pauldmccarthy / fsleyes

This is a mirror. Feel free to use the issue tracker. PRs welcome.
https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/
Other
22 stars 11 forks source link

GLXBadCurrentWindow \ GLXBadContent #79

Closed Rokujo001 closed 3 years ago

Rokujo001 commented 3 years ago

Hi, I hope someone could hep me. I'm using a linux subsystem (Ubuntu 18.04) on windows I get this error: The program 'fsleyes' received an X Window System error. This probably reflects a bug in the program. The error was 'GLXBadContext'. (Details: serial 7215 error_code 154 request_code 149 minor_code 5) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)

I updated everything (the only thing I can't update is Conda for some reason) FLSeyes version 1.1.0.dev0

What should I do?

Thanks!

pauldmccarthy commented 3 years ago

Hi @Rokujo001 can you give me a few more details?

Rokujo001 commented 3 years ago

Hi!

I'm sorry if I'm not accurate, but I'm trying to do this on my own and I have no back experience with Linux...

pauldmccarthy commented 3 years ago

Ok, how have you installed FSLeyes? Using pip or conda, or via some other means?

If you used conda, you should be able to find the version of wxpython by typing conda list

pauldmccarthy commented 3 years ago

Also, it appears that your WSL environment has access to an old OpenGL version - did you deselect Native OpenGL and select Disable access control in the Extra Settings panel when starting XLaunch?

Rokujo001 commented 3 years ago

I used python /mnt/c/Users//Downloads/fslinstaller.py after downloading the fslinstaller.py! conda list says command not found

Now the error does not show up, and FSLeyes loads, but it does not respond for example to the line fsleyes all_FA -b 0,0.8 mean_FA_skeleton -b 0.2,0.8 -l Green as the fsl window closes as soon as it opens...


fsleyes all_FA mean_FA_skeleton -l Green
unrecognized arguments: -l Green

FSLeyes version 1.0.11

Usage: fsleyes [options] file [displayOpts] file [displayOpts] ...

Options for 'volume' overlays
        [-n NAME] [-d] [-a PERC] [-b PERC] [-c PERC] [-ll] [-lh] [-or LO HI]
        [-un] [-dr LO HI] [-cr LO HI] [-mr LO HI] [-g REAL] [-ls]
        [-ch {R,G,B,A}] [-ic] [-cm CMAP] [-nc CMAP] [-cmr INT]
        [-in {none,linear,spline}] [-inc] [-i] [-ma] [-ns INT] [-bf REAL]
        [-bi] [-s INT] [-r INT] [-nis INT]
        [-m {intersection,union,complement}] [-v INT] [-cp POS AZI INC]
        [-cl FILE] [-mi FILE]

I can manually visualize in fsleyes dragging and dropping the "All_Fa" file , though

pauldmccarthy commented 3 years ago

Ok, that's good news. The new error you are encountering looks like you are passing invalid arguments to the fsleyes command - fsleyes is a different program to fslview, and has a different command-line interface - you can read more about it here: https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/command_line.html

To run the equivalent command with fsleyes, you will need to do something like this:

fsleyes all_FA -dr 0 0.8 mean_FA_skeleton -dr 0.2 0.8 -cm green

Rokujo001 commented 3 years ago

Oh ok! I used fsleyes because a message said that fslview was deprecated. I tried you version of the command but it says unrecognized arguments: all_FA -dr 0 0.8 mean_FA_skeleton -dr 0 0.8 -cm green , I have to check the link you posted, thanks. I hope I can come up with the equivalent of that command!

pauldmccarthy commented 3 years ago

Did you run the command from the correct directory, i.e. the one that contains the all_FA.nii.gz and mean_FA_skeleton.nii.gz files?

Rokujo001 commented 3 years ago

Yes, that was the error. I was in the wrong directory. Thank you very very much!!!!

