[Mne_analysis] mne.gui.coregistration - coloured fiducial

FAIRS Amie amie.FAIRS at univ-amu.fr
Thu Jul 9 04:31:52 EDT 2020
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Thanks for the help - I've run the mesa override code before launching spyder and then found that within the coreg gui, if I click on display option and unselect 'use advanced OpenGL' I can see at least the MRI head shape and fiducial points, so I can align them.

I'm going to update my linux system though and have seen the PR so I can try to make sure my mesa version is up to date on the new system. I can report back if I also end up with plotting issues again.

Thank you again!

Best,

Amie

Message: 1
Date: Wed, 8 Jul 2020 08:05:53 -0400
From: Luke Bloy <luke.bloy at gmail.com>
Subject: Re: [Mne_analysis] mne.gui.coregistration - coloured fiducial
To: Discussion and support forum for the users of MNE Software
	<mne_analysis at nmr.mgh.harvard.edu>
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	<CAG5Ru-pGgLHNTdqRD2b1n6tw4TVuqvUb9Re+NGBqCpWR3-Hipg at mail.gmail.com>
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It's going to be annoying to find and adjust the opacity of the right points in `mne coreg` since there are so many things plotted. There might be a global mayavi setting that disables all opacity but I'm not sure.

I suspect the issue is related to the version of mesa that you and I are using but I don't have a suggestion of what version you should try that will work. I did open an issue (
https://github.com/mne-tools/mne-python/issues/7977) to hopefully find a good way to evaluate this.

On Wed, Jul 8, 2020 at 4:20 AM FAIRS Amie <amie.FAIRS at univ-amu.fr> wrote:

>         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 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.
>
> 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.
> >>>
> >>>
> >>> _______________________________________________
> >>> Mne_analysis mailing list
> >>> Mne_analysis at nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >> _______________________________________________
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