Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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 Andreas Bartsch 01 Jul '26

01 Jul '26

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

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Reply - apply mri_synthmorph transform to a set of coordinates
by Ezequiel Mikulan 01 Jul '26

01 Jul '26

External Email - Use Caution Dear Malte, thanks for your reply. I need to apply a deformable transform. I've been using ANTs (antsRegistrationSyN and ApplyTransformsToPoints) and I would like to update that part of the pipeline with mri_synthmorph. Do you think it will be possible in the near future? Best, Ezequiel ________________________________________ Hi Ezequiel, Yes, this is supported by mri_label2label if you save the coordinates in a .label file with vox2ras=3Dscanner in the header. These are simple text fil es; you can find examples in the label subfolder of a FreeSurfer-processed subject. However, this currently only works for rigid or affine transforms, that is, LTA files. What kind of transform are you looking to apply? Best wishes, Malte ________________________________________ From: Ezequiel Mikulan <emikulan(a)yahoo.com> Sent: Monday, June 22, 2026 07:40 To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] apply mri_synthmorph transform to a set of coordinates External Email - Use Caution Hi, I would like to know whether it is possible to apply a transform estima ted 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 subje ct's native space and the MNI152 template. If this is not currently supported, is this something that might be added i= n the future? Thanks a lot for your tools. Best, Ezequiel

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Inquiry about the segmentation of deep-white structure (stria medullaris of thalamus)
by asada.reo.42z＠st.kyoto-u.ac.jp 01 Jul '26

01 Jul '26

External Email - Use Caution Dear Professor Iglesias and the FreeSurfer Development Team, I hope this email finds you well. My name is Reo Asada, and I am a sixth-year medical student at the Department of Psychiatry, Kyoto University. I am currently working on a neuroimaging research investigating the subcortical structures associated with Major Depressive Disorder (MDD) led by my senior collaborator, Dr. Takahiko Inagaki, who will be the first author and is CC'd on this email. For our structural analysis, we are utilizing your NextBrain atlas.I would like to thank you for providing such an exceptionally powerful resource to the imaging community. I am writing to kindly seek your guidance regarding an issue I encountered with the segmentation of the stria medullaris of the thalamus (SMe) (Label 201). When running the NextBrain pipeline on our dataset, the resulting SMe segmentations appear significantly fragmented and frequently mislocalize into the adjacent fornix area. My environment is Freesurfer 8.2.0 with the latest fix applied on Ubuntu 22.04 For reference, I have attached a screenshot demonstrating this issue. The background image is T1w_acpc_dc_restore.nii (processed via the HCP pipeline in native ACPC space, 0.8 x 0.8 x 0.8 mm resolution, image from HC). The overlays shown are: * white_matter_of_forebrain (Label 7, light green) * pons (Label 580, deep green) * stria_medullaris_of_thalamus (Label 201, red) [cid:5f940ad8-d72b-4c18-b956-df48f2a3eae8] The command used to create the segmentation is : mri_histo_atlas_segment_fireants --i /mnt/h/Habenula_Test_Retest/HCPPipeline/Nextbrain/Images/NLH121/run01/T1w/T1w_acpc_dc_restore.nii.gz --o /mnt/h/Habenula_Test_Retest/HCPPipeline/Nextbrain/Images/NLH121/run01/T1w/NextBrain --device cuda --mode invivo --threads 20 --side left (I think that this follows the standard command for mri_histo_altas_segment_fireants) Given the highly delicate nature of the SMe, I would deeply appreciate your advice on the following points: 1. Are there specific command-line flags, resolution adjustments, or preprocessing steps you recommend to improve the continuity and boundaries of such small tracts in NextBrain? 2. Is this level of fragmentation expected when operating on standard isotropic T1w resolutions, or could this point to an issue with the underlying registration/priors for this specific structure? Thank you very much for your time, consideration, and continued support of the community. Sincerely, Reo Asada Sixth-year Medical Student Faculty of Medicine, Kyoto University

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Re: freeview segemantation fault
by fsbuild 01 Jul '26

