Freesurfer June 2026

freesurfer@nmr.mgh.harvard.edu

24 participants
29 discussions

UCLA NIH-Supported Clinical fMRI Presurgical Planning Course, Quick Survey (5 min, response by July 3)
by Robert Welsh 26 Jun '26

26 Jun '26

External Email - Use Caution Dear Colleague, We are in the planning stages of a NIH-supported national course on Clinical fMRI-Based Presurgical Planning and are reaching out to ask for 5 minutes of your time. UCLA has run one of the highest-volume clinical fMRI presurgical programs in the country for over 20 years. We are building on that foundation to develop a structured training course for postdoctoral fellows, clinical fellows, and junior faculty from neuropsychology, neuroradiology, neurology, and neurosurgery. We have designed a short survey for two groups — potential trainees and program directors or senior faculty who might support a trainee in attending. We would be grateful if you would complete it yourself and forward it to current trainees in your program who might benefit from this type of course. https://secure-web.cisco.com/194vKw1t3DrVnYSyoLEYoRronsZ1vGrs1mEBNvE09z2MOX… We are hoping to hear from you by July 3, 2026. Your responses will directly shape the course design and support our NIH grant application. With thanks, Robert Welsh, PhD Professor-in-Residence, UCLA Patricia Walshaw, PhD Clinical Associate Professor, UCLA Vincent Koppelmans, PhD Research Associate Professor, University of Utah Christina Caldera Course Administrator, UCLA ----------------------------------- Robert C Welsh, PhD Professor Director and Technical Director CCN Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics Department of Psychiatry and Biobehavioral Sciences Semel Institute for Neuroscience and Human Behavior David Geffen School of Medicine UCLA Adjunct Professor Department of Psychiatry Huntsman Mental Health Institute University of Utah

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Postdoc & RA Positions available at Northwestern University Chicago
by Amber Leaver 26 Jun '26

26 Jun '26

External Email - Use Caution Postdoctoral and Research Assistant positions are available with Dr. Amber Leaver in the Department of Radiology at the Feinberg School of Medicine at Northwestern University in Chicago. Dr. Leaver leads the Integrative Neuromodulation MRI Research group, which uses multimodal brain MRI to study and improve noninvasive brain stimulation methods to treat depression, chronic tinnitus, and other conditions. Open positions will support federally funded research (R01MH141178) involving large-scale multi-site MRI data analysis of brain networks relevant to therapeutic and pathological seizures in electroconvulsive therapy (ECT) and epilepsy. Opportunities to collaborate on translational neuroimaging projects related to depression and chronic tinnitus are also available. Responsibilities: Primary responsibilities will be to manage, preprocess, and analyze multi-site brain MRI data and write manuscripts. Emphasis will be placed on fostering research independence through activities appropriate to career stage, including first-author publications, applications for postdoc fellowships, and conference submissions. Qualifications: Candidates must have degree(s) in neuroscience or fields relevant to neuroimaging. For the postdoc position, a PhD is required, and recent PhD graduates are particularly encouraged to apply. For both positions, candidates should have experience analyzing neuroimaging data using standard software packages (e.g., FSL, Freesurfer), command-line interface, and scripts/code (R, bash, Python). Successful applicants will have strong written and oral communication skills, and the ability to work both independently and collaboratively with scientists across a range of disciplines and career stages. People with interests in translational neuroimaging, neuropsychiatry, and brain stimulation are particularly encouraged to apply. Familiarity with Connectome Workbench, fMRIPrep, Docker, and/or complex multi-site MRI datasets is also a plus. Positions are initially for one year with extensions possible. To apply, send your CV and a brief research statement describing your research experience, interest in the position, and career goals to amber.leaver(a)northwestern.edu<mailto:amber.leaver@northwestern.edu>. Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Hiring is contingent upon eligibility to work in the United States. ________________________________________ Amber Leaver PhD Research Associate Professor of Radiology Track Lead, HSIP Medical Imaging Feinberg School of Medicine Northwestern University sites.northwestern.edu/inmri<https://secure-web.cisco.com/1VIJ2ro_aJgKkPGGuZTTD-pMLdjMBBZ_kWNWPMeu2nF9k_…>

