Freesurfer June 2026

freesurfer@nmr.mgh.harvard.edu

24 participants
28 discussions

Research Study Question - FreeSurfer Use
by Kasperek, Jessica 05 Jul '26

05 Jul '26

External Email - Use Caution Hello, One of my research studies, a retrospective Multiple Sclerosis (MS) study, is looking to conduct analyses on volumetric changes in brain MRI scans of MS patients during the course of their treatment. Specifically, it is looking for these items: * Overall brain volume change * Total lesion load * Cervical spine lesion * New MRI lesions * Asymmetrical atrophy between left and right hemispheres * Hippocampus * Thalamus * Basal ganglia * Prefrontal cortex * Cerebellum * Cortical GM Each patient has approx. 10 MRI scans or so. Is this a doable project for FreeSurfer? Any recommendations on how to approach this with the software? Any help is appreciated. Thanks, Jessica Jessica Kasperek Research Coordinator Neurology Department - Clinical Research Unit 1 Endeavor Health 2650 Ridge Avenue, Burch Building Room 310, Evanston, IL 60201 (p) 847-570-1864 (e) jessica.kasperek(a)endeavorhealth.org [cid:b190731c-8276-47fe-a322-7bde2a6cf3c8] ******************* PLEASE NOTE ******************* This message and any documents accompanying this transmission may contain information that is privileged, confidential, and/or exempt from disclosure under applicable law and is intended solely for the addressee(s) named above. If you are not the intended addressee/recipient, you are hereby notified that any use of, disclosure, copying, distribution, or reliance on the contents of this message is strictly prohibited and may result in legal action against you. Please reply to the sender advising of the error in transmission and immediately delete/destroy the message and any accompanying documents. Thank you.

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infant_recon_all: could not open aseg.16.mgz
by Dierker, Donna 02 Jul '26

02 Jul '26

External Email - Use Caution Hi infant freesurfer gurus, I need help with infant_recon_all. I have existing third-party segmentations for six month old babies' T1w's. I have relabeled them with label indices that bibsnet would output. Then I tried running nibabies like so: docker run --rm -i -u 1697:10 -v /usr/local/pkg/freesurfer7.3/.license:/opt/freesurfer/license.txt:ro -v /my_file_system/rawdata:/data:ro -v /my_file_system/derivatives/nibabies:/out -v /my_file_system/work/nibabies/sub-01:/work -v /my_file_system/derivatives/bibsnet:/deriv1 nipreps/nibabies:25.2.1 /data /out participant --participant-label 01 -s 6mo -w /work --verbose --derivatives /deriv1 --anat-only --fd-spike-threshold 0.2 --age-months 6 --surface-recon-method infantfs --cifti-output 91k --debug registration --project-goodvoxels --multi-step-reg --norm-csf --omp-nthreads 8 --mem 300000 --nprocs 8 --stop-on-first-crash --output-spaces fsLR MNIInfant:cohort-3 MNI152NLin6Asym:res-2 anat It runs 30-60 minutes and seems to make some surfaces before bailing like so: writing spherical brain to /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix spherical transformation took 0.0770 hours FSRUNTIME@ mris_sphere 0.0770 hours 8 threads #VMPC# mris_sphere VmPeak 929720 mris_sphere done /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/surf /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix lh.qsphere.nofix cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/rh.qsphere.nofix rh.qsphere.nofix /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall mri_or /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/wo rk/aseg.16.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/wm.nonscaled.mgz processing 3 input files processing input volume 1 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz processing input volume 2 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz processing input volume 3 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz error: mghRead(/out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz, -1): could not open file Segmentation fault (core dumped) I suspect aseg.16.mgz is the Brain-Stem, and these third-party segmentations did not separate the brainstem into pons, medulla, and midbrain, so I left the brainstem unlabeled. But after running into this issue, I tried relabeling the brainstem to label index 16 and ran nibabies again -- same error. I have been looking at these web pages for possible work-arounds, but I could use some help, if you have any ideas: https://secure-web.cisco.com/1kXsEAk5LcnODg46NZQ42ThUNHIoft_7-54OwfS8OeJsNP… https://secure-web.cisco.com/1E2XdEVYlFV-azzD0J4zRpK1RYhrDPSVxPfxg3Eqx3SHiC… Sorry for the long message and odd question, but as you know this timepoint is very challenging, and the segmentations are otherwise promising. Thank you for any ideas you have for working around this issue, Donna ________________________________ 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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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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Freesurfer June 2026