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

[Ricardo Licona]

        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 <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 <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 <mailto: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 <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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