01 Jul '26

External Email - Use Caution The freesurfer install and/or the freeview application may not be an issue.  If you are using NVIDIA graphics drivers instead of the system X.org drivers, then it might be that changing graphics setting in an X-windows application like freeview may not work for every possible setting you can choose in the application.  I see quite a few postings online about X-windows applications having graphics/font scaling issues on Ubuntu24 depending upon how the system is setup.  If there is no error displayed in the terminal session, you could look in the system log /var/log/syslog to see if there is any graphics related errors listed there. -R. On Jun 30, 2026, at 15:47, Andreas Bartsch <bartsch(a)radvisory.net> wrote:        External Email - Use Caution        Hi,I had sucessfully installed freesurfer 8.2.0 on Ubuntu 24.04 LTS Noble Numbat.Freeview was running.I then changed the font size under preferences from 12 to 14.Since then, I am getting a segmentation fault when I want to run freeview.I even didsudo apt purge freesurfer sudo apt install ./freesurfer_ubuntu24-8.2.0_amd64.deb sudo FREESURFER_HOME=/usr/local/freesurfer/8.2.0 bash fs820_updates.sh for a fresh clean re-installation but am still getting a crash of freeview whenever I am trying to start it.Any remedy?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/1seaLxin619QkjMydLmDPoUTWo857BJnWSchPVpjMA8tPx…

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Re: GPU Ubuntu 24.04 LTS Noble Numbat with a 20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop
by fsbuild 30 Jun '26

30 Jun '26

External Email - Use Caution The fs_install_cuda script does not install all the needed files and using it was removed from the setup notes on the wiki page,https://secure-web.cisco.com/1EArXUNKJci0kAcgvP3KiwS7GZE6BNY1DDZmBRa4I… It was an oversight it was still included in the 8.2.0 release. - R. On Jun 30, 2026, at 15:33, Maurilio Genovese <mauriliogenovese(a)gmail.com> wrote:        External Email - Use Caution        So fs_install_cuda script won't be useful for synthstrip? Thanks,Maurilio_______________________________________________ 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/1s3WKwG6xTvGVKu-diYA6zPCDIYSkCt2n8A9EWeqlSo-c7…

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Re: GPU Ubuntu 24.04 LTS Noble Numbat with a 20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop
by Maurilio Genovese 30 Jun '26

30 Jun '26

External Email - Use Caution So fs_install_cuda script won't be useful for synthstrip? Thanks, Maurilio

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Re: GPU Ubuntu 24.04 LTS Noble Numbat with a 20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop
by fsbuild 30 Jun '26

30 Jun '26

External Email - Use Caution Hello Andreas, Freesurfer releases are primarily built to use the generic system (CPU, GPU) hardware and do not include CUDA software/support because not everyone has CUDA devices, it may not work with different CUDA drivers, we should not re-distribute files with some copyrights, etc.  On machines like the arm64 Macs, I think commands will end up using the built-in GPU’s anyway, e.g., with tensorflow-metal. - R. On Jun 30, 2026, at 11:35, Andreas Bartsch <bartsch(a)radvisory.net> wrote:        External Email - Use Caution        Hi,I am trying to run:20240702165833_t2_spc_flair_sag_34.nii.gz -o brain.nii.gz -m mask.nii.gz -d dist.nii.gz --gpubut am getting:Error: -g flag provided but CUDA is not available on Ubuntu 24.04 LTS Noble Numbat with a 20 × 13th Gen Intel® Core™ i7-13700H, NVIDIA GeForce RTX 3050 6GB Laptop.CUDA, CUDA-toolkit and cudnn are installed, and fsl-gpu-tools are, in fact, running.Also, __NV_PRIME_RENDER_OFFLOAD=1 __VK_LAYER_NV_optimus=NVIDIA_only __GLX_VENDOR_LIBRARY_NAME=nvidia DRI_PRIME=1 mri_synthstrip -i 20240702165833_t2_spc_flair_sag_34.nii.gz -o brain.nii.gz -m mask.nii.gz -d dist.nii.gz --gpuresults in the same error.--gpu=0 does not seem to be the solution, either.Any ideas why -g does not work and how to get it to work?Cheers,AndreasAm 19.06.26 um 22:09 schrieb Andreas Bartsch: 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/1HFJI7-QmPHJz1lStDl4bW3afBpmFCKbUK3frcgcXWjaJ-…

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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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