External Email - Use Caution        


From your first email, w/o seeing more of the crash log, I would infer something went wrong communicating with the Xming server, which caused the thread to abort.  WSL continues to be a moving target and people have found the XMing settings for WSL1 no longer work with WSL2.  Some WSL users have switched to using MobaXterm (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mobaxterm.mobatek.net) and find it easier to configure compared XMing, though I have not tried it.  Others have switched to using the VirtualVox VM we provide with freesurfer pre-installed (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/VM_67) since the X-Server runs in the VM (no 3rd party X-server to install and configure settings for).   While that VM runs Ubuntu 18 out of the box, you could uninstall freesurfer, upgrade to Ubuntu 22, and then install the freesurfer 7.3.2 Ubuntu 22 .deb file into it.

- R.

On Apr 18, 2023, at 19:00, Keith E Moore <kem1@stanford.edu> wrote:

        External Email - Use Caution        


Okay, so it does look like it is the LIBGL bandwidth.  I went back and downgraded WSL to version1.0 (non-VM).  Yes, a bit draconian, but wanted to see if this was a lack of shared memory accessibility.
Used:
Cmd> wsl –set-version ubunto 1
 
Then reran and got the expected image:
 
$<image001.png>
 
So looks like there is an issue when interacting with X11 servers when the client  is in a VM?  Anyway,  I’ll work with  this… but would be grateful if there’s a better configuration.
 
Keith
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Keith E Moore
Sent: Tuesday, April 18, 2023 3:21 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] ABORT error when running freeview
 

        External Email - Use Caution        

Okay, found one issue.  My .bashrc had:
export LIBGL_ALWAYS_INDIRECT=1
I then went to unpacked tutorial  and ran:
 
$ 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
 
and got:
 
  <image002.png>
 
So most is working except the image isn’t showing… any ideas?
 
Keith Moore
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard..edu> On Behalf Of Keith E Moore
Sent: Tuesday, April 18, 2023 2:53 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ABORT error when running freeview
 

        External Email - Use Caution        

Hi, when I try to use freeview on ubuntu under WSL, I’m getting a brief show of a X window and then an ABORT.
 
I’m running in ubunto 22.04 (jammy)  under WSL on windows using an Xming 6.9.0.31
xMing is configured with a X11 server on localhost:0.0
 
I did a clean install of ubunto using:
Cmd> wsl –install ubuntu
 
Then in ubunto:
$ sudo apt update -y
$sudo apt-get upgrade -y
$sudo apt install x11-apps
$sudo apt install xterm
 
I installed freesurfer using:
$sudo apt install ./freesurfer_ununtu22-7.3.2_amd64.deb
 
Then added:
$export DISPLAY=”:0.0”
$export FS_LICENSE=<location of my license file>
$export FREESURFER_HOME=/usr/local/freesurfer/7..3.2
$export XDG_RUNTIME_DIR=/home/<myaccount>/..xdg
$export SUBJECTS_DIR=<location of subjects>
$source $FREESURFER_HOM/SetUpFreeSurfer.sh
 
$ freeview
Aborted
 
$sudo apt install gdb
$gdb freeview
(gdb) run
 
An Xwindow pops up which is blank/black that has the title “FreeView”.
 
And gdb reports:
 
<image003.png>
 
 
I’m sort of stuck… any idea what to try next?
 
Keith Moore
 
 
 
 
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer