External Email - Use Caution Thanks very much for the suggestions. It turns out I needed to add “vglrun” before my “freeview” command, but maybe more importantly also edit the fsxvfb script where Xvfb is called, and add the parameters “-screen 0 640x480x24”, since specifically the color depth had to be 24. I guess different systems might have different requirements. (And as a reminder for anyone else reading this who is using an HPC cluster, you need to run this on a gpu node.)
And thanks for the warning about the Ubuntu version too. Best, Dani From: fsbuild <fsbu...@contbay.com> Date: Friday, October 20, 2023 at 4:54 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Cc: Dani Del Rubin <rubin...@ohsu.edu> Subject: [EXTERNAL] Re: [Freesurfer] fsxvfb error: Falling back to using screens root_visual I could be wrong, but it reads like those errors are from the libqt5xcb.so running into errors communicating with X windows. Since freeview runs fine displaying those images on the machine when not exec'd thru fsxvfb, then maybe fsxvfb cannot capture because it is not expecting freeview to (still) run using Qt graphics and X-windows . I believe the release notes say fsxvfb does not need an X-server and so perhaps it is trying to capture images directly from the graphics hardware. Could be something is not up to date on your system with the graphics hardware drivers/system libraries. Another thing to consider is the freesurfer 7.4.1 release was not built for nor tested on Ubuntu 16 - the minimum version tested was Ubuntu 18. Given you are running it from the path /usr/global/freesurfer/7.4.1 then I suspect you did not download and run the 7.4.1 debian package installer for Ubuntu 18 as recommended on the freesurfer download page, https://secure-web.cisco.com/1sQhP6jhhRk7Hm5moyc_wtd5uc3B4ruQIC5CVQeu2hkid5bmNIbTNvP-tirHY_7jdCBfXreSLhHyMd3qm3mHGj2cMoBGFEWEwT0IOz2yJk7GYay9VqCWBKz3gze_TpY8hmi2U-qIH83DoaxdDUs4EobUJSd61kpowpi_wCHH6A1NKbElzXKDCCNrMejgoctPqmqdn9cxun-UUh5rpaMlAlKsTtfoz2b_8_Bxfugczn-zWR1mAQQ_8iLPu7DUD2LQojBOPOB-8rS19CcPy6WkjQpXYMPf5zcAjomI0sQq7c35Pr4upIV02N5bTbOMAV1pr/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7download<https://secure-web.cisco.com/1QwF2lY14p7-3u4QSleVoIR6_bAEEJ0Jjin5M-f-a7Bukwcw50ndTBbX_iKw9YwvQTUJ6p7AfORj_xWam3sy5nDSRmJFvagB2v621dC3iP0NDFGDoEd4qYAe6clHAIldcUiq5Nwi3uJ0TrXdRYzZlm0yQJ87MSjMGJIUEhomFzZYMes5OiVb-9P_hH0RwtikXjXVdT9bc4pM9tBQYgvJY3mHSrSKRZb-nVizXipkH5IY1a4b9D7_0zSKhAyWBSImOlHvmi_YwqQKMXRgYmoxShaqnisL5C8280sE5JtDnPlTCLJDeD3SUn_NstODngbMP/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7download__;!!Mi0JBg!Nw8_Nt11xBN3c1g28-jTHsaG3AP66MBVy1uB2ndoLmFKsb68L6qMUJuM4koZXQLiC7NJNwwpDMLe15TH6w$> (which would install under /usr/local/freesurfer). It would not be surprising for the Ubuntu 18 binary installer to fail trying to update an Ubuntu 16 system, but you could try running it. You can decline/abort the installation if you don't approve of the system updates it reports are needed before installing freesurfer. Even if the installer succeeds, we can't guarantee 7.4.1 will work correctly on Ubuntu 16. - R. On 10/19/23 17:50, Dani Del Rubin (rubin...@ohsu.edu) wrote: QXcbConnection: XCB error: 1 (BadRequest), sequence: 167, resource id: 133, major code:
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