Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30051 discussions

longitudnial thalamus segmentation (subnuclei)
by Isabella Rossellini 10 Feb '26

10 Feb '26

External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2). Our team has longitudinal data with 3 time points (e.g., T1, T2, T3), which has been analyzed with the main FreeSurfer longitudinal stream. So we have: ID_base (within-subject template), ID_T1.long, ID_T2.long, ID_T3.long. We decided to look at the thalamic nuclei, but we are not sure how to run it for the 3 time points. 1) Can we just run the segmentThalamicNuclei.sh on ID_T1.long, ID_T2.long and ID_T3.long? (without using the base) 2) Or: Are we supposed to run it on the base/ (within-subject template) first and that will transfer to T1/T2/T3_long data? Are we supposed to run the recon-all -long again to get the thalamic nuclei data for the 3 timepoints? I guess the second option would not be that productive because we need to rerun the longitudinal runs and edit the data again (to correct the pial surfaces etc.). Thank you for your help! Sincerely, Isa Rossellini

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fixing pial boundary: brainmask edits
by Ramirez, Josephine 10 Feb '26

10 Feb '26

External Email - Use Caution Hi there, I am attempting to fix pial boundary issues for a specific subject. I made edits to the brainmask volume as I noticed that the parts of the brain that need to be included were not considered brain. Then, I ran the command recommended when edits are made only to the brain mask to recreate pial surfaces. After running the command, I noticed that the brainmask volume was updated. The parts excluded were now considered brain. However, the pial boundary still did not include them. The aseg volume also did not update to include the parts previously exluded from the brainmask. This is especially strange to me because other participants with similar errors did have successful changes to brainmask and aseg volumes as well as pial surfaces when performing the same edits and running the exact same command. Freesurfer Version: freesurfer/6.0.0-ncf Command Used: recon-all -autorecon-pial -subjid $SUBJ Any troubleshooting suggestions? Not too sure what could be happening for this specific subject and its edits. With Kindness, Josie Ramirez Research Coordinator - H. Kosakowski Lab USC Dana and David Dornsife University of Southern California

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Please unsubscribe my email from the list
by 蒋劲男 08 Feb '26

08 Feb '26

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: 13251475309(a)163.com Thanks

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recon-all doesn't find 001.mgz in mri/orig
by Angelika Wolman 05 Feb '26

05 Feb '26

External Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute recon-all on my nii files. It seems it doesn't find 001.mgz in mri/orig *Subject does not have a bstampfile, copying /opt/fox_cloud/share/app/imaging/freesurfer/7.3.2-1/build-stamp.txt* I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275 Platform: Linux PlatformVersion: 3.10.0-1160.119.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 2) Platform: *CentOS Linux release 7.9.2009 (Core)* 3) uname -a: *Linux fox-c18 3.10.0-1160.119.1.el7.x86_64 #1 SMP Tue Jun 4 14:43:51 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux* 4) recon-all.log: see attached 5) script used: attached (T1_recon_all2.sh) Thank you ! Angelika

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Please unsubscribe my email from the list
by Juncen Wu 05 Feb '26

05 Feb '26

External Email - Use Caution Hi Freesurfer Team Please unsubscribe my email from the list Email: wujc2024(a)shanghaitech.edu.cn <mailto:wujc2024@shanghaitech.edu.cn> Thanks

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Fw: SuperSynth equivalent of quantifyHAsubregions.sh
by Dierker, Donna 05 Feb '26

05 Feb '26

External Email - Use Caution I don't think this message made it to the list. ________________________________ From: Dierker, Donna Sent: Wednesday, January 21, 2026 10:14 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: SuperSynth equivalent of quantifyHAsubregions.sh Hi Dr. Iglesias, We tried SuperSynth (development version downloaded 11/7/2025) on several subjects, and it worked very well. It took 12 minutes per subject (though we still needed to run Freesurfer 8 for the cortical parcels — this took longer). The PI will use the extra-cerebral regions for her study, though it will be a while before we have a paper to cite you. I wondered, though, whether there was a counterpart to quantifyHAsubregions.sh for SuperSynth (i.e., extract stats into NumSubjects x NumParcels spreadsheet)? Thanks for the great tools, 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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Making Matlab visible to Freesurfer?
by alex han 04 Feb '26

04 Feb '26

External Email - Use Caution Hello, I am running freesurfer 7.4.1 on Ubuntu 22, and am trying to run local GI on subjects but am having trouble making Matlab visible to freesurfer. I have tried using the runtime script in the wiki and currently have Matlab 2014b downloaded after getting an academic license. I tried using the cd <FreeSurferRootDirectory> && ln -s <MatlabRootDirectory> MCRv84 as well. In both cases running the recon-all -s <subj> -localGI command outputs the error in the log attached. I'm new to freesurfer and matlab, so I'm not sure how to start. I scrolled through the email archives, but couldn't find anyone with as simple a problem as mine on the same versions I'm using. Any help would be appreciated. Thank you very much