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Re: Rocky 8 support and tar.gz archives
by fsbuild 26 Jun '26

26 Jun '26

External Email - Use Caution Freesurfer releases require various linux system libraries/packages to be installed on the system in order for the binaries to run.  Expanding a tar archive does not perform any dependency checks or subsequently try to install what is needed for everything to run, i.e., it is not practical for us to try and troubleshoot an individual users setup and identify what is missing when a binary fails to run.  We can't prevent someone from expanding the installer packages like tar files into some arbitrary location, but we only support linux setups where an actual install has been done with the .rpm or .deb file.  One option is to test running a new version of freesurfer in a container or VM where you should have admin/root privileges to do the install. - R. On 6/25/26 07:15, Hewitt, Manuel (manuel.hewitt(a)med.uni-goettingen.de) wrote: Hi, we have been using FS 7.4.1 on Rocky 8 and would like to use FS 8.x, specifically 8.2.0.Before we installed FS in a user directory, not system-wide.For 8.x there are no releases as tar.gz archives anymore. Even the Rocky 9 archive was only added half a year later. Have these archives been discontinued? MFG, Manuel Hewittwissenschaftlicher Mitarbeiter UNIVERSITÄTSMEDIZIN GÖTTINGENGEORG-AUGUST-UNIVERSITÄTKlinik für NeurologieRobert-Koch-Straße 4037075 GöttingenBriefpost 37099 GöttingenTelefon +49 551 39-62355Fax +49 551 39-8126Email manuel.hewitt@med.uni-goettingen.dehttps://neurologie.umg.eu/          External Email - Use Caution         _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1QI5Jp55uVxO5nHVTQ0oAoIirelSqEhOLb-Zm1G0FWMrux… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/15DpN-5nqAKgW2CNTxkMlhTawoT0_yltL_OpHVSOA9_ptQ… <https://secure-web.cisco.com/1z0Kb0bpJbwJTSLYptBCtwDQfBqUPmw3smkhLNbv1UMCC7vlJDlS65pHsMUx_bdm_c5C5JyXYfO3jvhTt5XRbhfT9iI_sljnMVZ-Oc-vpv4lSC9lt3VNNDi21oxINBnfVlAq0A8iF2E3WphHVsd9iyB7EuxVDYWbl8O_YSAeVr7vvMHFnbXkQgm86sbh-8kgc3-GtKlzF2Gh_IwU-yRU6GiT_k59uyHriJx4v7_qZlHayMEzGlt5dwOlFjEr-Zewl_SbYstRYXOCMDV2v0oFfJig903aCPkttBKHeQjPaEIxESDgjK5kw1s6FEwizlGRJowAPUGfVvVoww0YOVdoEyQ/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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apply mri_synthmorph transform to a set of coordinates
by Ezequiel Mikulan 25 Jun '26

25 Jun '26

External Email - Use Caution Hi, I would like to know whether it is possible to apply a transform estimated with mri_synthmorph to a set of coordinates (i have them in RAS space). These are SEEG electrode positions, and the transform maps between a subject’s native space and the MNI152 template. If this is not currently supported, is this something that might be added in the future? Thanks a lot for your tools. Best, Ezequiel

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Rocky 8 support and tar.gz archives
by Hewitt, Manuel 25 Jun '26

