Freesurfer April 2026

freesurfer@nmr.mgh.harvard.edu

33 participants
36 discussions

Large discrepancy in left and right volumes of perirhinal cortices on FreeSurfer 7.1.1- Dissertation Help
by Schade, Rachel 28 Apr '26

28 Apr '26

External Email - Use Caution Dear FreeSurfer Developers, I was examining the perirhinal regions from BA_exvivo_thresh.stats when I noted a significant discrepancy between the left and right hemispheres, particularly obvious on the perirhinal volumes. On a set of 166 older adults, I found the following discrepancy: Left Mean (SD) Left Range Right Mean (SD) Right Range Volume 1694.01 (473.09) 872–3087 943.80 (244.34) 514–1638 Thickness 2.83 (0.27) 2.18 - 3.72 2.98 (0.31) 2.25 - 3.76 Surface Area 492.47 (83.31) 329 - 703 259.76 (38.55) 170 - 357 As you can see the mean and range are almost double that of the right for volume and surface area, though thickness seems relatively unaffected. I have included my colleague who looked at one participant with the most extreme asymmetry and found the following, where it looks like the entorhinal cortex is overlapping the perirhinal. Attached is a screen shot. I am using this for my dissertation due in a month and would love to know if this is a bug that could be resolved. Thank you for your time! Best. Rachel [UF] Rachel Schade Doctoral Candidate Public Health & Health Professions | Clinical & Health Psychology University of Florida rschade1(a)ufl.edu<mailto:rschade1@ufl.edu>

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Re: need license.txt urgently
by fsbuild 27 Apr '26

27 Apr '26

External Email - Use Caution Please try filling out and submitting the form at, https://secure-web.cisco.com/1T2tXCzg9gdR2IrrwN7O4uIv2RG-stuYEFyrM7wVo-on6U… The license file will be mailed to the email address you provide. - R. On 4/26/26 14:22, 马婧 (majing20000714(a)gmail.com) wrote:         External Email - Use Caution         I am so sorry to bother you.But I need FreeSurfer license.txt urgently for academic use.Thank you for your help. Name: MA JING Institution: JUNTENDO University  Email: majing20000714(a)gmail.com _______________________________________________ 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/1V5q9v0KJD9gU1usgVlg9iDjqzyifOArj_r7gCpnIJ3vxq… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1v4afNXIwJMdtkMisJBAXPZW0i6xnjRAMDRTibxQ-93nOu… <https://secure-web.cisco.com/1dWhB7785W_Lw1N9t1WR5J1NlBRCOpPLTHSjxx5pQO9IPApq-2EX3XFSwiND5tR4OycQ92gx9X_AENRTzLdj79jPwGB7beqLkqTVrfLvNlycVpvwo1SYdb99ZJv0HW9Bt5lr50qAH3mvt9YvJtoUWTXdwR5PGW3KWl2kZp3pL7-4xpIQvjWKnQDoYh9MOXMAjwpBymMVIxCuF0mcNSIL7_BmjSGHXgnH76DfTayaFbE2Bt2TQlLyXrphYhOjoYplYk1SG0TMdTW2qalvsvYVFSX58kwI1KhNk7ygGzPgrUxkjZmK7Wu4zBz4e__PPK9RiOUVVgEr2tK2UKQZprwaBBA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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reply
by Lepus Li 27 Apr '26

27 Apr '26

External Email - Use Caution confirm b54752357af3c9c3243ab66e4ca4f9805f5d93ec

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Confirm
by 許嘉琪 27 Apr '26

27 Apr '26

External Email - Use Caution confirm b54752357af3c9c3243ab66e4ca4f9805f5d93ec ᐧ

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need license.txt urgently
by 马婧 26 Apr '26

26 Apr '26

External Email - Use Caution I am so sorry to bother you.But I need FreeSurfer license.txt urgently for academic use.Thank you for your help. Name: MA JING Institution: JUNTENDO University Email: majing20000714(a)gmail.com

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confirm
by 許嘉琪 26 Apr '26

26 Apr '26

External Email - Use Caution confirm f7ac57421691dbb0f3dd3d33588d33bf4bc5878b ᐧ

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Dockerhub image missing python3
by Dan Fitch 24 Apr '26