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FR[AI]ME - a MacOS QuickLook plugin built with FreeSurfer in mind
by Ross Callaghan 04 Feb '26

04 Feb '26

External Email - Use Caution Dear FreeSurfer mailing list, We are pleased to announce the availability of FR[AI]ME by AINOSTICS™, a new macOS QuickLook extension for previewing common neuroimaging file formats that we hope will be beneficial to the FreeSurfer community. What is FR[AI]ME? FR[AI]ME is a lightweight macOS QuickLook extension that provides instant previews of common neuroimaging file formats directly in Finder. By pressing the spacebar, users can quickly visualize DICOM (.dcm, .IMA), NIfTI (.nii, .nii.gz), and FreeSurfer (.mgh, .mgz) files without launching a full imaging application. Why did we develop it? Recent changes in macOS 15.0 deprecated the long-standing DTI-TK QuickLook plugin that many in the neuroimaging community relied on. FR[AI]ME was developed as a modern replacement for the DTI-TK plugin, incorporating new features not previously possible. What's new in FR[AI]ME? FR[AI]ME includes a number of improvements over the original DTI-TK plugin, including support for new file formats such as DICOM and a choice of colourmaps per image. An exciting new feature in v2.0.0 enables folder previews, allowing you to view images overlaid over one another - for instance, to view segmentations directly over their base images. How can FR[AI]ME help FreeSurfer workflows? FR[AI]ME v2.0.0 is built with FreeSurfer workflows in mind, automatically displaying FreeSurfer segmentations using the standard lookup table. The folder preview feature further enables you to view FreeSurfer segmentation files directly overlaid on the base anatomical image. Why we ask for your support FR[AI]ME includes a free mode with limited metadata previews. A small annual subscription, comparable to the cost of coffee in a working week, unlocks full image previews. This helps cover ongoing development costs for AINOSTICS™, a small UK-based startup, as well as Apple's mandatory developer and distribution fees. Your support enables us to maintain and improve the plugin, delivering new features like those in v2.0.0. We hope FR[AI]ME is a useful replacement for those who relied on the DTI-TK QuickLook plugin and can be a helpful tool for all FreeSurfer users. FR[AI]ME is available as a simple install on the Mac App Store at the link below. https://secure-web.cisco.com/1GU-ttFUL-B535GgpEoSSSP7-QZ7w4XHxrpuNq2IUQiwt0…

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Normalization of cervical cord area or volume
by AJ 03 Feb '26

03 Feb '26

External Email - Use Caution What’s the best way of normalizing spinal cord area or volume: by TIV, brain volume, or regression? All these methods are used, but wanted your expert opinion Many thanks. AJ

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recon-any on the dev version: MODEL NOT FOUND
by Hajer Karoui 03 Feb '26

03 Feb '26

External Email - Use Caution Hello, I am trying to build my recon-any docker container, however, there aren't any recon-any models under /usr/local/freesurfer/models . I used the dev version as instructed on the recon-any page<https://secure-web.cisco.com/1IWMAnbFsrK7hUPXbUYFFyownliON0lfj8kai-AYb1tFVM…> : https://secure-web.cisco.com/1wqyV9QaH0DR_i5QozZC-H1CIPo692K7W9DuzDSMFhjOld… The line in the recon-any script (on the github repo<https://secure-web.cisco.com/1Y6OZwVR9AsipMHQdhwC2Wt__u5i2tFQbtRNBzaKMK2KTM…>) to download the model contains a work that doesn't actually work. I get Exit code 8 from wget (server error / HTTP error). So the URL is likely wrong or the file doesn't exist at that location. https://secure-web.cisco.com/1qWCICkPxU-ruG3rUhQv-XwI8SbaLM4OiAg-DKIR3Xbp1P… Looking forward to your advice and thanks. Best regards, Hajer Karoui Research Assistant | PhD Student King's College London Centre for Neuroimaging Sciences LinkedIn<https://secure-web.cisco.com/1m-CuDAw710ERnIYdy9wPywd9tq2n2rHaqU9MWNw-h0t4X…> [cid:d18f3379-74d7-4db2-8404-74031e6a6706] UNITY<https://secure-web.cisco.com/1MANCssXgEvlewAf2IUiy48lbi4V8lg_RU7S56W3fR0TAe…>

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