[Mne_analysis] BEM mesh error while downsampling vertices

Eric Larson larson.eric.d at gmail.com
Tue Oct 6 17:19:24 EDT 2020
Search archives:

        External Email - Use Caution        

From the code I pasted above, you should in principle be able to get the
X/Y/Z coordinates of any vertex you need. They are stored in the rows of
"rr". From that vertex number and the X/Y/Z coordinates, Blender probably
provides a way to select (or remove) points, and probably also fix
topological defects. But I don't really use Blender so I'm not sure.

Eric


On Tue, Oct 6, 2020 at 3:39 PM Kadwani, Manorama <MKADWANI at mgh.harvard.edu>
wrote:

> Thanks for the instructions.
>
> Do you know which one is the vertex with less than 3 neighboring triangles?
>
> Manorama
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Eric Larson <
> larson.eric.d at gmail.com>
> *Sent:* Tuesday, October 6, 2020 2:29 PM
> *To:* Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
> *Subject:* Re: [Mne_analysis] BEM mesh error while downsampling vertices
>
>
>         External Email - Use Caution
>
> Repo: https://github.com/mne-tools/mne-python
> Contributing instructions:
> https://mne.tools/dev/install/contributing.html#contributing
> FAQ file:
> https://github.com/mne-tools/mne-python/blob/master/doc/overview/faq.rst#my-watershed-bem-meshes-look-incorrect
>
> Eric
>
>
> On Tue, Oct 6, 2020 at 2:18 PM Kadwani, Manorama <MKADWANI at mgh.harvard.edu>
> wrote:
>
> Can you share the repo link where I can make a PR?
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Kadwani, Manorama <
> MKADWANI at mgh.harvard.edu>
> *Sent:* Tuesday, October 6, 2020 12:39 PM
> *To:* Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
> *Subject:* Re: [Mne_analysis] BEM mesh error while downsampling vertices
>
> Hi Eric,
>
> I forgot to turn off the digest mode, so I can't reply to your email
> directly.
>
> Thanks for the code.
> I could only see a subset of those vertices. Also, couldn't see how to
> edit those vertices, so I used Blender for editing.
> Using the vertices shown in the PyVista plot, I tried to zoom in at the
> location of those vertices in Blender. But I couldn't find the exact vertex
> which has fewer than 3 neighbouring triangles.
>
> I found many free-floating vertices, so deleted those. Then the number of
> vertices in the surface reduced a lot. I have shown an image of those
> vertices.
>
> Also attached is an image of the area where the Pyvista plot showed a
> vertex marked in red. All of the vertices have atleast 3 neighbour
> triangles.
>
> Sure, I can put a Github pull request.
>
> Thanks,
> Manorama
>
> ------------------------------
> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Kadwani, Manorama <
> MKADWANI at mgh.harvard.edu>
> *Sent:* Wednesday, September 30, 2020 6:16 PM
> *To:* Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
> *Subject:* [Mne_analysis] BEM mesh error while downsampling vertices
>
> Hi,
>
> I got a runtime error while making a BEM model (using mne.make_bem_model)
> that :
> "Surface inner skull has topological defects: 12 / 20484 vertices have
> fewer than three neighboring triangles [733, 1014, 2068, 7732, 8435, 8489,
> 10181, 11120, 11121, 11122, 11304, 11788]"
>
> As mentioned in this link-
> https://github.com/mne-tools/mne-python/issues/6127 I tried to visualize
> the inner skull surface but didn't know how to find those vertices. I have
> attached an image of the inner skull surface. I could see some small
> triangles at places I wouldn't expect them. So I tried to smoothen out any
> irregularities in Freeview using the smoothing tool. That didn't help. I
> still got the runtime error but with different vertices:
> "RuntimeError: Surface inner skull has topological defects: 12 / 20479
> vertices have fewer than three neighboring triangles [733, 1014, 2068,
> 7730, 8433, 8487, 10179, 11118, 11119, 11120, 11302, 11786]"
>
> Any idea on how to view and edit these vertices?
>
> Thanks,
> Manorama
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20201006/1c3c1a6f/attachment-0001.html 


More information about the Mne_analysis mailing list