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

Luke Bloy luke.bloy at gmail.com
Tue Jul 7 23:25:46 EDT 2020
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That is assuming the issue is the same one I have.


On Tue, Jul 7, 2020, 10:54 PM Luke Bloy <luke.bloy at gmail.com> wrote:

> 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-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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