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/BugReporting

------

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.

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