Rokujo001 commented 3 years ago

One last thing....I'm having trouble converting the lines from fslview of this tutorial into FSLeyes... such as: fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.8 tbss_tstat1 -l Red-Yellow -b 3,6 tbss_tstat2 -l Blue-Lightblue -b 3,6

fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.7 tbss_tfce_corrp_tstat1 -l Red-Yellow -b 0.95,1

fslview mean_FA -b 0,0.6 mean_FA_skeleton -l Green -b 0.2,0.7 tbss_fill -l Red-Yellow

Can anyone help me? Thanks in advance

pauldmccarthy commented 3 years ago

In brief:

So your commands would be:

fsleyes $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -cm Green -dr 0.2 0.8 tbss_tstat1 -cm Red-Yellow -dr 3 6 tbss_tstat2 -cm Blue-Lightblue -b 3 6

fsleyes $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -cm Green -dr 0.2 0.7 tbss_tfce_corrp_tstat1 -cm Red-Yellow -dr 0.95 1

fsleyes mean_FA -dr 0 0.6 mean_FA_skeleton -cm Green -dr 0.2 0.7 tbss_fill -cm Red-Yellow

FSLeyes has an extensive command line interface - every single image display setting can be specified through the command line - type fsleyes -fh (short for --fullHelp) for a comprehensive list (warning - it is quite long).

pauldmccarthy commented 3 years ago

P.S. Feel free to re-open this issue, or open a new one, if you have any more problems.

Rokujo001 commented 3 years ago

Thank you so much!!!!

aaroneg commented 2 years ago

If you found this issue from google and it wasn't the problem above with bad arguments, updating to vcxsrv 1.20.9.0 seemed to fix a similar issue with fsleyes with no arguments in 6.0.5

AndreaAtanasov commented 1 year ago

Can you explain how you solved the initial problem that started the topic. I successfully installed FSL last week using the official tutorial but was met with this problem today and it took me by surprise. Thanks in advance!

pauldmccarthy commented 1 year ago

Hi @AndreaAtanasov, can you check whether glxgears is working? It should pop up a window displaying three spinning gears. If glxgears doesn't work, could you try this:

Could you also let me know what X server you are using? If you are using vcxsrv, could you double check that you have unchecked Native OpenGL, and selected Disable access control when starting it up?

AndreaAtanasov commented 1 year ago

I installed FSL in advance a week or two ago using the official tutorial and FSLeyes worked fine. As

Hi @AndreaAtanasov, can you check whether glxgears is working? It should pop up a window displaying three spinning gears. If glxgears doesn't work, could you try this:

  • Check whether the LIBGL_ALWAYS_INDIRECT variable is set by running echo $LIBGL_ALWAYS_INDIRECT. If it is set it should print out 1. Unset it by running unset LIBGL_ALWAYS_INDIRECT, then try running glxgears again.

Could you also let me know what X server you are using? If you are using vcxsrv, could you double check that you have unchecked Native OpenGL, and selected Disable access control when starting it up?

I am using Vcxsrv and typing GlxGears in does open the little window with spinning gears on it which I suppose is good enough. I followed the advice you had given for when it doesn't work, just in case, and checked Xlaunch settings but the problem is still present.

pauldmccarthy commented 1 year ago

I installed FSL in advance a week or two ago using the official tutorial and FSLeyes worked fine.

Is there anything about your system that has been changed since then, e.g. OS updates?

Also, are you using WSL 1 or 2? You can find out by running this command in a PowerShell: wsl -l -v

AndreaAtanasov commented 1 year ago

I installed FSL in advance a week or two ago using the official tutorial and FSLeyes worked fine.

Is there anything about your system that has been changed since then, e.g. OS updates?

Also, are you using WSL 1 or 2? You can find out by running this command in a PowerShell: wsl -l -v

I am not sure about OS updates, and Powershell tells me Ubuntu is running version 2 which I suppose is WSL2. I have tried switching between the two on another computer of mine where I faced the very same issues, but it didn't really do anything benefitial.

pauldmccarthy commented 1 year ago

@AndreaAtanasov Are you using Ubuntu 18.04? Can you paste the full error that is printed when you try to run FSLeyes, and also the output of running these commands?

AndreaAtanasov commented 1 year ago

@AndreaAtanasov Are you using Ubuntu 18.04? Can you paste the full error that is printed when you try to run FSLeyes, and also the output of running these commands?

