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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 http://secure-web.cisco.com/1OIbiZUZzpMZLVXGKj-AwW4K8SnoS4EHxuX0Nm7vR74Z11Fx... ------
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. [image: image.png]
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