24 Apr '26

External Email - Use Caution Hi folks, In the freesurfer/freesurfer:8.2.0 image from Dockerhub, straightforward `recon-all -all ...` runs have: env: 'python3': No such file or directory in STDERR. I'm running on a HTCondor cluster so I'm getting STDERR and STDOUT in separate files and can't see where this is exactly. It's the first line output to STDERR, followed by a bunch of INFO: using NIfTI-1 sform (sform_code=1) threshold mask volume at 0.001 ... that looks normal. When I converted the Dockerfile to a singularity conf and created my own rockylinux:9 8.2.0 container, I didn't see this issue. I've confirmed that going into the container in writable mode and running `yum install python3` fixes it. (As a side note, recent updates being released as in-place patches with the same version number [instead of using minor version changes] is a bit confusing in places like dockerhub. I'm sure you all have a reason for doing it this way, but there are disadvantages too.) Dan Fitch Research Engineer University of Wisconsin-Madison Institute on Aging

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7t
by Miriam Taza 23 Apr '26

23 Apr '26

External Email - Use Caution Hello, Im wondering if you know if sclimbic would work well on 7T data? Thanks Miriam

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FS version 8 for 7-T mp2rage UNI
by Huaiyu Liu 23 Apr '26

23 Apr '26

External Email - Use Caution Dear FreeSurfer Developers, I am attempting to preprocess my 7T MP2RAGE UNI image (0.65 mm isotropic resolution, TR = 5000 ms, TE = 2.54 ms) using FreeSurfer 8.2.0 with the following recon-all command: recon-all -all -i sub-01_t1w.nii -s sub-01 According to a discussion thread I found in the FreeSurfer archive<https://secure-web.cisco.com/1LCAbAxlUHY-wISqgMbjgKwSDIJ2615y8K3UxjFEuQ_26m…>, it seems that it is acceptable to run the default recon-all pipeline directly on raw MP2RAGE UNI images without prior skull stripping. 1. May I know that whether this is still the recommended approach for FreeSurfer 8.2.0? 2. Additionally, if I want to use FreeSurfer version 7, would it be preferable to perform skull stripping beforehand, or is it still advisable to use the raw UNI image directly? Thank you very much for your guidance and/or suggestions. Best regards, 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: Updates/bug fixes available for the 8.2.0 release
by fsbuild 22 Apr '26

22 Apr '26

External Email - Use Caution As of 04/22/26 there are some new updates for the 8.2.0 release as listed below.  If you previously downloaded the patch script from,https://secure-web.cisco.com/1qCx9Ci-0IiJiQhCxDnRpJLjd0jhRddADqK1i_Bg1… - there is no need to download it again.  Just re-run the script to pick up the latest updates according to the instructions listed here that match your system,https://secure-web.cisco.com/1v_nsy-KSg4QUEFw9AiqUXudF57zbV9lCe77-My… - R. ../bin/mri_histo_atlas_segment_fireantsUpdated citations in mri_histo_atlas_segment_fireants ../bin/mri_glmfitRe-added Logan KM ../bin/segmentHA_T2.shFix typos in segmentHA_T2.sh ../bin/SegmentAAN.shPrint right path of output in SegmentAAN.sh ../bin/mri_tumorsynthFixing the problems with i++ exit status that was incompatible with set -e ../bin/create_nnUNet_v1.7_env.shUpgrade python version to 3.9 to allow nnUnet installation for mri_tumorsynth ../python/packages/SuperSynth/scripts/inference.pyReinstating logic that was unintentionally dropped during refactor On Mar 28, 2026, at 22:49, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         As of 3/28/26 here has been an update to a previously patched file, so please run the update script again; nothing should change if everything is up to date. - R. On 3/25/26 17:55, fsbuild (fsbuild(a)contbay.com) wrote:         External Email - Use Caution        Some updates/bug fixes are available for an existing installation of a Freesurfer 8.2.0 release.   These include fixes for recon-all expert options and an update on Ubuntu24 only for gems bindings.  Please see the instructions at, https://secure-web.cisco.com/1v_nsy-KSg4QUEFw9AiqUXudF57zbV9lCe77-MykJwrZf2… _______________________________________________ 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/1XWi_TGfR4IiDaI_ZYrbuJA_sSMnZbvJJc6pDpYQAi7Wio…

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Freesurfer April 2026