  • env
  • $FSLDIR/fslpython/bin/conda list -n fslpython

So here goes: The program 'fsleyes' received an X Window System error. This probably reflects a bug in the program. The error was 'GLXBadContext'. (Details: serial 7170 error_code 154 request_code 149 minor_code 5) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.)

env LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:.tar=01;31:.tgz=01;31:.arc=01;31:.arj=01;31:.taz=01;31:.lha=01;31:.lz4=01;31:.lzh=01;31:.lzma=01;31:.tlz=01;31:.txz=01;31:.tzo=01;31:.t7z=01;31:.zip=01;31:.z=01;31:.Z=01;31:.dz=01;31:.gz=01;31:.lrz=01;31:.lz=01;31:.lzo=01;31:.xz=01;31:.zst=01;31:.tzst=01;31:.bz2=01;31:.bz=01;31:.tbz=01;31:.tbz2=01;31:.tz=01;31:.deb=01;31:.rpm=01;31:.jar=01;31:.war=01;31:.ear=01;31:.sar=01;31:.rar=01;31:.alz=01;31:.ace=01;31:.zoo=01;31:.cpio=01;31:.7z=01;31:.rz=01;31:.cab=01;31:.wim=01;31:.swm=01;31:.dwm=01;31:.esd=01;31:.jpg=01;35:.jpeg=01;35:.mjpg=01;35:.mjpeg=01;35:.gif=01;35:.bmp=01;35:.pbm=01;35:.pgm=01;35:.ppm=01;35:.tga=01;35:.xbm=01;35:.xpm=01;35:.tif=01;35:.tiff=01;35:.png=01;35:.svg=01;35:.svgz=01;35:.mng=01;35:.pcx=01;35:.mov=01;35:.mpg=01;35:.mpeg=01;35:.m2v=01;35:.mkv=01;35:.webm=01;35:.ogm=01;35:.mp4=01;35:.m4v=01;35:.mp4v=01;35:.vob=01;35:.qt=01;35:.nuv=01;35:.wmv=01;35:.asf=01;35:.rm=01;35:.rmvb=01;35:.flc=01;35:.avi=01;35:.fli=01;35:.flv=01;35:.gl=01;35:.dl=01;35:.xcf=01;35:.xwd=01;35:.yuv=01;35:.cgm=01;35:.emf=01;35:.ogv=01;35:.ogx=01;35:.aac=00;36:.au=00;36:.flac=00;36:.m4a=00;36:.mid=00;36:.midi=00;36:.mka=00;36:.mp3=00;36:.mpc=00;36:.ogg=00;36:.ra=00;36:.wav=00;36:.oga=00;36:.opus=00;36:.spx=00;36:.xspf=00;36: HOSTTYPE=x86_64 FSLWISH=/usr/local/fsl/bin/fslwish FSLDIR=/usr/local/fsl LESSCLOSE=/usr/bin/lesspipe %s %s LIBGL_ALWAYS_INDIRECT=1 LANG=C.UTF-8 DISPLAY=172.27.80.1:0 FSLMACHINELIST= WSL_INTEROP=/run/WSL/8_interop WSL_DISTRO_NAME=Ubuntu-18.04 FSLTCLSH=/usr/local/fsl/bin/fsltclsh FSLREMOTECALL= USER=maki PWD=/home/maki HOME=/home/maki NAME=DESKTOP-KVVLRQI XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop FSLLOCKDIR= FSLGECUDAQ=cuda.q SHELL=/bin/bash TERM=xterm-256color SHLVL=1 LOGNAME=maki PATH=/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu18.04onWindows_1804.2020.827.0_x64__79rhkp1fndgsc:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Users/pc/AppData/Local/Microsoft/WindowsApps:/snap/bin FSLOUTPUTTYPE=NIFTIGZ FSLMULTIFILEQUIT=TRUE WSLENV= LESSOPEN=| /usr/bin/lesspipe %s =/usr/bin/env

