[Neuroimaging] Running pysurfer under Ubuntu 18.04:

[Michael Waskom]

It's very likely not a pysurfer problem per se so I doubt that changing the
version of that will help.

Someone has reported the error to mayavi:
https://github.com/enthought/mayavi/issues/621. But I don't understand the
resolution.

It's likely some incompatibility between mayavi / vtk / the GUI library.
Trying a different GUI library (e.g. Qt) would be my first step.

I've used pysurfer/mayavi on ubuntu without issue, but that is installing
things using conda and not pip.

On Fri, Jul 6, 2018 at 4:16 PM, Yaroslav Halchenko <yoh at onerussian.com>
wrote:

> What about version which comes with Ubuntu?
> According to http://neuro.debian.net/pkgs/python-surfer.html it is 0.7 ,
> so you need fresher one and we need to update packaging?
>
>
> On July 6, 2018 2:46:17 PM EDT, "KEVEEN RODRÍGUEZ ZAPATA" <
> keveen.rodriguez at udea.edu.co> wrote:
>>
>> 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
>>> _______________________________________________
>>> Neuroimaging mailing list
>>> Neuroimaging at python.org
>>> https://mail.python.org/mailman/listinfo/neuroimaging
>>>
>>
>>
>> --
>>
>> Keveen Rodríguez Zapata
>> Estudiante de Bioingeniería e Ingeniería Informática
>> GRUNECO
>> Universidad de Antioquia
>> <http://www.biomaterialesudea.com.co>
>>
>>
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> --
> Sent from a phone which beats iPhone.
>
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