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30051 discussions

Clarification on FreeSurfer recon-all Output and Preprocessing Steps
by Akanksha Upadhyay 23 Feb '26

23 Feb '26

External Email - Use Caution Hello FreeSurfer Developers, Greetings of the day. I am attempting to replicate a previously published work and have applied the recon-all pipeline on our structural MRI data (T1w.nii) using FreeSurfer. After segmentation and normalization, the output we are obtaining appears unusual to us. I would like to confirm whether these results are expected or if additional preprocessing steps are required prior to running recon-all . I have also attempted reorientation of the input image; however, I was only able to find GUI-based orientation options. I would appreciate your guidance on the following points: 1. Whether the observed segmentation and normalization outputs are expected, or if further preprocessing steps (such as reorientation, intensity correction, or format conversion) should be performed before running recon-all. 2. If manual reorientation is recommended, how should the orientation be determined (e.g., reference axes, alignment criteria, or specific angles)? 3. Any best practices for preparing T1w.nii files to ensure optimal processing with FreeSurfer. I am attaching screenshots of the normalization and segmentation results (aseg output) for your reference. Kindly guide me on how to proceed further. Thank you very much for your time and support. [image: Normalisation_results.jpg] [image: Segmentation_output_aseg.jpeg] -- *Regards* *Akanksha Upadhyay* *Department of Computer Science* *University of Delhi*

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Pineal Gland on v8
by Thakore, Radha 23 Feb '26

23 Feb '26

External Email - Use Caution Hello, I had a quick question about pineal gland segmentation. I heard that it would be possible to run pineal gland segmentation using FreeSurfer v.8. However, I am unsure about the Terminal input code with recon-all to specifically do that. Would you be able to help me with quantification of the pineal gland? Thank you! Sincerely, Radha Thakore M.D. Student | Class of 2028 Creighton University School of Medicine | Phoenix Campus

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License Registration Issue - 504 Gateway Timeout
by Alice Chen 18 Feb '26

18 Feb '26

External Email - Use Caution Dear FreeSurfer Team, I am writing to request a license file for FreeSurfer. I attempted to register via the online form (https://secure-web.cisco.com/177L6Jl_Bcj3JUMv1gTQIJ3dvJDC9gvlPAjizrI3y5crM0…) but I am repeatedly receiving a "504 Gateway Timeout" error. I am a researcher at the University of New South Wales (UNSW) and will be using FreeSurfer for non-profit research. Here are my registration details: Name: Alice Chen Title: Dr. (or your actual title) Institution: University of New South Wales (UNSW), Sydney, Australia Email: alice.chen3(a)unsw.edu.au<mailto:alice.chen3@unsw.edu.au> Operating System: Linux (HPC Cluster) Type of use: Non-profit education/research Could you please provide me with a license.txt file so I can proceed with my analysis? Thank you for your time and assistance. Best regards, Alice Ruiye Chen, PhD, MD Postdoctoral Research Fellow | School of Psychology, UNSW Sydney Visiting Postdoctoral Fellow | NeuRA W: http://secure-web.cisco.com/1jUJcMHl6XyXsg47bCeTsMPAF5dhUkWbQJBJXMFNDxi5WYh…<http://secure-web.cisco.com/1tEO6JgURwv0QF4P_BSmKpSw5o-_Epu524hdJjD2Ti66Zhf…> Google scholar<https://secure-web.cisco.com/1A5jBnt_pbS4abQ5DBdY56gImIMJcHn7zyR0Gct_3Qm4sz…> I pay my respects to Aboriginal and Torres Strait Islander peoples past and present, their cultures and traditions and acknowledge their continuing connection to land, sea and community. This email and any files transmitted with it may contain confidential information. If you believe you have received this email or any of its contents in error, please notify me immediately by return email and destroy this email. Do not use, disseminate, forward, print or copy any contents of an email received in error.