$FSLDIR/fslpython/bin/conda list -n fslpython

packages in environment at /usr/local/fsl/fslpython/envs/fslpython:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_kmp_llvm conda-forge alabaster 0.7.12 py_0 conda-forge alsa-lib 1.2.3.2 h166bdaf_0 conda-forge aom 3.5.0 h27087fc_0 conda-forge apptools 5.1.0 pyh44b312d_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py38h0a891b7_2 conda-forge asttokens 2.0.8 pyhd8ed1ab_0 conda-forge atk-1.0 2.36.0 h3371d22_4 conda-forge attrdict 2.0.1 pyhd8ed1ab_1 conda-forge attrs 22.1.0 pyh71513ae_1 conda-forge awscli 1.25.92 py38h578d9bd_0 conda-forge babel 2.10.3 pyhd8ed1ab_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bash 5.1.16 hd863ed2_0 conda-forge bash_kernel 0.8.0 pyh1a96a4e_1 conda-forge bcrypt 3.2.2 py38h0a891b7_0 conda-forge beautifulsoup4 4.11.1 pyha770c72_0 conda-forge bleach 5.0.1 pyhd8ed1ab_0 conda-forge blosc 1.21.1 h83bc5f7_3 conda-forge bokeh 2.4.3 pyhd8ed1ab_3 conda-forge botocore 1.27.91 pyhd8ed1ab_0 conda-forge brotli 1.0.9 h166bdaf_7 conda-forge brotli-bin 1.0.9 h166bdaf_7 conda-forge brotlipy 0.7.0 py38h0a891b7_1004 conda-forge brukerapi 0.1.5 pyhd8ed1ab_0 conda-forge brunsli 0.1 h9c3ff4c_0 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge c-blosc2 2.4.2 h7a311fb_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.2.0 pyhd8ed1ab_0 conda-forge cairo 1.16.0 h6cf1ce9_1008 conda-forge certifi 2022.9.24 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py38h4a40e3a_0 conda-forge cfitsio 4.1.0 hd9d235c_0 conda-forge charls 2.3.4 h9c3ff4c_0 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 py38h578d9bd_0 conda-forge cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge commonmark 0.9.1 py_0 conda-forge configobj 5.0.6 py_0 conda-forge cryptography 38.0.2 py38h2b5fc30_0 conda-forge curl 7.85.0 h7bff187_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cytoolz 0.12.0 py38h0a891b7_0 conda-forge dask 2022.10.0 pyhd8ed1ab_1 conda-forge dask-core 2022.10.0 pyhd8ed1ab_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge dav1d 1.0.0 h166bdaf_1 conda-forge dbus 1.13.6 h5008d03_3 conda-forge dcm2niix 1.0.20220720 h924138e_0 conda-forge debugpy 1.6.3 py38hfa26641_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.3.5.1 pyhd8ed1ab_0 conda-forge distributed 2022.10.0 pyhd8ed1ab_1 conda-forge docutils 0.16 py38h578d9bd_3 conda-forge double-conversion 3.1.7 h9c3ff4c_0 conda-forge eddy_qc 1.0.3 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel eigen 3.4.0 h4bd325d_0 conda-forge elfutils 0.186 he364ef2_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge envisage 6.0.1 pyhd8ed1ab_0 conda-forge executing 1.1.1 pyhd8ed1ab_0 conda-forge expat 2.4.9 h27087fc_0 conda-forge ffmpeg 4.3.2 h37c90e5_3 conda-forge file-tree 1.1.0 pyhd8ed1ab_0 conda-forge file-tree-fsl 0.2.1 pyhd8ed1ab_0 conda-forge flit-core 3.7.1 pyhd8ed1ab_0 conda-forge fmrib-unpack 3.5.2 pyhd8ed1ab_0 conda-forge fmrib-unpack-fmrib-config 1.3.0 pyhd8ed1ab_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.0 hc2a2eb6_1 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.37.4 py38h0a891b7_0 conda-forge freetype 2.12.1 hca18f0e_0 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge frozendict 2.3.4 py38h0a891b7_0 conda-forge fsl-add_module 0.3.2 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl-get_standard 0.1.0 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl-pyfeeds 0.9.5 py_0 conda-forge fsl-tirl v2.1.3b1 py38h7703b5b_1 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl_mrs 1.1.8 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl_sub 2.6.1 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl_sub_plugin_sge 1.5.0 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsl_sub_plugin_slurm 1.4.1 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel fsleyes 1.4.6 py38h578d9bd_0 conda-forge fsleyes-props 1.8.2 pyhd8ed1ab_0 conda-forge fsleyes-widgets 0.12.3 pyhd8ed1ab_0 conda-forge fslpy 3.9.5 pyhd8ed1ab_0 conda-forge fsspec 2022.8.2 pyhd8ed1ab_0 conda-forge future 0.18.2 py38h578d9bd_5 conda-forge gdk-pixbuf 2.42.8 hff1cb4f_1 conda-forge