[Neuroimaging] Problem with PySurfer module in Python3

[Kadwani, Manorama]

Hi Eric,

I did take care of modifying the command and used 'python3 -m pip' instead of just 'pip'. Sorry I didn't specify that in my previous email.

Ok, I installed VTK using that command, but it shows version 8.2.0 instead of 8.1.2 that came in the Mayavi-master package:

mne:           0.20.0
numpy:         1.18.1 {blas=mkl_rt, lapack=mkl_rt}
scipy:         1.4.1
matplotlib:    3.1.3 {backend=Qt5Agg}

sklearn:       0.22.1
numba:         0.48.0
nibabel:       3.1.0
cupy:          Not found
pandas:        1.0.1
dipy:          Not found
mayavi:        4.7.1 {qt_api=pyqt5, PyQt5=5.9.2}
pyvista:       Not found
vtk:           8.2.0

When I again tried installing PySurfer, it said that 'Requirement already satisfied: PySurfer in /usr/local/lib/python3.6/dist-packages'. Python3 still can't find PySurfer module.

Also, I had installed VTK-9.0.0 previously using the configuration steps in https://vtk.org/Wiki/VTK/Building/Linux. There they mentioned configuring VTK with the path to the Qt build and path to VTK. Where is the location of VTK in that archive if I need to modify the cmakeList?

Thanks,
Manorama

________________________________
From: Neuroimaging <neuroimaging-bounces+mkadwani=mgh.harvard.edu at python.org> on behalf of Eric Larson <larson.eric.d at gmail.com>
Sent: Thursday, June 11, 2020 11:48 AM
To: Neuroimaging analysis in Python <neuroimaging at python.org>
Subject: Re: [Neuroimaging] Problem with PySurfer module in Python3


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But Python3 gives me an error that this module was not found. Any ideas on what I missed?

On some systems you have to be careful about `python` vs `python3` and `pip` vs `pip3`. You might need to use `pip3`, or more explicitly perhaps `python3 -m pip` to run the command, i.e.:

python3 -m pip install PySurfer

You might currently hit a problem with Mayavi because they haven't released an update to deal with VTK9, in which case you might also need to do:

python3 -m pip install vtk https://github.com/enthought/mayavi/archive/master.zip

And then try the PySurfer line.

Eric



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