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Re: LGI make_outer_surface error
by fsbuild 15 Feb '26

15 Feb '26

External Email - Use Caution Before the assertion, the mri_mc command segfaults.  I don’t know that code to judge the correctness of the command, but my guess is ending up with a surface with 0 faces and 0 vertices caused recon-all to exit. The beginning of the log shows the 7.4.1 release for Ubuntu 22 running on the Windows subsystem for Linux (WSL2).  I’m not sure the 15G of free memory listed there is actually available to recon-all running in WSL2.  On some windows systems, memory inside WSL2 was limited to 1/2 of the system memory so running WSL2 + linux applications did not deprive the host Windows OS of memory.   A segfault could occur because something ran out of memory, although I don’t see any memory notifications.   Freesurfer requires a minimum of 16G of free RAM, i.e., 16G free inside WSL2 apart from the memory WSL2 is using and apart from the memory used by the Windows OS together with any running Windows applications. The setting of FREESURFER_HOME indicates the standard install of freesurfer under /usr/local/freesurfer was not done with the freesurfer_ubuntu22-7..4.1_amd64.deb package.   So some freesurfer binaries may not run, but I don’t see errors about that in the log. It looks an external Matlab distribution is in use and generating warnings.  Freesurfer was tested using the matlab run time environment as installed by the fs_install_mcr script to be located inside the freesurfer distribution.  Information about that is under the section SETUP A MATLAB DISTRIBUTION,https://secure-web.cisco.com/13044hq9EdebE9_JMyWEvQec0wCBES_jb… - Our online freesurfer course requires participants with Windows machines to install Oracle Virtual Box in order to run a Freesurfer Ubuntu 22 Virtual Box VM, i.e., we don’t officially support running Freesurfer in WSL2.   It can be impractical for us to troubleshoot a system where freesurfer was not installed with the Linux .deb or .rpm file.  - R. On Feb 14, 2026, at 17:38, alex han <alexhan160(a)gmail.com> wrote:

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LGI make_outer_surface error
by alex han 14 Feb '26

14 Feb '26

External Email - Use Caution Hello Freesurfer developers, I'm currently attempting to run recon-all -s sub-GE101 -localGI, but I continue to get this error: { Error using make_outer_surface (line 57) mri_mc failed: changing type of input volume to 8 bits/voxel... ASSERTION FAILED: /home/rd521/space_freesurfer/build/docker_ubuntu22/trunk/rd521-7.4.1/utils/mrisurf_metricProperties.cpp:4249 mris->dist_nsize == 0 >>ERROR: make_outer_surface did not create output file I have not seen any email threads with a similar error on this version, and I'm unsure how to approach this issue. Freesurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 uname -a: Linux not-urs 6.6.87.2-microsoft-standard-WSL2 #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux Platform: Ubuntu 24.04.3 LTS Recon-all log attached to this email. Respectfully, Alex Han.

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Fwd: Postdoc & PhD calls at Uni Vienna
by Douglas N. Greve 13 Feb '26

13 Feb '26

-------- Forwarded Message -------- Subject: Postdoc & PhD calls at Uni Vienna Date: Fri, 13 Feb 2026 14:51:20 +0000 From: Narly Golestani <narly.golestani(a)univie.ac.at> To: Narly Golestani <narly.golestani(a)univie.ac.at> CC: External Email - Use Caution Dear colleagues, I would be very grateful if you could please circulate the below information regarding calls for PhD and postdoc positions at University of Vienna to your groups and/or networks. For both calls I’m listed as a potential supervisor, so it could be an opportunity for a PhD and/or for a female postdoctoral to come and work with the Brain and Language Lab, which remains jointly affiliated with Universities of Vienna and of Geneva. * Postdoc (STEM fields, for women): https://careers.univie.ac.at/en/postdoc/e-steem <https://secure-web.cisco.com/1X7ev915mhsa9-jI3OxVRLBZNasFaljei5oQP4yVf_dh4s…> * PhD (social sciences, for all): https://careers.univie.ac.at/en/praedoc/praedoc-ssh <https://secure-web.cisco.com/1nlnN3F0t3UFhCNnzKSoCvKzE4wDmRyHw8fUf88Hehwo-F…>. Deadlines for both: March 2^nd at 14h. Interested individuals are welcome to email me if they would like to apply with me as a potential host. Many thanks, and all the best, Narly. **-----------------------------------------------------------------------------------------** *Brain and Language Lab* **Prof. Narly GOLESTANI* * Cognitive Science Hub Dept. of Cognitive and Behavioural Biology, *University of Vienna,* & Department of Psychology, *University of Geneva* ** <https://secure-web.cisco.com/1A9kPz3YFuTIAzhPN_e1J2BU6V4a5pByU5Q6Vn0CWdkZ2c…>http://www.brainandlanguagelab.org <http://secure-web.cisco.com/1r7k88oQMZ9SDO9eVZdtBgUZLLYh9Ern2ZB2Jyc8V4PPAuA…> https://twitter.com/brain_lang_lab <https://secure-web.cisco.com/1oX00SA75EX3HkVcolpRwe8vrYODwAFKFubkyl8rHqptYr…> *-----------------------------------------------------------------------------------------*