gettext 0.21.1 h27087fc_0 conda-forge ghalton 0.6.1 py38h2bc3f7f_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel giflib 5.2.1 h36c2ea0_2 conda-forge gl2ps 1.4.2 h0708190_0 conda-forge glew 2.1.0 h9c3ff4c_2 conda-forge glib 2.74.0 h6239696_0 conda-forge glib-tools 2.74.0 h6239696_0 conda-forge gmp 6.2.1 h58526e2_0 conda-forge gnutls 3.6.13 h85f3911_1 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge graphviz 2.50.0 h85b4f2f_1 conda-forge gst-plugins-base 1.18.5 hf529b03_3 conda-forge gstreamer 1.18.5 h9f60fe5_3 conda-forge gtk2 2.24.33 h539f30e_1 conda-forge gts 0.7.6 h64030ff_2 conda-forge h5py 3.3.0 nompi_py38h9915d05_100 conda-forge harfbuzz 2.9.1 h83ec7ef_1 conda-forge hdf4 4.2.15 h9772cbc_4 conda-forge hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge heapdict 1.0.1 py_0 conda-forge hlsvdpropy 2.0.1 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel html5lib 1.1 pyh9f0ad1d_0 conda-forge icu 68.2 h9c3ff4c_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge imagecodecs 2022.9.26 py38h67e265d_1 conda-forge imageio 2.22.0 pyhfa7a67d_0 conda-forge imagesize 1.4.1 pyhd8ed1ab_0 conda-forge importlib-metadata 4.11.4 py38h578d9bd_0 conda-forge importlib_metadata 4.11.4 hd8ed1ab_0 conda-forge importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge indexed_gzip 1.7.0 py38h3b715e4_0 conda-forge ipykernel 6.16.0 pyh210e3f2_0 conda-forge ipython 8.3.0 py38h578d9bd_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 8.0.2 pyhd8ed1ab_1 conda-forge isodate 0.6.1 pyhd8ed1ab_0 conda-forge jasper 1.900.1 h07fcdf6_1006 conda-forge jedi 0.18.1 pyhd8ed1ab_2 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge joblib 1.2.0 pyhd8ed1ab_0 conda-forge jpeg 9e h166bdaf_2 conda-forge jsoncpp 1.9.4 h4bd325d_3 conda-forge jsonschema 4.16.0 pyhd8ed1ab_0 conda-forge jupyter 1.0.0 py38h578d9bd_7 conda-forge jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge jupyter_console 6.4.4 pyhd8ed1ab_0 conda-forge jupyter_core 4.11.1 py38h578d9bd_0 conda-forge jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 3.0.3 pyhd8ed1ab_0 conda-forge jxrlib 1.1 h7f98852_2 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py38h43d8883_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge lcms2 2.12 hddcbb42_0 conda-forge ld_impl_linux-64 2.39 hc81fddc_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 h9c3ff4c_0 conda-forge libarchive 3.5.2 hccf745f_1 conda-forge libavif 0.11.0 h5cdd6b5_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_7 conda-forge libbrotlidec 1.0.9 h166bdaf_7 conda-forge libbrotlienc 1.0.9 h166bdaf_7 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libclang 11.1.0 default_ha53f305_1 conda-forge libcurl 7.85.0 h7bff187_0 conda-forge libdeflate 1.14 h166bdaf_0 conda-forge libdrm 2.4.113 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libevent 2.1.10 h9b69904_4 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_18 conda-forge libgd 2.3.3 h6ad9fb6_0 conda-forge libgfortran-ng 12.2.0 h69a702a_18 conda-forge libgfortran5 12.2.0 h337968e_18 conda-forge libglib 2.74.0 h7a41b64_0 conda-forge libglu 9.0.0 he1b5a44_1001 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge liblapacke 3.9.0 16_linux64_openblas conda-forge libllvm10 10.0.1 he513fc3_3 conda-forge libllvm11 11.1.0 he0ac6c6_4 conda-forge libmicrohttpd 0.9.75 h7f98852_0 conda-forge libnetcdf 4.8.1 nompi_hcd642e3_100 conda-forge libnghttp2 1.47.0 hdcd2b5c_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libopencv 4.5.3 py38h5627943_1 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libpciaccess 0.16 h516909a_0 conda-forge libpng 1.6.38 h753d276_0 conda-forge libpq 13.5 hd57d9b9_1 conda-forge libprotobuf 3.16.0 h780b84a_0 conda-forge librsvg 2.52.5 hc3c00ef_1 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libspatialindex 1.9.3 h9c3ff4c_4 conda-forge libsqlite 3.39.4 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_18 conda-forge libtheora 1.1.1 h7f98852_1005 conda-forge libtiff 4.4.0 h55922b4_4 conda-forge libtool 2.4.6 h9c3ff4c_1008 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp 1.2.4 