[Neuroimaging] Running pysurfer under Ubuntu 18.04:

KEVEEN RODRÍGUEZ ZAPATA keveen.rodriguez at udea.edu.co
Fri Jul 6 14:46:17 EDT 2018

Hi Dr. Tim Schäfer, the same thing happened to me recently, it happens that
the library of mayavi contains other sublibraries of VTK, for it reinstalls
mayavi, or failing to do everything with conda (Anacona package), so it
will probably work properly.

El jue., 5 jul. 2018 a las 13:51, <ts+ml at rcmd.org> escribió:

> Dear list,
> I'm trying to run the PySurfer 'Basic Visualization' example script from
> the Example Gallery [1] under Ubuntu 18.04 and I am getting the following
> error:
> [ts at box:~/develop/comp_neuro_science/python_visualization_pysurfer] $
> python plot_basics.py
> ********************************************************************************
> WARNING: Imported VTK version (8.1) does not match the one used
>          to build the TVTK classes (6.3). This may cause problems.
>          Please rebuild TVTK.
> ********************************************************************************
> Basic Visualization
> ===================
> Initialize a basic visualization session.
> X Error of failed request:  BadWindow (invalid Window parameter)
>   Major opcode of failed request:  10 (X_UnmapWindow)
>   Resource id in failed request:  0x2e00018
>   Serial number of failed request:  53
>   Current serial number in output stream:  55
> The warning before the error is pretty clear, but I'm neither sure whether
> it is the cause of the problem, nor how to fix it. When the command is run,
> the warning is displayed, then a empty display window opens for a split
> second and closes again, and the script terminates with the error given
> above.
> Some system info:
> -Operating system: The OS is Ubuntu 18.04 (64bit).
> -python version (OS default): Python 2.7.15rc1
> -pip version (OS default): pip 9.0.1 from /usr/lib/python2.7/dist-packages
> (python 2.7)
> I have FreeSurfer installed and its environment setup (FREESURFER_DIR,
> SUBJECTS_DIR, etc) in case that matters (I guess fsaverage will be taken
> from $SUBJECTS_DIR?).
> The output of `pip -list` is pretty long and can be found at
> https://paste.ubuntu.com/p/RXQCmCJMSY/. Note that tvtk (mentioned in the
> warning above) is NOT in the list.
> How I installed PySurfer:
> I followed these instructions: https://pysurfer.github.io/install.html,
> so I did:
> sudo apt-get install python-pip
> pip install numpy scipy ipython nibabel matplotlib mayavi imageio pysurfer
> The command did not give any errors.
> Any suggestions on what I should try next?
> What I already tried:
> 1)
> $ pip install vtk==6.3
> Collecting vtk==6.3
>   Could not find a version that satisfies the requirement vtk==6.3 (from
> versions: 8.1.0, 8.1.1)
> No matching distribution found for vtk==6.3
> 2)
> $ pip install tvtk
> Collecting tvtk
>   Could not find a version that satisfies the requirement tvtk (from
> versions: )
> No matching distribution found for tvtk
> Thanks in advance,
> Tim
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> [1]
> https://pysurfer.github.io/auto_examples/plot_basics.html#sphx-glr-auto-examples-plot-basics-py
> _______________________________________________
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> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging


Keveen Rodríguez Zapata
Estudiante de Bioingeniería e Ingeniería Informática
Universidad de Antioquia


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