It looks like there are a lot of defects as I see a lot of these messages
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from
wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
Try following those instructions
On 6/14/2022 5:37 PM, Wang, Yu wrote:
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
<http://secure-web.cisco.com/1iPjG6_yDpeRBXccjdFdxifv54y1GvmJtNQuC-KaFzx3NzAM79VncTDzeOsHzRjZXnNBtfoaUmJp-iqE4rmlb_37cgVnP3yoki6Hp6iDUWG3J7O_20a1Pt0eBKm4QhifNMlGWguI5yCIPrx5roSppTd3PlAL7k5JfTjaFrGD1Ogx4sy6MWpeqn3cWM2ox5FY9fPhWkCMZnY4RcShAJveekgUswk3t5qqqGNBK9kILalsHRBCIKK35oVStKCn7nAaCv0gXMdgLUdoM1OJyAI6Aa6OkZIfE6MM8BVu5_1htGYbtk48IVxo1d8kVfjrOGsnqdjvbyuTBrBrM_T-Y7zKIZA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>*
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 May8 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
4. 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
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