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.
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I've used Freesurfer version 7.4.1 without this error in my computer.
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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
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
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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
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