[Mne_analysis] mne.gui.coregistration - coloured fiducial

[FAIRS Amie]

        External Email - Use Caution        

Thanks for the tip! I'll test it out tomorrow and come back if I run into more problems.

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.

Date: Tue, 7 Jul 2020 22:54:18 -0400
From: Luke Bloy <luke.bloy at gmail.com>
Subject: Re: [Mne_analysis] mne.gui.coregistration - coloured fiducial
	dots not showing
To: Discussion and support forum for the users of MNE Software
	<mne_analysis at nmr.mgh.harvard.edu>
Message-ID:
	<CAG5Ru-rVwLXjF1NioxnqivEFNQfP2P-NcEpR=kaqc140=ZfQ9Q at mail.gmail.com>
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Those won't help unfortunately. The problem is that it won't render any points with an alpha not equal to one. If you change the alpha, using the mayavi settings they will show up.

Eric, I think one of the cis might match the llvm driver and opengl that is causing the problem so maybe we have a place to test so we can submit a bug report to vtk? I just need to confirm with your new PR.

On Tue, Jul 7, 2020, 11:32 AM Eric Larson <larson.eric.d at gmail.com> wrote:

>         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-m
>> ne-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 Universit?
>>>
>>> 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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>>> Mne_analysis at nmr.mgh.harvard.edu
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>>
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