25 Jun '26

Hi, we have been using FS 7.4.1 on Rocky 8 and would like to use FS 8.x, specifically 8.2.0. Before we installed FS in a user directory, not system-wide. For 8.x there are no releases as tar.gz archives anymore. Even the Rocky 9 archive was only added half a year later. Have these archives been discontinued? MFG, Manuel Hewitt wissenschaftlicher Mitarbeiter UNIVERSITÄTSMEDIZIN GÖTTINGEN GEORG-AUGUST-UNIVERSITÄT Klinik für Neurologie Robert-Koch-Straße 40 37075 Göttingen Briefpost 37099 Göttingen Telefon +49 551 39-62355 Fax +49 551 39-8126 Email <mailto:manuel.hewitt@med.uni-goettingen.de> manuel.hewitt(a)med.uni-goettingen.de <https://secure-web.cisco.com/10RBM1M-alXji3WAezqAzDUhRJBMv3Sb3vcdT1jYbICAE0…> https://secure-web.cisco.com/10RBM1M-alXji3WAezqAzDUhRJBMv3Sb3vcdT1jYbICAE0… External Email - Use Caution

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Re: latest freesurfer for Ubuntu 24.04 LTS Noble Numbat on 20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop GPU
by fsbuild 19 Jun '26

19 Jun '26

External Email - Use Caution The latest Freesurfer release is 8.2.0 from 3/2026 as listed here,https://secure-web.cisco.com/1SCAeqA5D30l01clq4hqLiGOlk9ojDnnCLiRfX54I… - and the link to the Ubuntu24 installer package is,https://secure-web.cisco.com/18VvOMJBSFuFEfxflOqrMc6d4XCs1qNkqKYD8HYVsKH… After installation, you should apply all the 8.2.0 patch updates per the instructions,https://secure-web.cisco.com/11gwvkh46pKGNAueq3gjYK7xWYkb6lcCj… If you are planning on running recon-all then your laptop should probably have 32G or more total system RAM.  Also probably a good idea for your boot partition to have 10G+ free space. - R. On Jun 19, 2026, at 16:09, Andreas Bartsch <bartsch(a)radvisory.net> wrote:        External Email - Use Caution        Hi,what is the latest Freesurfer version suitable for Ubuntu 24..04 LTS Noble Numbat on Intel (20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop GPU)?Where is the download, and where are installation instructions?Thanks!Cheers-Andreas_______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1tVrgCdE4iFOJbNj4i4C1nM3KuKrMLMxJcb5iVcGaFxQ3d…

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Late-breaking abstracts for IST 2026 (Banff): submit July 22 to August 19
by Graham Little 18 Jun '26

18 Jun '26

External Email - Use Caution Dear colleagues, Registration for IST 2026 in Banff is open, and we are adding a late-breaking abstract window for work that wasn't ready by the spring deadline. If you have new results, this is a second route onto the program. Conference dates: October 25 to 29, 2026 Location: Banff Centre for Arts and Creativity, Banff National Park, Canada Late-breaking window: July 22 to August 19, 2026 Submit here: https://secure-web.cisco.com/1hTbr2SlzD_B_jC1AaDUDw3pWAno3LE830EyIPTlWNzd8Q… IST 2026 is the society's second annual meeting. It runs across the full tractography workflow, from anatomy and validation through methods and clinical applications, with time set aside for direct conversation with the people using and building the tools. What's on the program: - Keynotes from Neda Jahanshad (Keck School of Medicine, USC; ENIGMA), Luis Concha (Institute of Neurobiology, UNAM), and Forrest Collman (Allen Institute for Brain Science) - Masterclasses in three tracks: Anatomy and Validation, Analysis and Methods, and Clinical Applications - A program where every trainee presents, with a power pitch and a poster The window closes August 19, and there are fewer late-breaking slots than in the main round, so send yours in early once submissions open. Best regards, The IST 2026 Organizing Committee

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FR[AI]ME 3.0 — Now with full 4D NIfTI and diffusion MRI support on macOS QuickLook
by Ross Callaghan 15 Jun '26

