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

[Eric Larson]

        External Email - Use Caution        

Hey Ricardo,

This is great information! Would you be up for making a Pull Request on
GitHub to modify this tutorial with updated instructions?

https://github.com/mne-tools/mne-python/blob/master/tutorials/source-modeling/plot_fix_bem_in_blender.py

This is what gets rendered to create the HTML tutorial.

Eric


On Tue, Oct 27, 2020 at 2:15 AM Ricardo Licona <ricklicona at me.com> wrote:

>         External Email - Use Caution
>
> Dear all,
>
> I solved the problem for Subject 09. In the Blender edit images that I
> sent you, there are no intersections (I analyzed the plot in detail); for
> this case, I only modified the outer skin. However, when I changed the
> outer skull solely, the problem finished. I exclusively employed
> mne.viz.plot_bem, although also I would consider Eric's options.
>
> For new users, I recommend make little modifications in Blender, then
> check the BEM plots (mne.viz.plot_bem) and save the plots. The idea is that
> you detect step by step, which parts of the surfaces to modify and
> eliminate the intersections between the surfaces. Here is the original
> tutorial:
> https://mne.tools/stable/auto_tutorials/source-modeling/plot_fix_bem_in_blender.html#sphx-glr-auto-tutorials-source-modeling-plot-fix-bem-in-blender-py
> .
>
> Only the next keyboard keys are necessaries in Blender:
>
>    - TAB: To change to EDIT mode
>    - C: To get a 'circle form' and select the parts that you want to
>    change
>    - G: To enlarge or reduce the pieces set (elemental)
>
>
> Here the plot and other important files (download:
> https://correoipn-my.sharepoint.com/:f:/g/personal/jliconam1700_alumno_ipn_mx/ElKGzCPCRXtNorraicEzoDsBPkjYyqD5RbBB-NMHmCZ9EA?e=8gstBV
> ):
>
>    - Graph with outer skull changed
>    - Blender image of the region changed
>    - Outer skull .surf file
>    - Outer skull fixed .obj file
>
>
> 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)
>
> Thanks for all.
>
> Best,
> Ricardo.
>
>
>
>
>
> El 26 oct 2020, a las 9:49, Eric Larson <larson.eric.d at gmail.com>
> escribió:
>
>         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:*MailScanner has detected a possible fraud
>> attempt from "correoipn-my.sharepoint.com" claiming to be*
>>  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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