SUMA Visualization Issue

djohn · October 12, 2018, 2:12pm

Hi,

I’m doing a surfaced-based analysis on my data, and am trying to use SUMA for visualization purposes. I ran Freesurfer’s recon-all on my data, then used @SUMA_Make_Spec_FS to create the SUMA directory and files. Once I finished preprocessing my data, I tried using SUMA with the command suma -spec ${subj}_lh.spec -sv ${subj}_SurfVol+orig. &

The output from the command line is as follows:

libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #1/6(Local Domain Parent), loading …

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #2/6 (mappable via Local Domain Parent), loading …

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #3/6 (mappable via Local Domain Parent), loading …

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #4/6 (mappable via Local Domain Parent), loading …

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #5/6 (mappable via Local Domain Parent), loading …

vvvvvvvvvvvvvvvvvvvvvvvvvvvvSurface #6/6 (mappable via Local Domain Parent), loading …
SUMA_Engine: Starting to listen …

The SUMA GUI comes up with a blank window, and I am unable to load a view, where I get the error message: SUMA_LoadVisualState: Can’t open file

I was wondering whether my SUMA issue is due to the error message about loading drivers, or if there is something wrong with my files?

Thank you for the help.

ptaylor · October 12, 2018, 2:19pm

Hi, Dan-

What’s the output of


afni_system_check.py -check_all

and also what happens if you just type


suma

in a terminal? Does the visualizer open up with some kind of image (a random one)?

–pt

djohn · October 12, 2018, 2:38pm

Hi,

The output from afni_system_check.py is:

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 3.10.0-862.11.6.el7.x86_64
version: #1 SMP Fri Aug 10 16:55:11 UTC 2018
distribution: Red Hat Enterprise Linux Server 7.5 Maipo
number of CPUs: 24
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /N/soft/rhel7/afni/18.0.13/afni
afni version : Precompiled binary linux_openmp_64: Feb 5 2018
: AFNI_18.0.12
AFNI_version.txt : AFNI_18.0.12, linux_openmp_64, Feb 05 2018
which python : /N/soft/rhel7/python/2.7.13a/bin/python
python version : 2.7.13
which R : /N/soft/rhel7/r/3.3.1/bin/R
R version : R version 3.3.1 (2016-06-21) – “Bug in Your Hair”
which tcsh : /usr/bin/tcsh

instances of various programs found in PATH:
afni : 1 (/gpfs/hps/soft/rhel7/afni/18.0.13/afni)
R : 1 (/gpfs/hps/soft/rhel7/r/3.3.1/bin/R)
python : 2
/gpfs/hps/soft/rhel7/python/2.7.13a/bin/python2.7
/usr/bin/python2.7
python2 : 2
/gpfs/hps/soft/rhel7/python/2.7.13a/bin/python2.7
/usr/bin/python2.7
python3 : 0

testing ability to start various programs…
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success

checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE

    oo Warning: 
       These packages are not installed on the computer: afex!
    These packages are not installed on the computer: phia!

checking for $HOME files…
.afnirc : missing
.sumarc : found
.afni/help/all_progs.COMP : missing

------------------------------ python libs -------------------------------
** python module not found: PyQt4
– PyQt4 is no longer needed for an AFNI bootcamp

-------------------------------- env vars --------------------------------
PATH = /N/u/dlevitas/Carbonate/bin/ants/bin/:/N/u/dlevitas/Carbonate/.local/bin/:/N/u/dlevitas/Carbonate/dbus/:/N/u/dlevitas/Carbonate/jq/:/N/u/dlevitas/Carbonate/inkscape-0.92.3/:/N/u/dlevitas/Carbonate/mricrogl_lx/pigz/:/N/u/dlevitas/Carbonate/mricrogl_lx/build/dcm2niix/bin/:/N/u/dlevitas/Carbonate/BrainSuite15c/bin/:/N/u/dlevitas/Carbonate/c3d-1.0.0-Linux-x86_64/bin/:/N/u/dlevitas/Carbonate/sublime_text_3/:/opt/moab/bin:/opt/moab/bin:/N/u/dlevitas/Carbonate/bin/ants/bin/:/N/u/dlevitas/Carbonate/.local/bin/:/N/u/dlevitas/Carbonate/dbus/:/N/u/dlevitas/Carbonate/jq/:/N/u/dlevitas/Carbonate/inkscape-0.92.3/:/N/u/dlevitas/Carbonate/mricrogl_lx/pigz/:/N/u/dlevitas/Carbonate/mricrogl_lx/build/dcm2niix/bin/:/N/u/dlevitas/Carbonate/BrainSuite15c/bin/:/N/u/dlevitas/Carbonate/c3d-1.0.0-Linux-x86_64/bin/:/N/u/dlevitas/Carbonate/sublime_text_3/:/N/soft/rhel7/singularity/2.5.2/bin:/N/soft/rhel7/cmake/gnu/3.11.4/bin:/N/soft/rhel7/freesurfer/6.0.0/freesurfer/bin:/N/soft/rhel7/fsl/5.0.11b/bin:/N/soft/rhel7/fsl/5.0.11b/extras/bin:/N/soft/rhel7/fsl/autoPtx/0.1.1:/N/soft/rhel7/libmng/2.0.3/bin:/N/soft/rhel7/lcms/2.8/bin:/N/soft/rhel7/matlab/2017a/bin/:/N/soft/rhel7/afni/18.0.13:/N/soft/rhel7/libpng/1.6.29/bin:/N/soft/rhel7/r/3.3.1/bin:/N/soft/rhel7/java/1.8.0_131/bin:/N/soft/rhel7/curl/intel/7.54.0/bin:/N/soft/rhel7/gsl/gnu/2.3/bin:/N/soft/rhel7/git/gnu/2.13.0/bin:/N/soft/rhel7/quotas:/N/soft/rhel7/perl/gnu/5.24.1/bin:/N/soft/rhel7/python/2.7.13a/bin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/bin/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/bin:/N/soft/rhel7/gcc/6.3.0/bin:/opt/moab/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/N/u/dlevitas/Carbonate/bin

