External Email - Use Caution Dear FreeSurfer Team,
I am attempting to run Recon-all on practice cannabis data on the tutorial, using Ubuntu18 VM for Windows os (also I completely new to coding and Ubuntu). On my first attempt to run Recon-all, I got the error shown below: "ln: failed to create symbolic link 'lh.white.H': Operation not permitted." mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 25.993*4pi (326.639) --> -25 handles ICI = 146.8, FI = 1524.9, variation=23628.367 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2022:05:05:23:34:15 mris_curvature N 4 e 1.66 S 0.10 U 1.30 P 84% M 144988 F 3 R 39631 W 0 c 13 w 718 I 616 O 0 L 1.08 1.11 1.08 @#@FSLOADPOST 2022:05:05:23:34:17 mris_curvature N 4 1.08 1.11 1.08 rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not permitted Linux developer-VirtualBox 5.4.0-109-generic #123~18.04.1-Ubuntu SMP Fri Apr 8 09:48:52 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub101-sesBL exited with ERRORS at Thu May 5 23:34:17 EDT 2022 For more details, see the log file /home/developer/guest_shared/fs-subjects/sub101-sesBL/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1qOeaquoMOTkikWpYGZ4Zmm7T4aU7IdoLWz_R7WjwgxWoQGxY3cPBUDVV4WjL1HTzvXW83WzudLxHfUxd3VMjIW_onAfNPXVndE-taWDHNlTvxXSVt2XAWWGqV2_tqFc6xj1PgghG-vQD5NzYL7fMWU0fWUyVO3gu-hnNg-Nlw0SYtMFHU1Mpf_ezbHxFnHKFMhZR7-V9ztKJPq48qnxSxdaYp3f90UN5PtdDDL_YToCmUoLNZzThrPogT-MkRuyqenk7hzKn-vnr1u89-jcjkzLqvD1Zlp4rCTKFLJ1mv-WZ7GImSBJ-q_-ejSRyOeOLlCao4_RYJXLprXzFkq51bQ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting After searching through the archives, I see that other people have had the same problem in that their os is not able to create a symbolic link. I tried following one of the archives and did: developer@developer-VirtualBox:~/guest_shared/mv-ds000174-1.0.1-Cannabis/sub-101/ses-BL/anat$ cd /home/developer/guest_shared/fs-subjects developer@developer-VirtualBox:~/guest_shared/fs-subjects$ ln -s /home/developer/guest_shared/fs-subjects/fsaverage ln: failed to create symbolic link './fsaverage': Operation not permitted But I again received the "failed to create symbolic link. How can I allow symbolic links? Also, I was generally wondering how do you rerun recon-all starting from a specific step once I get this working? Does one have to rerun all of recon-all each time there is an error or can I start from where I left off? Thank you so much for your help! Best wishes, Joanna
_______________________________________________ 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.
