We have a user reported similar experience at https://github.com/freesurfer/freesurfer/issues/1292 They resolved the issue by upgrading their Mac arm64 OS version from Sonoma 14.7.4 to Sequoia 15.3.2

Hope this is helpful.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of ???(???? ??????) Sent: Monday, April 14, 2025 5:53 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_cc segementation fault during recon-all using FreeSurfer 8.0.0

External Email - Use Caution I'm attempting recon-all command with "-all -qcache" option with T1w nii.gz file. I got the following error in all of my subjects data. ------ freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a FreeSurferEnv.csh dev Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64 ~/Dropbox/KKY/Imaging/FS_subjects/05731016/mri ~/Dropbox/KKY/Imaging/FS_subjects/05731016/mri IsConformed yes Mon Apr 14 18:40:16 KST 2025 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta 05731016 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as transforms/cc_up.lta Segmentation fault ERROR: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta 05731016 Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64

recon-all -s 05731016 exited with ERRORS at Mon Apr 14 18:40:17 KST 2025

To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://secure-web.cisco.com/1OIbiZUZzpMZLVXGKj-AwW4K8SnoS4EHxuX0Nm7vR74Z11FxaGBWV0LOuWnzW1kb21t9ZYu9TmEHRUmLVyUB4I2qUUp1iPquRa1jBkTYEqGpfnb6uhF0OhTQFBSD_H0kOQrw8XHJMnRgmIuqamiZu5iGMSct6Uue0tnp49Jieg-T2tq0rYav0iAHBzWPDMO92UEbKyPWeya_xKaGOl5b01FnoLSzxobvLVxQYZTnpwmLdjYYylvpWTNc1hdqK_gNdJ_RZcFnaC_8GrmkRpBK-8NTr3swig1mZc4V2YvxzF44cei3JxH48oaswScm7TNOfffSNsgQTtnsM37XEw5TVQw/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting ------

I've used Freesurfer version 7.4.1 without this error in my computer. "aseg.auto_noCCseg.mgz" was only 16 bytes. And when I inspected "synthseg.vol.csv" in "stats" folder, the volume of all segments was 0. [cid:image001.png@01DBBE5B.FB6C4600]

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: MacOS X darwin_arm64 (64b) PKG installer (Silicon Macs with M1...M4 processors) -- with the latest version of Xquartz 2) Platform: macOS Somoma 14.1 3) uname -a: Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64 4) recon-all.log: see attached

Thank you for your cooperation.

Best regards KY, Kim

-- Keun You, KIM (김근유), MD, PhD Assistant Professor Department of Psychiatry (Geriatric Psychiatry) Severance Hospital Yonsei University College of Medicine Seoul, Republic of Korea