External Email - Use Caution        

Hi, FreeSurfer Developers,

 

 I am attempting to use the recon-all to reconstruction, I successfully run this command in some subjects, but it also failed in around 1/3 of subjects. And after running the recon-all of this 1/3 subjects. It will show “mri_watershed error:GLOBAL region of the brain empty” and I already solve this with the command “recon-all -skullstrip -no-wsgcaatlas -s smwrc1NT816”. And after working with this, I tried to use the command “recon-all -autorecon2 -autorecon3 -s smwrc1NT816” and it shows the output as without given some detailed reasons:

 

recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 CDT 2022

 

For more details, see the log file /Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log

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

 

I’ve searched over the internet and did not find the reasons and solutions of my problems. And I will attached the recon-all.log in case it's of any use.

 

I try to work out on two machine, and they show the same problems :

  1. FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b and freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
  2. Platform: MacOs 11.4 and ubantu 20.04.4
  3. uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel Version 20.5.0: Sat May  8 05:10:31 PDT 2021; root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 arm64

or: Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

  1. recon-all.log: see attached (this one is run by macOS)

 

I will be appreciated if you can give me a hand with these problems. And looking forward to your reply.

 

Sincerely,

Yu