Freesurfer September 2026

freesurfer@nmr.mgh.harvard.edu

19 participants
24 discussions

PhD positions in computational neuroscience at the University of South Carolina
by Z S 28 Sep '26

28 Sep '26

External Email - Use Caution Dear all, Dr. Sha’s lab (https://secure-web.cisco.com/1zZvkpEMU-2uxy_jpyQYDQwnfzCYLwW9h9_ymm0uoRbXBd…) at the University of South Carolina is seeking *PhD students in computational neuroscience *in the Department of Psychology. Our lab is affiliated with the Carolina Autism & Neurodevelopment Center, the Institute for Mind & Brain, and working closely with the McCausland Center for Brain Imaging in Columbia, center of SC Metropolitan Statistical Area. Our lab explores the mechanisms of atypical brain development and neurodevelopmental disorders (e.g., autism spectrum disorders) by leveraging computational modeling (e.g., deep learning models) to bridge neural circuitry, exposure (e.g., early life adversity) and psychopathological phenotypes, and treatment outcomes. These innovative projects will leverage state-of-the-art machine learning models and neuroimaging, supported by the brand-new Brain Imaging Center (with 3T and 7T MRI scanners) and the Biobehavioral Research Center at the University of South Carolina. This position provides an excellent opportunity for a self-motivated student to gain hands-on experience with neuroimaging (e.g., MRI) and biomedical research techniques. The candidate will have full access to rich in-house and public datasets, and advanced neuroimaging platforms. Our lab fosters a collaborative and productive environment, and we fully support PhD students in generating high-quality research publications, applying for fellowships and securing their future career paths. Requirements: · Bachelor’s or Master’s degree in a relevant field (e.g., neuroscience, math, data science, biostatistics, biomedical engineering) · Experience with neuroimaging MRI data analysis is preferred. · Candidates with coding experience are preferred. How to apply: Please submit your CV to Dr. Sha (zsha(a)mailbox.sc.edu) Best, Zhiqiang

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Re: FS 8.2.0 on Rocky 9 / RHEL 9
by fsbuild 25 Sep '26

25 Sep '26

External Email - Use Caution I would not say “ignore” the rocky9 installer. The rocky9 binaries should run more efficiently on rocky9 than the rocky8 binaries.   If you don’t need to run what you listed, then I would default to using the rocky9 installer, e.g., what you listed is not necessary to run recon-all or freeview on rocky9.  You will eventually need to abandon the rocky8 binaries as they are not expected to work going forward on newer OS’s like rocky10 (which is the current release). You can install only 1 instance of the freesurfer package using the .rpm installers.   So I would install the rocky9 .rpm on rocky9 and make that the default for users.  You could then manually unpack the rocky8 rpm, and copy the contents somewhere such that you can access it as a fallback on the rocky9 machine in case someone needs to try and run those older binaries. - R. On Sep 3, 2026, at 02:54, Anderson Winkler <anderson.winkler(a)utrgv.edu> wrote:

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Question about holes in the FreeSurfer 8 ICC mask
by Cajgfinger, Thomas 25 Sep '26

25 Sep '26

External Email - Use Caution Hello, I am using FreeSurfer 8.2.0 and noticed some enclosed holes in the intracranial cavity (ICC) mask produced by recon-all. The holes appear in several slices, and they account for approximately 3% of voxels in one subject. Could you let me know: 1. Is this expected behavior for the ICC mask? 2. Is there a FreeSurfer option or recommended command to avoid or fill these holes? I have attached an anonymized screenshot showing an example. [cid:0c624e69-4e2b-463c-a0cc-5181c59362b3] Thanks, Thomas Cajgfinger --Confidentiality Notice: This e-mail transmission may contain restricted, confidential, and/or legally privileged information that is intended only for the individual(s) or entity(ies) named in the e-mail address(es), or the individual(s) or entity(ies) reasonably understood to be the intended recipient(s) via the content or context of the transmission. If you are not the intended recipient, any disclosure, copying, distribution, or reliance upon the contents of this e-mail is by you is prohibited. If you have received this transmission in error, please reply directly to the sender to notify them of their error then immediately delete the message.

