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Your Linux image could be missing system files and/or graphics card driver updates needed for the version of Qt included with Freeview to display graphics via X-Windows.  So I would first remove whatever currently exists under /usr/local/freesurfer and then follow the instructions on the Wiki page to do an install from scratch using the actual installer (instead of the tar file).  The instructions are here,

https://surfer.nmr.mgh.harvard.edu/fswiki/FS7_wsl_ubuntu

After you install Freesurfer and setup the X-server on the Windows host - stop and verify basic graphics are working by running glxgears.  If communication from Linux running under WSL is working with the X-server on the Windows host, then you will see an X-Window open and display the spinning gears via the following Linux commands,

$ sudo apt-get install mesa-utils
.... answer Y to all prompts ... output deleted ...
$ which glxgears
/bin/glxgears
$ glxgears

The instructions on the wiki page end with running the "freeview" command with no arguments in order to test freeview can at least open and display an empty window.

If that works try displaying one of the volume files included in freesurfer,

$ freeview  $FREESURFER_HOME/subjects/bert/mri/brain.mgz

If that works, then try displaying one of your surfaces/volumes with your own freeview command.

If however glxgears worked, but the freeview command failed to open a window and/or display the volume as listed above, then the next step is to check for an upgrade to the OpenGL drivers on your Windows host.  Freeview needs newer revisions of OpenGL in order to display graphics.  Once you update the drivers, try running the freeview commands listed above again.

BTW - please remember to change SUBJECTS_DIR from $FREESURFER_HOME/subjects in your shell environment to a path your normal userid can write to w/o sudo/admin privs.  That could be in your home directory e.g.,

$ cd
$ mkdir subjects
$ export SUBJECTS_DIR=$HOME/subjects

You could put that export command in your shell init, e.g., $HOME/.bashrc file

- R.


On 1/6/24 13:25, Flemister, Abeoseh B. (flemistera@missouri.edu) wrote:
I’m using Ubuntu. 

Abeoseh Flemister
From: Flemister, Abeoseh B. <flemistera@missouri.edu>
Sent: Saturday, January 6, 2024 12:24:40 PM
To: fsbuild <fsbuild@contbay.com>; freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
No, I installed using tar.gz

freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz

Abeoseh Flemister
From: fsbuild <fsbuild@contbay.com>
Sent: Friday, January 5, 2024 9:35 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Flemister, Abeoseh B. <flemistera@missouri.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
 
Did you install Freesurfer 7.4.1 using the Debian installer package ?
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer_ubuntu22-7.4.1_amd64.deb
- R.

On Jan 5, 2024, at 22:18, Flemister, Abeoseh B. <flemistera@missouri.edu> wrote:

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Thanks, but the issue isn't that graphics aren't displaying, it's that freeview won't load because qt can't be initialized.. 

Abeoseh Flemister
From: fsbuild <fsbuild@contbay.com>
Sent: Friday, January 5, 2024 8:27 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Flemister, Abeoseh B. <flemistera@missouri.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
 
For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output", 

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg76229.html

In case the link to the Freesurfer WIKI talking about WSL is garbled in the URL above, that link is,

https://freesurfer.net/fswiki/FS7_wsl_ubuntu

- R.

On Jan 5, 2024, at 21:08, Flemister, Abeoseh B. <flemistera@missouri.edu> wrote:

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Hi Yujing,

Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized.

I saw an email on this topic but I don't think it was ever answered.. Apologies if I'm reading the thread wrong. Any help would be greatly appreciated!

Abeoseh Flemister
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Sent: Friday, January 5, 2024 3:05 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS
 
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.
This is from your recon-all.log
“
mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz

 

mri_convert: extra argument ("/usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz")
“

 

There is a space in your path to nii.gz.. Can you remove the space by renaming the directory?

 

Also, your SUBJECTS_DIR points to your Freesurfer install directory - /usr/local/freesurfer/subjects. You might run into permission or symbolic link problems later. It is a good idea to set SUBJECTS_DIR to some other directory where you have write permissions.

 

Best,

 

Yujing

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Flemister, Abeoseh B.
Sent: Friday, January 5, 2024 3:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

 

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Hi FreeSurfer Team,

 

I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our dataset and using .nii files and got the same result. I saw a recent thread where someone's issue was improperly labeled WM lesions but my dataset is composed of healthy brains. 

 

I attached my recon-all.logs.. I am using a Linux virtual machine (FreeSurfer version freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460). Please let me know if you have any questions!

 

Thanks,
Abeoseh Flemister
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