Hi Renat, That 3rd defect is fairly large – normally it would hang but it’s possible you’re running out of memory. If you can zip the subject and file drop it to us, we can take a look:
https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange best, Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Yakupov, Renat /DZNE <renat.yaku...@dzne.de> Date: Friday, April 30, 2021 at 11:49 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Freesurfer 7 crashes during mris_fix_topology External Email - Use Caution Dear all, I have a subject whose Freesurfer processing crashes during topology fixing step. The last lines in `recon-all.log` are: After retessellation of defect 2 (v0=22890), euler #=-15 (110444,329616,219157) : difference with theory (-18) = -3 CORRECTING DEFECT 3 (vertices=8808, convex hull=2020, v0=31369) Segmentation fault (core dumped) Linux compute-0-2.local 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 81489f2bb-M12_T1_01 exited with ERRORS at Tue Apr 27 21:23:59 CEST 2021 For the full `recon-all.log` and `recon-all.error` files please see the attached files. I tried to follow the manual topology fixing instructions from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview<https://secure-web.cisco.com/1CVb3gwDr9GTwil5kr7FQYCZpGmZhLu9ovxhkC6nEa1QhFJIx6eypmT0rYaI6M3eFoajm5UGJThFtpEwrTovzNAg_qegvhWDxcy-m6gpWYAx55QHi7-eJxrS108DfdnILY9yauaca2pTGvSgA9CrUOR9Twoqnu5o6E2uJ_bMuvqjHfdZuxVU9dNQ0n1Pi4WCFH3_4H6PQilZLYZai-fJAGrNEqr7pFG9jzwrssq82FVnCamJT0vmbbW9I27W_DE1vKkW9T7lo9aEi6hbNTu3rdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTopologicalDefect_freeview>, but *.white and *.pial surface files are missing from `surf` directory. It only contains these files: lh.defect_borders lh.defect_labels lh.orig.nofix lh.smoothwm.nofix rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.qsphere.nofix rh.inflated.nofix rh.qsphere.nofix Which files can I use in place of white and pial surface files in order to look for WM segmentation defects? Some additional information about the data: - I am running Freesurfer 7.1 - overall, there are no gross errors in WM segmentation, although the subjects does have significant temporal lobe atrophy - there are two images acquired at different times, and processing fails for both images - interestingly, processing didnt crash with Freesurfer 6. Thank you and have a great weekend, Renat.
_______________________________________________ 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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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.