h522a892_0 conda-forge libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxkbcommon 1.0.3 he3ba5ed_0 conda-forge libxml2 2.9.12 h72842e0_0 conda-forge libxslt 1.1.33 h15afd5d_2 conda-forge libzip 1.9.2 hc869a4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge libzopfli 1.0.3 h9c3ff4c_0 conda-forge llvm-openmp 14.0.4 he0ac6c6_0 conda-forge llvmlite 0.36.0 py38h4630a5e_0 conda-forge locket 1.0.0 pyhd8ed1ab_0 conda-forge loguru 0.6.0 py38h578d9bd_1 conda-forge lxml 4.8.0 py38h0a891b7_2 conda-forge lz4 4.0.0 py38h1bf946c_2 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge lzo 2.10 h516909a_1000 conda-forge markupsafe 2.1.1 py38h0a891b7_1 conda-forge matplotlib 3.5.3 py38h578d9bd_2 conda-forge matplotlib-base 3.5.3 py38h38b5ce0_2 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge mayavi 4.7.2 py38h90e5726_5 conda-forge mesalib 21.2.5 h0e4506f_3 conda-forge mistune 2.0.4 pyhd8ed1ab_0 conda-forge mkl 2020.4 h726a3e6_304 conda-forge mkl-service 2.3.0 py38h1e0a361_2 conda-forge mock 4.0.3 py38h578d9bd_3 conda-forge msgpack-python 1.0.4 py38h43d8883_0 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-common 8.0.31 haf5c9bc_0 conda-forge mysql-libs 8.0.31 h28c427c_0 conda-forge nbclient 0.7.0 pyhd8ed1ab_0 conda-forge nbconvert 7.2.1 pyhd8ed1ab_0 conda-forge nbconvert-core 7.2.1 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.2.1 pyhd8ed1ab_0 conda-forge nbformat 5.7.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge nettle 3.6 he412f7d_0 conda-forge networkx 2.8.7 pyhd8ed1ab_0 conda-forge nibabel 3.2.2 pyhd8ed1ab_0 conda-forge nidmresults 2.1.0 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel nidmresults-fsl 2.2.0 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel nilearn 0.9.2 pyhd8ed1ab_0 conda-forge nlopt 2.7.1 py38h4ff0c24_1 conda-forge notebook 6.4.12 pyha770c72_0 conda-forge nspr 4.32 h9c3ff4c_1 conda-forge nss 3.78 h2350873_0 conda-forge numba 0.53.1 py38h8b71fd7_1 conda-forge numexpr 2.7.3 py38h43a58ef_1 conda-forge numpy 1.22.4 py38h99721a1_0 conda-forge opencv 4.5.3 py38h578d9bd_1 conda-forge openh264 2.1.1 h780b84a_0 conda-forge openjpeg 2.5.0 h7d73246_1 conda-forge openslide 3.4.1 h978ee9a_4 conda-forge openslide-python 1.2.0 py38h0a891b7_1 conda-forge openssl 1.1.1q h166bdaf_0 conda-forge packaging 21.3 pyhd8ed1ab_0 conda-forge pandas 1.4.4 py38h47df419_0 conda-forge pandoc 2.19.2 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge pango 1.48.10 hb8ff022_1 conda-forge paramiko 2.10.4 pyhd8ed1ab_0 conda-forge parse 1.19.0 pyh44b312d_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge partd 1.3.0 pyhd8ed1ab_0 conda-forge pathlib2 2.3.7.post1 py38h578d9bd_1 conda-forge patsy 0.5.3 pyhd8ed1ab_0 conda-forge pcre2 10.37 hc3806b6_1 conda-forge pexpect 4.8.0 pyh9f0ad1d_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 9.2.0 py38ha3b2c9c_2 conda-forge pip 22.3 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge plotly 5.10.0 pyhd8ed1ab_0 conda-forge progressbar2 4.0.0 pyhd8ed1ab_0 conda-forge proj 8.2.0 h277dcde_0 conda-forge prometheus_client 0.15.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.31 pyha770c72_0 conda-forge prompt_toolkit 3.0.31 hd8ed1ab_0 conda-forge prov 2.0.0 pyhd3deb0d_0 conda-forge psutil 5.9.2 py38h0a891b7_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pugixml 1.11.4 h9c3ff4c_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py-opencv 4.5.3 py38he5a9106_1 conda-forge pyasn1 0.4.8 py_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pydicom 2.3.0 pyh6c4a22f_0 conda-forge pydot 1.4.2 py38h578d9bd_2 conda-forge pyface 7.4.2 pyhd8ed1ab_0 conda-forge pygments 2.13.0 pyhd8ed1ab_0 conda-forge pyld 2.0.3 pyh9f0ad1d_0 conda-forge pymapvbvd 0.4.8 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py38h0a891b7_1 conda-forge pyopengl 3.1.6 pyhd8ed1ab_1 conda-forge pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge pyparsing 2.4.7 pyhd8ed1ab_1 conda-forge pypdf2 2.10.8 pyhd8ed1ab_0 conda-forge pypubsub 4.0.3 py_0 conda-forge pyqt 5.12.3 py38ha8c2ead_4 conda-forge pyqt5-sip 4.19.18 pypi_0 pypi pyqtchart 5.12 pypi_0 pypi