fsxvfb is just a script that sets up an env for running Xvfb. I wrote
this script and got it working, but I'm not an expert on Xvfb, so you'll
have to figure it out yourself. You can try to running another program
that brings up an image (eg, fsxvfb glxgears) to make sure it is not a
freeview thing. Otherwise, I'd suggest going through that script and
running the commands one at a time to see if you can find the failure point
On 10/19/2023 5:50 PM, Dani Del Rubin wrote:
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Hello Developers,
I’m trying to use fsxvfb to run freeview and save some snapshots, but
I can’t get it to run. The command I’m executing is:
“fsxvfb freeview -v brainmask.mgz -ss pic1.jpg --quit"
The output I get is:
this pid 23712
setting display to 86
[1] 23721
pid 23721
Starting command freeview -v brainmask.mgz -ss pic1.jpg --quit
Falling back to using screens root_visual.
Falling back to using screens root_visual.
Falling back to using screens root_visual.
Falling back to using screens root_visual.
Segmentation fault (core dumped)
Program exited normally.
No image is saved. If I run the command without fsxvfb, it executes
successfully ending up with a saved image, although it still gives an
error:
X server does not support XInput 2
QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id:
133, major code: 130 (Unknown), minor code: 47
QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id:
133, major code: 130 (Unknown), minor code: 47
Also, I can successfully run the AFNI command @snapshot_volreg to
output an image, and that script also uses xvfb, so I don’t believe
it’s a general problem with xvfb.
Finally, my environment by default uses freesurfer version 6.0.0, but
I’ve run the commands “export
FREESURFER_HOME=/usr/global/freesurfer/7.4.1” followed by “source
/usr/global/freesurfer/7.4.1/SetUpFreeSurfer.sh” to temporarily change
the version.
Other info:
1. Freesurfer version:
freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460
2. Platform: Ubuntu 16.04.7 LTS
3. uname -a: Linux [nodename] 4.4.0-206-generic #238-Ubuntu SMP Tue
Mar 16 07:52:37 UTC 2021 x86_64 x86_64 x864_64 GNU/Linux
4. I am connecting remotely via X2Go to a MATE setup, which then
connects to the compute node.
I only saw 5 questions referring to xvfb on the archive, and most
questions about xvfb I found online seem to not apply to my situation.
Thanks very much for any help!
Dani
--
*Dani Del Rubin, Ph.D.*(he/him)
Research Data Analyst, Psychiatry
Oregon Health & Science University
c: 301-437-7660 | rubin...@ohsu.edu
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