Freesurfer October 2026

freesurfer@nmr.mgh.harvard.edu

12 participants
15 discussions

FW: Postdoc opportunity at Oxford: 3D ultrasound reconstruction
by Fischl, Bruce R.,PHD 23 Oct '26

23 Oct '26

A great opportunity to work with Ana who is doing exciting research Bruce From: Ana Namburete <ana.namburete(a)cs.ox.ac.uk> Sent: Friday, October 23, 2026 6:10 AM Subject: Postdoc opportunity at Oxford: 3D ultrasound reconstruction External Email - Use Caution Dear colleagues, We're looking for a postdoc to join us at Oxford to work on 3D reconstruction of neonatal brain ultrasound, combining neural rendering, multi-view geometry, and ultrasound physics. The position is funded by an ERC Starting Grant (WOMB2COT). We're particularly keen to hear from people with a background in computer vision or 3D reconstruction. No medical imaging experience needed! If this could be relevant to someone in your group or network, I'd really appreciate it if you could pass it along. Here is the call: https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_c…<https://secure-web.cisco.com/1s2Lusf7P6hLvMkWrjWCYY_x1__QdyBn4Q0Pv40rKwTHB5…> Many thanks! Ana Prof. Ana Namburete Associate Professor of Computer Science Tutorial Fellow in Computer Science Department of Computer Science | Pembroke College 15 Parks Road | Oxford OX1 3QD University of Oxford E ana.namburete(a)cs.ox.ac.uk<mailto:ana.namburete@cs.ox.ac.uk> W Lab website<https://secure-web.cisco.com/1QD_KQKD-aga92FQgA1aYlbyalxO8-WfQWkargf8Uw72ZA…> Please don't feel obliged to read or respond to my email outside your own working hours

1 0

FR[AI]ME 4.0 - Preview medical images with macOS QuickLook
by Ross Callaghan 23 Oct '26

23 Oct '26

External Email - Use Caution Dear FreeSurfer users, We’re pleased to announce FR[AI]ME 4.0, an update to our macOS Quick Look extension for neuroimaging data. This release makes image previews available free and adds new ways to explore your data with Premium. What’s new in 4.0: * Image previews are now free — select an image in Finder and press the spacebar for a static three-plane preview, with metadata, colormaps, colourbar legends, and scale bars. For 4D images, free mode displays the first volume. * Free folder browsing — preview a parent directory and switch between its images using the sidebar. * DICOM series previews (Premium) — combine supported DICOM series into 3D or 4D previews. * Interactive slice navigation and voxel readout (Premium) — click within an image or use the cursor sliders to explore anatomical locations across three planes. * Time-series plots (Premium) — inspect how intensity at the selected voxel changes across volumes. Also included with Premium: * Image overlays with independent colormaps for comparing anatomical images, segmentations, and other maps. * 4D volume navigation for browsing fMRI, diffusion MRI, and other volumetric series. * An interactive b-vector sphere showing diffusion gradient directions and b-values. Place the corresponding .bvec/.bval files alongside your image and preview the parent directory. FR[AI]ME supports NIfTI (.nii/.nii.gz), FreeSurfer (.mgh/.mgz), and DICOM (.dcm), including automatic FreeSurfer lookup-table selection for recognised segmentation files. DICOM support remains experimental. FR[AI]ME 4.0 is available on the Mac App Store<https://secure-web.cisco.com/1JFevhqszJAHcZUpB8tb0783JDdSPstJX27N5zFkVXEaag…>. Static previews are free; interactive and advanced features require a Premium subscription. For questions or feedback, contact info(a)ainostics.com<mailto:info@ainostics.com>. We’d welcome suggestions from the FreeSurfer community.

1 0

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

21 Oct '26

External Email - Use Caution There is currently an issue affecting the servers though I cannot say for certain if it is causing the link,https://secure-web.cisco.com/1sJRnI9lGMxlTQGsADd31JOhZT3S6HrWKqwsj9KB3… to load.  I can try it again after the issue(s) have been resolved. - R.

1 0

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

1 0

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/

3 2

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/

2 1

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.

1 0

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

1 0

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

15 Oct '26

1 0

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.

2 1

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2026