Freesurfer

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30076 discussions

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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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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