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Repost: mri_gtmpvc error - segmentation ROIs disappear in PET space
by Qassim Alkassir 23 Sep '26

23 Sep '26

External Email - Use Caution Just reposting this to gently bump it since I did not see it on the forum: Hello, I am using PETSurfer/mri_gtmpvc for PET quantification in the WRAP Alzheimer's cohort. I am encountering a reproducible error when regions present in gtmseg.mgz have no voxels after the segmentation is mapped into PET space. I searched the mailing-list archives and found a previous discussion of the same error message involving segid 29. In our data, however, the affected labels differ between subjects, so I wanted to ask what the recommended general approach is. What I am trying to accomplish ------------------------------ We are processing motion-corrected, frame-averaged 11C-PiB PET images with PETSurfer. Our PET images are approximately: Matrix: 128 x 128 x 63 Voxel size: 2.574 x 2.574 x 2.425 mm Voxel volume: 16.07 mm^3 The corresponding gtmseg.mgz images have: Voxel size: 0.5 x 0.5 x 0.5 mm Voxel volume: 0.125 mm^3 Command ------- The relevant mri_gtmpvc options generated by our PETSurfer workflow are: mri_gtmpvc \ --psf 0 \ --no-tfe \ --seg gtmseg.mgz \ --default-seg-merge \ --auto-mask 10 0.01 \ --mgx 0.01 \ --no-reduce-fov \ --no-rescale \ --save-input \ ... I have attached the full PETSurfer log from a representative failed subject. It contains the complete generated command and output. Exact error ----------- For example: ERROR: creating region for nthseg=22, segid=78, Left-WM-hypointensities It may be that there are no voxels for this seg when mapped into the input space. I initially encountered this problem in another subject for segid 79 (Right-WM-hypointensities). Before changing the segmentation or adding replacement rules, I tested four additional independent PiB subjects using the same unmodified workflow. gtmseg completed successfully for all four subjects. PETSurfer completed successfully for one subject and failed during mri_gtmpvc for three subjects. Results ------- The regions producing mri_gtmpvc errors were: Subject SegID Region GTM vol PET vox ---------------------------------------------------------------- WRAP1 78 Left-WM-hypointensities 6 mm^3 0 WRAP1 79 Right-WM-hypointensities 5 mm^3 0 WRAP2 31 Left-choroid-plexus 6 mm^3 0 WRAP2 78 Left-WM-hypointensities 21 mm^3 0 WRAP2 79 Right-WM-hypointensities 1 mm^3 0 WRAP3 78 Left-WM-hypointensities 2 mm^3 0 We also have an informative within-subject comparison in WRAP3: segid 78: GTM volume = 2 mm^3 PET-space representation = 0 voxels mri_gtmpvc reports an error for segid 78 segid 79: GTM volume = 46 mm^3 PET-space representation = 1 voxel mri_gtmpvc does not report an error for segid 79 For the failing labels, we directly counted the voxels in both gtmseg.mgz and the PET-space segmentation at: no_pvc_6.0fwhm/aux/seg.nii.gz In every case listed above, the label is present in gtmseg.mgz but has zero voxels in the PET-space segmentation. This makes us suspect that the immediate failure occurs when a region retained in the GTM definition receives no voxel representation after mapping the segmentation onto the much coarser PET grid. One detail that of note was that total region volume alone does not determine whether a label survives. For example, segid 78 in WRAP2 occupies 21 mm^3 in gtmseg.mgz, which is greater than the volume of one PET voxel (16.07 mm^3), but it still maps to zero PET voxels. Questions --------- 1. What is the recommended PETSurfer/mri_gtmpvc approach when a valid region in gtmseg.mgz has zero voxels after mapping into PET space? 2. For segids 78 and 79 (Left/Right-WM-hypointensities), is --merge-hypos intended for this situation? 3. We also see the same problem for segid 31 (Left-choroid-plexus). Should choroid plexus be merged/replaced for GTM analysis, or should this be handled differently? 4. More generally, should very small regions be merged before GTM construction, or is there another recommended way to handle regions that disappear at PET resolution? Additional FreeSurfer context ----------------------------- The anatomical FreeSurfer reconstructions were originally generated with FreeSurfer 8. The PETSurfer/gtmseg environment currently uses FreeSurfer 7.4.0. Because the FreeSurfer 8 reconstructions did not contain the classical talairach.m3z expected by the FreeSurfer 7.4 gtmseg, we generated talairach.m3z using FreeSurfer 7.4 mri_ca_register. gtmseg subsequently completes successfully for all subjects tested. The error described above occurs later during mri_gtmpvc. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.0-20230510-e558e6e 2) Platform: Ubuntu Linux, x86_64 3) uname -a: Linux hpclogin.sri.utoronto.ca 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) PETSurfer log: See attached. I have attached the PETSurfer log from WRAP2, which demonstrates the failure for three different labels (31, 78, and 79). Thank you, Qassim Alkassir

