. The Software has been designed for research purposes only and has not been reviewed or approved by the Food and Drug Administration or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Any commercialization of the Software is at the sole risk of the party or parties engaged in such commercialization. ... The license also states that use is subject to all the terms of the sub-licenses (3rd party licenses) cited in the distribution, 3. This Software License does not grant any rights with respect to third party software, except those rights that MGH has been authorized by a third party to grant to you, and accordingly you are solely responsible for (i) obtaining any permissions from third parties that you need to use, reproduce, make derivative works of, display and distribute the Software, and (ii) informing your sublicensees, including without limitation your end-users, of their obligations to secure any such required permissions. Various 3rd party licenses can be found here (but I would also check the source code),https://secure-web.cisco.com/1t4quIjwQZEU0TLUWioxZu5rgoMaI_VdfGmF2F56… My understanding is that once you bundle Freesurfer with any software or service that is a commercial product or charges a fee, then you are subject to the *commercial* terms of any 3rd party licenses.  That could require paying for a commercial license from one or more of the 3rd party license holders.   Your organizations legal counsel or legal department should review all the licenses and their terms. - R.

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[RE] Publishing a docker container with Freesurfer inside
by JOUBERT Alice 15 Oct '26

15 Oct '26

External Email - Use Caution Hello, I am very sorry for asking again, if you answered it seems it did not reach me and I would like to do things properly : Thanks for developing FreeSurfer ! My lab uses it regularly, especially along our own software Clinica. I had a question regarding your license limitations. We plan on making Docker containers that would include both Clinica and external software such as FreeSurfer. Would you be okay with it if we made it (ie FreeSurfer binaries) openly available ? It would be free/open-source and users would still need to mount their own FreeSurfer License to the container. Best, Alice Joubert, Research Engineer at ARAMIS Paris Brain Institute

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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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Freesurfer October 2026