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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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<http://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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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://www.massgeneralbrigham.org/complianceline
<https://www.massgeneralbrigham.org/complianceline> .
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.
