Orientation issue when plotting BEM surfaces

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1

Hi all, lovely to be on a forum again, it’s just like the early 2010s… I have a small problem with visualizing my BEM meshes which have been produced with freesurfer. It seems that no matter how I generate them, they look right in freeview and yet they’re upside down with mne.viz.plot_bem()

  • MNE-Python version: 0.22.0
  • operating system: Ubuntu 18.04 LTS (running in Windows Subsystem for Linux 2 in Windows 10 Professional)

I have included a code snippet but you probably need the actual MRI I was using – it’s open source data from the Donders Institute MOUS study and has been defaced.

Freeview screenshot (T1.mgz, outer skin surface made using mri_watershed:

image
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Freeview screenshot (T1.mgz, outer skin surface made using mri_watershed (with -useSRAS flag)):

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mne.viz.plot_bem(subject=‘sub-A2034’, orientation=‘coronal’, mri=‘T1.mgz’):

Using surface: /home/neurons/subjects/sub-A2034/bem/inner_skull.surf
Using surface: /home/neurons/subjects/sub-A2034/bem/outer_skull.surf
Using surface: /home/neurons/subjects/sub-A2034/bem/outer_skin.surf

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import os
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import mne

subjpath = '/home/neurons/subjects/'
mne.set_config('SUBJECTS_DIR',subjpath)
mne.viz.plot_bem(subject='sub-A2034', orientation='coronal', mri='T1.mgz')

Anyone have any ideas? Let me know if you need more info. Thanks.

2

are you sure it’s the same files used in both cases?

can you replicate for all subjects?

do you have the pb with mne sample data?

Alex

3

I’ll look into it, thanks…

4

Okay, looks like the issue fixed itself after running

recon-all -all -s sub-A2034

Now everything looks aligned in mne. Sorry for the waste of a topic.

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5

Thanks for reporting back! Also if you regenerated the surfaces using a newer version of MNE-Python it we might have been that, too – we’ve had some fixes for BEM meshes over the last couple releases.

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