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 (https://secure-web.cisco.com/1zZzK3bvGd5zsB2uABu9OZeWvaxLdkpnrA0kBfX1S3S3NDG4JCd6MHums0esqOipz3Gf0t3HYAoGOVrVL-0rPYz2_hU5HV_dEtffv-yeIo-lhjJ343fvw9AQWvEB6tTi_wVutqzRu6BQoEe7Qs71oMWkf1oYc54_JT-YDZt7Fzxfk1DGJC5znW6i2UbrXJ6MSPCn_mCYHl5HpG3dmHMzSRO4qlGFs9hOk1LaD7NiwaQLJ5zTjChTWvrslsCWhhyuOchRonnC04ZyRn8XPksO0-3xVqbFTAgQG9pSwc3uAD3JzJakNSUVgIvFzy95R-WAw/https%3A%2F%2Fmobaxterm.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 (https://secure-web.cisco.com/1fhOwedIcHgfE4tyeSK9G0oaBhabx6_ZVJc7Vr6kaXK3UynOTGEj0KbWvmoGLmm-priyEPi8SjSdwjQR531hso6fbbrHOEyECccpWfpE3_1iRPT9XjjdRvIpu-uUOCwvnjgnltoUzkUaggwgTgd88pb-nnCE1NmIM9j6ah87VddIeG8U8uNnnPTOnK6cKUCPiMbGumVNDXEcZyQX7ehp2k0fI1SquBgrE6Wxmr_ND0RRYuLT6YfS-3mNEmzykLQ2EjktfiOuZYGRC1_1RcsD2qsWtVpq5NURW-cUAqoz5Gq05BjHzmutpxctvHr7irvIg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_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 <k...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh..harvard.edu> On Behalf Of Keith E MooreSent: Tuesday, April 18, 2023 3:21 PMTo: Freesurfer support list <freesur...@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=1I 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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr..mgh.harvard.edu> On Behalf Of Keith E MooreSent: Tuesday, April 18, 2023 2:53 PMTo: freesur...@nmr.mgh.harvard.eduSubject: [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 6.9.0.31xMing 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 $ freeviewAborted $sudo apt install gdb$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 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
