[Mne_analysis] mne.gui.coregistration - coloured fiducial dots not showing

[Eric Larson]

        External Email - Use Caution        

(For the antialias option, you'll need to try latest MNE-Python master, not
0.20.7)

On Tue, Jul 7, 2020 at 11:30 AM Eric Larson <larson.eric.d at gmail.com> wrote:

> If the rendering is done in a VM it's likely to be using MESA GL software
> rendering, can you see if any of these help?
>
>
> https://mne.tools/dev/install/advanced.html#off-screen-rendering-in-mne-python-on-linux-with-mesa
>
> Eric
>
>
> On Tue, Jul 7, 2020 at 9:33 AM FAIRS Amie <amie.FAIRS at univ-amu.fr> wrote:
>
>>         External Email - Use Caution
>>
>> Dear mne community,
>>
>>
>>
>> Sorry again for another error message. I’m trying to run
>> mne.gui.coregistration, but while the MRI appears to load (there is a head)
>> there are no fiducials plotted. There is a fiducial file that is found in
>> the watershed folder for my subject, but I cannot see any of the fiducials
>> plotted so cannot edit them if needs be.
>>
>>
>>
>> I’m running mne python via spyder on linux, but not through anaconda,
>> because anaconda clashed with something in my VM and so previously the GUI
>> wouldn’t even launch. My sys info is below. One thing to note: I don’t have
>> pyvistaqt because when trying to install it there is an error with pyqt5
>> version 5.15 and that dependency cannot be loaded, so pyvistaqt also failed
>> to install.
>>
>>
>>
>> Do you know why the fiducial points are not visible in the GUI?
>>
>> As an aside, the linux system I am using is the one bundled with
>> freesurfer as a VM for running freesurfer on windows. A bit off topic but
>> do I need a different linux distribution to make this work?
>>
>>
>>
>> Any help would be really appreciated.
>>
>>
>>
>> mne.sys_info()
>>
>> Platform:      Linux-5.3.0-62-generic-x86_64-with-Ubuntu-18.04-bionic
>>
>> Python:        3.6.9 (default, Apr 18 2020, 01:56:04)  [GCC 8.4.0]
>>
>> Executable:    /usr/bin/python3.6
>>
>> CPU:           x86_64: 6 cores
>>
>> Memory:        19.8 GB
>>
>>
>>
>> mne:           0.20.7
>>
>> numpy:         1.19.0 {blas=openblas, lapack=openblas}
>>
>> scipy:         1.5.1
>>
>> matplotlib:    3.2.2 {backend=module://ipykernel.pylab.backend_inline}
>>
>>
>>
>> sklearn:       0.23.1
>>
>> numba:         0.50.1
>>
>> nibabel:       3.1.1
>>
>> cupy:          Not found
>>
>> pandas:        1.0.5
>>
>> dipy:          1.1.1
>>
>> mayavi:        4.7.1 {qt_api=pyqt5, PyQt5=5.11.3}
>>
>> pyvista:       0.25.3
>>
>> vtk:           8.1.2
>>
>>
>>
>> Best,
>>
>>
>>
>> Amie
>>
>>
>>
>> ------------------
>>
>> Dr. Amie Fairs
>>
>> Post-doctorant
>>
>> Aix-Marseille Université
>>
>> Laboratoire Parole et Langage (LPL) | CNRS UMR 7309 | 5 Avenue Pasteur |
>> 13100 Aix-en-Provence
>>
>> Email : amie.fairs at univ-amu.fr
>>
>>
>>
>> While I may send this email outside of typical working hours, I have no
>> expectation to receive an email outside of your typical hours.
>>
>>
>> _______________________________________________
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>
>
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