[Mne_analysis] Editing BEM meshes (Blender) {Disarmed}

[Eric Larson]

        External Email - Use Caution        

The first image did not come through. But in the second (corrected) one, in
the lower left plot you can see the outer skull (yellow) surface come very
close to the outer skin (peach) surface. `plot_bem` by default only shows
some slices -- if you use mne Report to render the bem with `decim=1`
you'll get an interactive slider where you can see all slices. There are
probably some slices for which they do intersect. You can also plot them in
3D using `plot_alignment` with the `surfaces` argument, or use FreeView --
or there is probably a way to view them in Blender to see where they
intersect.

Could you slightly expand downward (and smooth -- it's quite jagged) the
outer skin surface in blender?

Eric


On Sun, Oct 25, 2020 at 2:36 PM Ricardo Licona <ricklicona at me.com> wrote:

>         External Email - Use Caution
>
> Dear all,
>
> I had problems with BEM surfaces of FreeSurfer, thus I tried to correct
> them with the software Blender. After manual editing, according to plots,
> the intersections between the outer skull and outer skin disappear.
> However, when I run my Python script to create the 3-layer BEM model
> (conductivity = (0.3, 0.006, 0.3)), I have the same error message: “FAILED
> to create 3-layer BEM for sub009: Surface outer skull is not completely
> inside surface outer skin.”
>
> I am using the ds117 dataset.
>
> Plots (subject 9):
>
> * Original plot without edit:
>  https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/Ee725N_sYlhHtVMvMVDq7UABDrd6yjCwE9unGYMVVj3UvQ?e=co8vb4
> <https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/Ee725N_sYlhHtVMvMVDq7UABDrd6yjCwE9unGYMVVj3UvQ?e=co8vb4>
>
> * Plot after Blender edit:
> https://correoipn-my.sharepoint.com/:i:/g/personal/jliconam1700_alumno_ipn_mx/EQjGk_LZgyNItO-sJ8dYLZgB9a6W1HfqzqtiIEZYy6dlQA?e=KAlbM4
>
>
> Any advice?
>
> OS: Mac Os X (Catalina 10.15.7)
> MNE: 0.21.0
> FreeSurfer: 6.0 (due to some problems with the recent versions and Mac Os
> X)
>
> Best,
> Ricardo.
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