Issue in computing the head model

Dear Brainstormers,

I have some problem in computing the head model for few subjects in my sample size. Specifically I have computed the BEM surfaces and I got a really bad result:

sub-82

I worked on it and I fix the outer_skin surface using other software (e.g. headreco, FreeSurfer etc.). Now the surfaces are fine but I am not able to compute the head model since I keep receiving this message:

Screen Shot 2020-03-29 at 11.06.41

Initially, I was thinking that it might be related to the different number of faces, vertices. So I fixed this and now they are the same for all of surfaces but nothing has changed.

Do you have any suggestions?

Thanks in advance

  1. The end of the message is missing.
    Please copy-paste it from the Matlab command window

  2. While this error message is on your screen, please zip the Brainstorm temporary folder, upload it somewhere and post the download link here. It will help the OpenMEEG developers debugging this problem.
    The folder to zip is typically in your home folder ($HOME/.brainstorm/tmp on Linux). If you're not sure, execute bst_get('BrainstormTmpDir') in your Matlab command window while Brainstorm is running

@Alexandre @papadop @mclerc @sik

Dear Francois,

thanks for your reply. Please find below what you requested:

  1. *************************************************************************** ** Error: OpenMEEG call: om_assemble -HM ** "/home/davide/.brainstorm/tmp/openmeeg.geom" ** "/home/davide/.brainstorm/tmp/openmeeg.cond" ** "/home/davide/.brainstorm/tmp/openmeeg_hm.mat" ** OpenMEEG error #1: ** ./om_assemble version 2.4.1 compiled at Aug 29 2018 08:19:44 using OpenMP ** Executing using 12 threads. ** ** | ------ ./om_assemble ** | -HM ** | /home/davide/.brainstorm/tmp/openmeeg.geom ** | /home/davide/.brainstorm/tmp/openmeeg.cond ** | /home/davide/.brainstorm/tmp/openmeeg_hm.mat ** | ----------------------- ** (DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): /home/davide/.brainstorm/tmp/openmeeg.geom ** This geometry is a NESTED geometry. ** Info:: Mesh name/ID : 1 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 8.85089e-06 ** Max Area : 8.3238e-05 ** Info:: Mesh name/ID : 2 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 7.82514e-06 ** Max Area : 7.80443e-05 ** Info:: Mesh name/ID : 3 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 9.79692e-07 ** Max Area : 0.000167025 ** Info:: Domain name : Scalp ** Conductivity : 1 ** Composed by interfaces : +1 -3 ** Interface "1"= { mesh "1" } ** Interface "3"= { mesh "3"(outermost) } ** Info:: Domain name : Skull ** Conductivity : 0.0125 ** Composed by interfaces : +2 -1 ** Interface "2"= { mesh "2" } ** Interface "1"= { mesh "1" } ** Info:: Domain name : Brain ** Conductivity : 1 ** Composed by interfaces : -2 ** Interface "2"= { mesh "2" } ** Info:: Domain name : Air ** Conductivity : 0 ** Composed by interfaces : +3 ** Considered as the outermost domain. ** Interface "3"= { mesh "3"(outermost) } ** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ** !!!!!!!!!!! WARNING !!!!!!!!!!! ** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ** 2 meshes are intersecting ! ** Info:: Mesh name/ID : 1 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 8.85089e-06 ** Max Area : 8.3238e-05 ** Info:: Mesh name/ID : 3 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 9.79692e-07 ** Max Area : 0.000167025 ** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ** !!!!!!!!!!! WARNING !!!!!!!!!!! ** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ** 2 meshes are intersecting ! ** Info:: Mesh name/ID : 2 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 7.82514e-06 ** Max Area : 7.80443e-05 ** Info:: Mesh name/ID : 3 ** # vertices : 1922 ** # triangles : 3840 ** Euler characteristic : 2 ** Min Area : 9.79692e-07 ** Max Area : 0.000167025 ** ** For help with OpenMEEG errors, please refer to the online tutorial: ** https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#Errors

  2. https://drive.google.com/file/d/1NsEksFY6uUphyALAo2uRkouPbbVPsu6H/view?usp=sharing

Hope to hearing from you soon

Best

Thanks, this might help the OpenMEEG team.

Could you also post a screen capture of the three surfaces in Brainstorm, with the edges displayed and a different color for the middle layer?

Hi Francois,

Sure, please find attached the surfaces in Brainstorm with both the edges displayed

Screen Shot 2020-04-01 at 13.29.36

If you need anything else please do not hesitate to contact me

Looking forward to hearing from you

The error message in OpenMEEG says that it can't run because the surfaces are interesting.
And in you figure, it is obvious that the "outer skull" layer is intersecting the "scalp" layer. It is not possible to compute a BEM solution in these conditions.

You need to fix your surfaces before trying to run OpenMEEG.
Some possible options (many others possible):

  1. Use the same tools you used to generate the skull surface to generate the head
  2. Generate the BEM surfaces using the Brainstorm tools
  3. Update Brainstorm and use the new option I added a few days ago to generate the BEM surfaces using FieldTrip (you need to download FieldTrip and set the FieldTrip path in the Brainstorm preferences) - this is still undocumented

Dear Francois,

I generated the BEM surfaces using FieldTrip and this is what I got:

Screen Shot 2020-04-10 at 18.33.20

It's much better than before but it still weird at the bottom. Do you think it is fine to run the source analysis with this BEM or should I try to fix it?

Moreover, for other subjects the BEM surfaces are not good at all even using FieldTrip

Screen Shot 2020-04-10 at 18.48.47

Any suggestion would be highly appreciate

Thanks

No, you should try to fix this...

If you can't find any way to obtain correct surfaces, you could always either use a spherical head model, an anatomy template, or a template warped to fit the positions of the electrodes (if you have individual electrode positions: https://neuroimage.usc.edu/brainstorm/Tutorials/TutWarping).