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Issue with MP2RAGE Surface Reconstruction (Process Stalls)
by Philemon Deusch 12 Feb '26

12 Feb '26

External Email - Use Caution Hello everyone, I am a beginner in using FreeSurfer. My goal is to achieve good cortical segmentation using an MP2RAGE scan acquired on a 7T MRI. I am using FreeSurfer 8.1.0 on Ubuntu 22.04. FreeSurfer starts running without any problems; however, during the surface reconstruction step, a major defect repeatedly occurs. The process then continues running for several days without finishing, so I stopped it after about three days. I tried making small adjustments, but the defect remained unchanged. The recon-all.log file is attached. I would greatly appreciate any advice or suggestions. Best regards, Phil

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trgvtxno = -1 < 0
by Izumi, Masaki 11 Feb '26

11 Feb '26

External Email - Use Caution Hello FreeSurfer Developers, I attempted to run recon-all in cerebellum hypo case, but it resulted in an error. The message indicated “trgvtxno = -1 < 0.” When I inspected the data in Freeview, I noticed that the left and right white matter and pial surfaces were intersecting near the corpus callosum. Therefore, I mannually removed the white matter around the corpus callosum in wm.mgz and reran recon-all -autorecon2-wm -autorecon3 -subjid <subject>. However, the same error continues to occur, and left and right surface isn't separated. (https://secure-web.cisco.com/1C9t-jL1GVEMftdXHKe19QFSQcOKzZdZalLfUD3e4RKaX6…) 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-macOS-darwin_x86_64-8.1.0-20250718-f30dfed 2) Platform: macOS Tahoe Version 26.1 3) uname -a: Darwin RELMPEDFAC27837 25.1.0 Darwin Kernel Version 25.1.0: Mon Oct 20 19:26:51 PDT 2025; root:xnu-12377.41.6~2/RELEASE_X86_64 x86_64 4) recon-all.log: see attached Masaki Izumi

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samseg stats files format question FS 7.2.0 FS 8.1.0
by Roderick McColl 11 Feb '26

11 Feb '26

External Email - Use Caution I have used FS 7.2.0 and run_samseg on many subjects and (finally) realized that samseg.stats is not in a format amenable to use with asegstats2table however after installing FS 8.1.0 and run_samseg again on a few subjects I see there is now a file called samseg.fs.stats generated in addition to the samseg.stats file and the data is the same except for the addition of the label number, and this file is amenable to asegstats2table as far as I can tell. Is there a FS 8.1.0 command which can generate a samseg.fs.stats from a combo of samseg.stats and seg.mgz or other combo existing with 7.2.0 analyses? Thanks -roddy ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Pediatric cortical/thalamic parcellation
by Damiana Bergamo 10 Feb '26

10 Feb '26

External Email - Use Caution Dear all, I am a postdoctoral researcher working on developmental neuroimaging data. I am writing to ask whether there are any atlases available within FreeSurfer that are specifically suitable for children and adolescents aged approximately 3 to 16/18 years, both for cortical parcellation and for thalamic segmentation, similar to what is available for infants (0–2 years). So far, I have been using the standard adult atlas, but I am wondering whether this is the most appropriate choice for this age range, or whether age-specific alternatives are recommended. Thank you Damiana

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