Freesurfer

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30065 discussions

Inquiry about the segmentation of deep-white structure (stria medullaris of thalamus)
by asada.reo.42z＠st.kyoto-u.ac.jp 24 Jun '26

24 Jun '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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apply mri_synthmorph transform to a set of coordinates
by Ezequiel Mikulan 22 Jun '26

22 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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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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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 19 Jun '26

19 Jun '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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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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Recon-all for multiple subjects on parallel
by Huaiyu Liu 09 Jun '26

09 Jun '26

External Email - Use Caution 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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Re: Question About 8.2.0 Arm64 Mac Release Update
by fsbuild 08 Jun '26

08 Jun '26

External Email - Use Caution https://secure-web.cisco.com/16COGs9Xf9FKM8v1Ci_oDQXeV8-AvFh3_rWW0AtsOrgd4L… … lists there is an update for mri_tumorsynth included (for all OS’s).  It looks to me like the updates do not change the output but makes running it more reliable/stable.  For darwin_arm64,  the SynthSeg update is needed if you intend to run recon-all (and there is also an update to the recon-all script for all OS's). - R.

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