15 Jun '26

External Email - Use Caution Dear FreeSurfer users, We are excited to announce a major update to FR[AI]ME, the macOS QuickLook extension for neuroimaging data. This release adds full 4D image support, making it significantly more useful for researchers working with time-series and diffusion MRI data. What's new in 3.0: * 4D volume navigation — scrub through fMRI runs, perfusion series, or any 4D NIfTI directly in Finder. No need to open FSLeyes, FreeView, ITK-SNAP etc. just to check a volume. * Diffusion MRI b-vector/b-value visualisation — an interactive 3D sphere plots every gradient direction on its b-shell, highlighting the currently selected volume. Just place .bvec/.bval files alongside your image and preview the parent directory. What else can FR[AI]ME do: * Image overlay — select a parent directory to preview and choose any two images as base/overlay with independent colour maps and opacity. * Multiple colour maps including FreeSurfer LUT, Inferno, Magma, Spectral, and more. * Supported formats: NIfTI (.nii/.nii.gz), FreeSurfer (mgh/mgz), DICOM. FR[AI]ME 3.0 is available now on the Mac App Store: https://secure-web.cisco.com/1Ssvdc_JbHZr2U5adh3sFA47HI87hMEilgW-UwPDDyIBHD… For questions or feedback, contact info(a)ainostics.com<mailto:info@ainostics.com>.

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Question Regarding Synth Tools for Quantitative Atrophy Analysis
by John Anderson 12 Jun '26

12 Jun '26

External Email - Use Caution Hello, Could an expert in the Synth collection of tools please confirm whether these tools are intended for reliable use in patient populations, or primarily in healthy brains? Specifically, we would like to understand whether the Synth tools can preserve and reproduce cortical atrophy measurements in a manner comparable to the full recon-all pipeline. Practically, it appears that recon-all and the Synth tools may produce different measurements for the same brains, so we would like to clarify the expected use case. For example, if we have a pooled MRI dataset from patients with different neurological pathologies, including Alzheimer’s disease, amyotrophic lateral sclerosis, and other disorders, each condition may have a distinct cortical atrophy pattern. Are the Synth tools able to perform segmentation while preserving these disease-specific pathological patterns, or should they not be used for quantitative atrophy analysis? Any advice would be appreciated. Thank you. John

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Re: Recon-all for multiple subjects on parallel
by Finn, Quentin 09 Jun '26

09 Jun '26

External Email - Use Caution Not a developer, but this is something that comes up frequently in most analysis situations. For qsub, you should be able to just make separate scripts for each subject and submit them all at once and let the scheduler node handle the rest. E.g. If you have sub1.sh, sub2.sh,....subn.sh as the submission scripts you can just submit them all: for j in sub*.sh; do qsub ${j} done You may consider writing a wrapper that will create all the subscripts based on an input...e.g.: SUBNAME=$1 Echo "#!/bin/bash #$ -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 $SUBJECTS_DIR env | grep -E "FREESURFER|FS_LICENSE|SUBJECTS_DIR" recon-all -all -i /data/holly-host/UserName/anat/${SUBNAME}_t1w.nii -s sub-01 SegmentAAN.sh sub-01 " > ${SUBNAME}.sh ________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, June 9, 2026 9:36 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 268, Issue 8 Caution: This message came from an external sender outside your organization. Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Recon-all for multiple subjects on parallel (Huaiyu Liu) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Jun 2026 14:35:49 +0000 From: Huaiyu Liu <huaiyu.liu(a)ucl.ac.uk> Subject: [Freesurfer] Re: Recon-all for multiple subjects on parallel To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <DB8PR01MB5899E8997D209D3F51B01799DB1D2(a)DB8PR01MB5899.eurp rd01.prod.exchangelabs.com> Content-Type: multipart/alternative; boundary="_000_DB8PR01MB5899E8 997D209D3F51B01799DB1D2DB8PR01MB5899eurp_" External Email - Use Caution Dear FS Developers, I recently asked a question about how to run recon-all in parallel for multiple subjects (like 4-8). Could someone give me some clues, I would be really apperciate. Best, Huaiyu ________________________________ From: Huaiyu Liu <huaiyu.liu(a)ucl.ac.uk> Sent: Thursday, May 28, 2026 18:21 To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Recon-all for multiple subjects on parallel 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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Freesurfer June 2026