pyqtwebengine 5.12.1 pypi_0 pypi pyrsistent 0.18.1 py38h0a891b7_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.6.1 py38hc386592_3 conda-forge python 3.8.13 h582c2e5_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.2 pyhd8ed1ab_0 conda-forge python-utils 3.3.3 pyhd8ed1ab_0 conda-forge python_abi 3.8 2_cp38 conda-forge pytz 2022.4 pyhd8ed1ab_0 conda-forge pywavelets 1.3.0 py38h71d37f0_1 conda-forge pyyaml 5.4.1 py38h0a891b7_3 conda-forge pyzmq 24.0.1 py38hfc09fa9_0 conda-forge qt 5.12.9 hda022c4_4 conda-forge qtconsole 5.3.2 pyhd8ed1ab_0 conda-forge qtconsole-base 5.3.2 pyha770c72_0 conda-forge qtpy 2.2.1 pyhd8ed1ab_0 conda-forge rdflib 6.2.0 pyhd8ed1ab_0 conda-forge rdflib-jsonld 0.6.2 py38h578d9bd_2 conda-forge readline 8.1.2 h0f457ee_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge rich 12.6.0 pyhd8ed1ab_0 conda-forge rsa 4.7.2 pyh44b312d_0 conda-forge rtree 1.0.1 py38h02d302b_0 conda-forge ruamel.yaml 0.17.21 py38h0a891b7_1 conda-forge ruamel.yaml.clib 0.2.6 py38h0a891b7_1 conda-forge s3transfer 0.6.0 pyhd8ed1ab_0 conda-forge scikit-image 0.19.3 py38h47df419_1 conda-forge scikit-learn 1.1.2 py38h0b08f9b_0 conda-forge scipy 1.8.1 py38hea3f02b_2 conda-forge seaborn 0.11.2 hd8ed1ab_0 conda-forge seaborn-base 0.11.2 pyhd8ed1ab_0 conda-forge send2trash 1.8.0 pyhd8ed1ab_0 conda-forge setuptools 65.5.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.1.9 hbd366e4_1 conda-forge snowballstemmer 2.2.0 pyhd8ed1ab_0 conda-forge sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge spec2nii 0.4.8 pyhd8ed1ab_0 conda-forge sphinx 5.1.1 pyhd8ed1ab_1 conda-forge sphinx_rtd_theme 1.0.0 pyhd8ed1ab_0 conda-forge sphinxcontrib-applehelp 1.0.2 py_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 2.0.0 pyhd8ed1ab_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.5 pyhd8ed1ab_2 conda-forge sqlite 3.39.4 h4ff8645_0 conda-forge stack_data 0.5.1 pyhd8ed1ab_0 conda-forge statsmodels 0.13.2 py38h71d37f0_0 conda-forge tbb 2020.2 h4bd325d_4 conda-forge tbb-devel 2020.2 h4bd325d_4 conda-forge tblib 1.7.0 pyhd8ed1ab_0 conda-forge tenacity 8.1.0 pyhd8ed1ab_0 conda-forge terminado 0.16.0 pyh41d4057_0 conda-forge textual 0.1.18 pyhd8ed1ab_1 conda-forge threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge tifffile 2022.10.10 pyhd8ed1ab_0 conda-forge tinycss2 1.1.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tornado 6.1 py38h0a891b7_3 conda-forge tqdm 4.64.1 pyhd8ed1ab_0 conda-forge traitlets 5.4.0 pyhd8ed1ab_0 conda-forge traits 6.4.1 py38h0a891b7_0 conda-forge traitsui 7.4.1 pyhd8ed1ab_0 conda-forge trimesh 3.15.3 pyh1a96a4e_0 conda-forge typing-extensions 4.4.0 hd8ed1ab_0 conda-forge typing_extensions 4.4.0 pyha770c72_0 conda-forge unicodedata2 14.0.0 py38h0a891b7_1 conda-forge urllib3 1.26.11 pyhd8ed1ab_0 conda-forge utfcpp 3.2.1 ha770c72_0 conda-forge vtk 9.0.3 no_osmesa_py38h7a5b95d_106 conda-forge wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.3 pyhd8ed1ab_0 conda-forge wire 1.0.0 py_0 https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel wxnatpy 0.4.0 pyhd8ed1ab_0 conda-forge wxpython 4.1.1 py38h1c15066_3 conda-forge x264 1!161.3030 h7f98852_1 conda-forge xarray 2022.10.0 pyhd8ed1ab_0 conda-forge xnat 0.4.2 pyhd8ed1ab_0 conda-forge xorg-damageproto 1.2.1 h7f98852_1002 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-glproto 1.4.17 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.7.2 h7f98852_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdamage 1.1.5 h7f98852_1 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h7f98852_1 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxrandr 1.5.2 h7f98852_1 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 conda-forge xorg-randrproto 1.5.0 h7f98852_1001 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-util-macros 1.19.3 h7f98852_0 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.4 h9c3ff4c_1 conda-forge zfp 1.0.0 h27087fc_1 conda-forge zict 2.2.0 pyhd8ed1ab_0 conda-forge zipp 3.9.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zlib-ng 2.0.6 h166bdaf_0 conda-forge zstd 1.5.2 h6239696_4 conda-forge

