[Freesurfer] FLAIR vs. T1 question

[aliyas...@yahoo.com]

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Dear FS mailing list,
My apologies if this is a naive question. I have FLAIR images that were 
acquired with much higher resolution than the T1 images for the same subject. 
Does it make sense to run recon-all using FLAIR as the input image? I tried it, 
and my segmentations look reasonable. I am mainly interested in volumetric WM 
segmentations. 
Am I missing something basic, or is there something else I can try that 
leverages the FLAIR (other than using it to refine the pial surfaces)?  

Thank you. 
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Re: [Freesurfer] Freeview not showing output

[Wang, Ruopeng]

What if you run glxgears command? Do you see 3D spinning gears or just a blank 
window?

Ruopeng

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Shawa, Zeena 

Sent: Wednesday, January 3, 2024 9:17:00 AM
To: 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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