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Update/fix for freesurfer license registration page
by fsbuild 22 Sep '26

22 Sep '26

External Email - Use Caution The freesurfer license registration form,https://secure-web.cisco.com/1eH4NN8hGQ-iq5ACClrSdWb_RLJ7QvNokZX4eXy95… - has been updated to try and prevent gateway timeout and other related errors.  Please try the form again if you have been unable to obtain a license.  As always, if you are accessing the web from behind an institutional, corporate or government firewall (and/or using a VPN), then your connection times may take longer or be interrupted and so may still fail.   But the response times seem improved from what we can see. - R.

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Failed talarach
by El_Duderino_422 22 Sep '26

22 Sep '26

External Email - Use Caution Hello All, I have got an issue with the procedure for dealing with a fail talairach registration. Failed talairach happen quite often for us. I go through the whole procedure of manually registering. I follow the procedure outlined in the URL. https://secure-web.cisco.com/13NWWpMXxUVWAfIn9KlHlBzoCyjMJjY8qB8jWk4-Z8YLCN… This never seems to work. Yesterday, I did some digging and I am a bit confused on the procedure and how it even works.. In the step where we run tkregisterfv --s tal_before --fstal When saving the transform it saves in the lta format. The file that need to be replaced is talairach.xfm. There is no way to save in a xfm format; if there is I could not figure it out. The talairach.lta is generated in the beginning of the autorecon2 step and is also a transform to register to a different target. After running the recon-all transform.xfm does not update. I followed the direction. Furthermore, the part were your check the registration with the command freeview -v tal_before/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm T1.mgz and brainmask.mgz are always registration. should the command be freeview -v fsaverage/mri/T1.mgz -v tal_before/mri/brainmask.mgz:reg=tal_before/mri/transforms/talairach.xfm Please correct me. I know I am completely misunderstanding things.

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License Not Received After Registration — FreeSurfer 8.2.0 / Ubuntu 24.04
by yilunshi2004 18 Sep '26

18 Sep '26

External Email - Use Caution Hello FreeSurfer team, I registered for a FreeSurfer license using this email address. I received the mailing-list confirmation and welcome messages, but no license.txt or license text. I also checked spam. Could you please check whether my license registration was completed and resend the license? If it was not completed, please help me resolve the registration issue. I plan to use FreeSurfer 8.2.0 on Ubuntu 24.04 for academic MRI research. Thank you.

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(无主题)
by cz1394004851＠163.com 18 Sep '26

18 Sep '26

External Email - Use Caution 你好能不能检查一下，为什么很多申请邮件都发到我这里

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FreeSurfer license not received after registration
by Chensj 18 Sep '26

18 Sep '26

External Email - Use Caution Hello FreeSurfer team, I registered for a FreeSurfer license using this email address. I received the mailing-list confirmation and welcome messages, but no license.txt or license text. I also checked spam. Could you please check whether my license registration was completed and resend the license? If it was not completed, please help me resolve the registration issue. I plan to use FreeSurfer 7.4.1 on Ubuntu 22.04 for academic MRI research. Thank you.

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FreeSurfer license not received after registration
by Chensj 18 Sep '26

18 Sep '26

External Email - Use Caution Dear FreeSurfer team, I submitted the FreeSurfer license registration using the email address from which I am sending this message. I have received the GNU Mailman confirmation and the Freesurfer mailing-list welcome message, but no license.txt file or license text. I have checked my inbox and spam folder. Could you please resend my license, or advise how to complete license issuance? I plan to run FreeSurfer 7.4.1 on Ubuntu 22.04 / Linux Intel for academic MRI research. Thank you for your help.

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Freesurfer September 2026