It appears your system has some problem displaying OpenGL content properly. I’m not familiar with Xming. Can you try some other x display for Windows such as mobaxterm?

https://mobaxterm.mobatek.net/



On Jan 4, 2024, at 6:11 AM, Shawa, Zeena <zeena.shawa.20@ucl.ac.uk> wrote:

        External Email - Use Caution        


Hi Ruopeng,
 
Thank you for your quick reply!
When running glxgears I just see a blank window.
 
Sincerely,
Zeena Shawa
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wang, Ruopeng
Sent: Wednesday, January 3, 2024 4:29 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freeview not showing output
 

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What if you run glxgears command? Do you see 3D spinning gears or just a blank window?
 
Ruopeng
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shawa, Zeena <zeena.shawa.20@ucl.ac.uk>
Sent: Wednesday, January 3, 2024 9:17:00 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freeview not showing output
 

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Hello FreeSurfer Developers and Community,
 
Hope your day has been going well and happy new year!
 
I'm attempting to visualise FreeSurfer outputs using freeview, as described on the “Introduction to Freesurfer Output” tutorial, under the “Viewing Volumes with Freeview” section (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview ). The viewer launches fine and seems to load everything, but instead of showing any output it simply shows a black screen in the middle (screenshot attached). There is no error outputted in the command line either. The viewer seems to work fine otherwise, and I have completed the Xming X-server setup as described here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FSL_wsl_xming .
 
I've searched the archives and GitHub issues and cannot find a similar error. I would appreciate any feedback on how to troubleshoot this issue.
Thank you very much for your understanding and help! 
 
  1. FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460
  2. Freeview version: Version 3.0, June 14 2023 build
  3. Xming versions: Xming fonts 7.7.0.10, Xming 6.9.0.31
  4. Platform: WSL2 Ubuntu 22.04.3 LTS
  5. uname -a: Linux LAPTOP-4153LQMG 5.15.133.1-microsoft-standard-WSL2 #1 SMP Thu Oct 5 21:02:42 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
  6. specific command: freeview -v \
good_output/mri/T1.mgz \
good_output/mri/wm.mgz \
good_output/mri/brainmask.mgz \
good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \
-f good_output/surf/lh.white:edgecolor=blue \
good_output/surf/lh.pial:edgecolor=red \
good_output/surf/rh.white:edgecolor=blue \
good_output/surf/rh.pial:edgecolor=red
 
 
Sincerely,
Zeena Shawa
 
Zeena Shawa
i4Health PhD Student
Alan Turing Institute – Roche Community Scholar
Research Group UCL Centre for Medical Image Computing
 
 
 
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