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Hi Freesurfer Developers,
I’m attempting to run recon-all but keep on coming across this same error:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta 1047
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 1047
recon-all -s 1047 exited with ERRORS at Wed Oct 29 18:32:30 GMT 2025
I found a couple reports of people encountering the same error, with some suggesting that upgrading macOS resolved the issue. Unfortunately, that solution didn’t work in my case. The problem closely matches the one described in this posthttps://secure-web.cisco.com/1eUJH1QOVis9V-ja_XistwYUH99s1WkkKGscZLAnWqIcpXLVxUw9eN85IV4YFrHtxySKFuLjkWczEUNE6AOPwhHw1w4YvzoRrh_oIaBppxWTuuy7t9Zk_WIA5oIIPMqZ7bCW3o4hotFhJyxwAgKpqYRNe_K97CVls3z91JTp3ZAsQV7eAvIXuaeIxE5S9KSPaE_XC0NJS248t_K5aQ6RMVItHqEw-yo3Uq4n_zWYa6CPJz-dGNc3itPDKQx8tSoIFqtG0JIitaWNDmo_7brQH0kFzNwImRviGVN6NRmv5hda46treMNdZ5eg9RkR-ndY-Ru4U3R5ISpKQQnRSUMlEJQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg77867.html and this posthttps://secure-web.cisco.com/1em4eF9GNBoGc5vVMCfPLPX9WS5q43YwfPAfj41wlBnIw_npxRCBd8H8o_YhE9GlBtg58BuoMG9VOmX1YUGN4-Uj0C7gcI6A4RuVwDKY8SA_0dADYs18b_MqwaaYkaMVWIlwRPsknDaaeW1X_dVRGdOxt07E8SaZpqpzocdA8v7-jjsbYhs2k4lmRUcdIgCqWkHA0n86gO5fRerrxP-4JQPHU4SJbf7pRqt2P4MmynyOoDbS-9Z5z3dkG3miHFtD8XA1tWu9JxqaoliquWHCn_Dc1haJS6GolcGrX8qjuWrCEfdiaDJ-uGYMVrQdY8B03mSxHOT2a5NAEZExt42muTg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F1292, where the file “aseg.auto_noCCseg.mgz” is only 16 bytes in size. Similarly, when I checked “synthseg.vol.csv” in the “stats” folder, the reported volumes for all segments were 0.
1. FreeSurfer version: freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed 2. Platform: macOS Tahoe 26.0.1 3. uname -a: Darwin 22SCompL011.local 25.0.0 Darwin Kernel Version 25.0.0: Wed Sep 17 21:41:45 PDT 2025; root:xnu-12377.1.9~141/RELEASE_ARM64_T6000 arm64 4. recon-all.log: see attached