pauldmccarthy commented 1 year ago

And does the error message change when you try to run FSLeyes after unsetting the LIBGL_ALWAYS_INDIRECT variable? i.e.

unset LIBGL_ALWAYS_INDIRECT
fsleyes
AndreaAtanasov commented 1 year ago

And does the error message change when you try to run FSLeyes after unsetting the LIBGL_ALWAYS_INDIRECT variable? i.e.

unset LIBGL_ALWAYS_INDIRECT
fsleyes

Error code has not changed although fsleyes does stay open for about 0.1 seconds longer than before, cannot say if this is just a coincidence.

pauldmccarthy commented 1 year ago

@AndreaAtanasov Would you be able to try using an alternate X server? I'd recommend mobaxterm

AndreaAtanasov commented 1 year ago

It did the same thing with mobaxterm, I didn't really play with any settings though.

pauldmccarthy commented 1 year ago

What happens if you run FSLeyes as root, i.e. sudo $FSLDIR/bin/fsleyes ?

AndreaAtanasov commented 1 year ago

What happens if you run FSLeyes as root, i.e. sudo $FSLDIR/bin/fsleyes ?

same error code

SomePersonSomeWhereInTheWorld commented 1 year ago

Not sure if this is related but when running FSL 6.0.5.2 installed in RHEL 8 and connecting via XQuartz on a Mac, with just a laptop and no external monitors the following crash happens:

MESA-LOADER: failed to open swrast (search paths /usr/lib64/dri)
The program 'fsleyes' received an X Window System error.
This probably reflects a bug in the program.
The error was 'GLXBadContext'.
  (Details: serial 1000 error_code 161 request_code 149 minor_code 6)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)

If I use > 1 monitor it at least opens but in order to see the menus I have to unplug a monitor to be able to get to the bottom right corner to drag the fsleyes window to shrink it. Is this the right place for this?

vogab commented 1 year ago

hi, a short message to let you know that I had the same issue and error message. I deselected Native OpenGL and select Disable access control in the Extra Settings panel when starting XLaunch as suggested here https://github.com/pauldmccarthy/fsleyes/issues/79#issuecomment-862267467

it solved my issue and I could run fsleyes smoothly