[Neuroimaging] Running pysurfer under Ubuntu 18.04:

Yaroslav Halchenko yoh at onerussian.com
Fri Jul 6 16:16:01 EDT 2018

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
>the library of mayavi contains other sublibraries of VTK, for it
>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
>> the Example Gallery [1] under Ubuntu 18.04 and I am getting the
>> 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
>> 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
>> second and closes again, and the script terminates with the error
>> 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
>> (python 2.7)
>> I have FreeSurfer installed and its environment setup
>> SUBJECTS_DIR, etc) in case that matters (I guess fsaverage will be
>> 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
>> warning above) is NOT in the list.
>> How I installed PySurfer:
>> I followed these instructions:
>> so I did:
>> sudo apt-get install python-pip
>> pip install numpy scipy ipython nibabel matplotlib mayavi imageio
>> 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
>> 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,
>> [1]
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>> Neuroimaging mailing list
>> 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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