you do not need the white or pial surfaces, just the orig.nofix.
On 6/19/2022 5:17 PM, Wang, Yu wrote:
External Email - Use Caution
Hi freesurfer expects,
I have tried to use this way to solve the problem, but it did not
work because I don’t have the files like lh.pial. But I tried to use
the command “recon-all -s c1NT816 -I smwrc1NT816_screen_mpr.nii
-no-ants-n4 -all ”. It seems this command can solve the problems and
it shows “finished without error” . But the segmentation looks very
strange on the freeview and I did not know what is going wrong. And I
will attach the strange figure with this email.
Thank you for answering my previous questions and looking forward to
your reply.
Thanks in advanced,
Yu
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Date: *Sunday, June 19, 2022 at 9:50 AM
*To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] recon-all -s exited with ERRORS
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 *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
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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
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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
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
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