PYTHONPATH = /N/soft/rhel7/python/2.7.13a/lib/python2.7/site-packages

R_LIBS =
LD_LIBRARY_PATH = /N/soft/rhel7/singularity/2.5.2/lib:/N/soft/rhel7/freesurfer/6.0.0/freesurfer/lib:/N/soft/rhel7/fsl/5.0.11b/lib:/N/soft/rhel7/fsl/5.0.11b/extras/lib:/N/soft/rhel7/libmng/2.0.3/lib:/N/soft/rhel7/lcms/2.8/lib:/N/soft/rhel7/libpng/1.6.29/lib:/N/soft/rhel7/zlib/gnu/1.2.11/lib/:/N/soft/rhel7/bzip2/1.0.6/lib/:/N/soft/rhel7/xz/5.2.3/lib/:/N/soft/rhel7/r/3.3.1/lib64/R/lib:/N/soft/rhel7/nlopt/2.4.2/lib:/N/soft/rhel7/curl/intel/7.54.0/lib:/N/soft/rhel7/gsl/gnu/2.3/lib:/N/soft/rhel7/perl/gnu/5.24.1/lib:/N/soft/rhel7/python/2.7.13a/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/intel64/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mpi/mic/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/ipp/lib/intel64:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/compiler/lib/intel64_lin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/tbb/lib/intel64/gcc4.7:/N/soft/rhel7/intel/18.0.2/debugger_2018/iga/lib:/N/soft/rhel7/intel/18.0.2/debugger_2018/libipt/intel64/lib:/N/soft/rhel7/intel/18.0.2/compilers_and_libraries_2018.2.199/linux/daal/lib/intel64_lin:/N/soft/rhel7/gcc/6.3.0/lib64:/N/soft/rhel7/gcc/6.3.0/lib:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/runtime/glnxa64:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/bin/glnxa64:/N/soft/rhel7/matlab/MATLAB_Compiler_Runtime/v92/sys/os/glnxa64

DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =

------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /N/soft/rhel7/afni/18.0.13

------------------------------ OS specific -------------------------------

========================= summary, please fix: =========================

login shell ‘bash’, trusting user to translate from ‘tcsh’
shell bash: consider sourcing (non-login) .bashrc from (login) .bash_profile
missing R packages (see rPkgsInstall)
consider running: cp /N/soft/rhel7/afni/18.0.13/AFNI.afnirc ~/.afnirc
consider running: apsearch -update_all_afni_help
insufficient data for AFNI bootcamp
consider installing PyQt4

Loading SUMA by typing suma on the command line only brings up the GUI, but no image is displayed. The command line output is:

suma:
No input specified, loading some toy surfaces…
Use ‘.’ and ‘,’ to cycle between them.
See suma -help for assistance.

libGL error: unable to load driver: swrast_dri.so
libGL error: failed to load driver: swrast
SUMA_Engine: Starting to listen …

ptaylor · October 12, 2018, 4:18pm

Hm, it looks a driver issue with OpenGL. Do you have special graphics/video drivers, by any chance?

From looking online, it seems like installing mesa-utils and libgl1-mesa-glx with your package manager is a first course of action, but that might depend on the drivers…

–pt

djohn · October 12, 2018, 5:26pm

I’m running AFNI and SUMA on my university’s HPC, so I’m not entirely sure off the top of my head if there are any special graphics/video drivers ( I can ask one of the admins though). Since I don’t have root privileges, I wouldn’t be able to install mesa-utils and libgl1-mesa-glx myself, but I’ll them about it first to see how to proceed.

Thanks,

Dan

benfulton · October 25, 2018, 6:42pm

Hi,

I am working with Dan on resolving this issue on our cluster. We installed mesa-dri-drivers and its dependencies, and verified that suma is able to display the test images correctly over X using Windows and XMing. However, it’s not able to display them on a Mac using XQuartz:


$ suma

suma:
     No input specified, loading some toy surfaces...
     Use '.' and ',' to cycle between them.
     See suma -help for assistance.

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
oo     Warning SUMA_XErrHandler (SUMA_display.c:4147):
Intercepted X11 error: BadValue (integer parameter out of range for operation)
Will attempt to proceed but trouble might ensue.
++     Notice SUMA_XErrHandler (SUMA_display.c:4148 @09:35:35):
Trace At Xerr
      SUMA_XErrHandler
     SUMA_glXMakeCurrent
    SUMA_graphicsInit
   SUMA_X_SurfaceViewer_Create
  suma
 Bottom of Debug Stack

We have the following packages installed:


$ rpm -qa | grep libGL
mesa-libGL-17.2.3-8.20171019.el7.x86_64
mesa-libGLU-9.0.0-4.el7.x86_64
mesa-libGLU-devel-9.0.0-4.el7.x86_64
mesa-libGL-devel-17.2.3-8.20171019.el7.x86_64

Any hints? Thanks!

Ben Fulton

pmolfese · October 25, 2018, 6:45pm

What version of XQuartz are you running?

benfulton · October 25, 2018, 7:42pm

We tried a few different Macs, but they all seem to be running XQuartz 2.7.11 (xorg-server 1.18.4).

–
Ben Fulton