Compute headmodel error: Error: OpenMEEG call: om_assemble -HM

[barehaco]

Hi All,

I am getting this error when I try to compute the headmodel.
Can anyone help?

Thank you!
Corinne

---

** Error: OpenMEEG call: om_assemble -HM
** "D:.brainstorm\openmeeg.geom"
** "D:.brainstorm\openmeeg.cond"
** "D:.brainstorm\openmeeg_hm.mat"
** OpenMEEG error #1:
** om_assemble version 2.4.0 compiled at Aug 22 2018 08:20:22 using OpenMP
** Executing using 2 threads.
**
** | ------ om_assemble
** | -HM
** | D:.brainstorm\openmeeg.geom
** | D:.brainstorm\openmeeg.cond
** | D:.brainstorm\openmeeg_hm.mat
** | -----------------------
** This geometry is a NESTED geometry.
** Info:: Mesh name/ID : 1
** # vertices : 998
** # triangles : 2000
** Euler characteristic : -2
** Min Area : 2.55657e-06
** Max Area : 0.000798526
** Info:: Mesh name/ID : 2
** # vertices : 1001
** # triangles : 1998
** Euler characteristic : 2
** Min Area : 2.57178e-06
** Max Area : 0.000409643
** Info:: Mesh name/ID : 3
** # vertices : 1090
** # triangles : 2176
** Euler characteristic : 2
** Min Area : 3.34257e-06
** Max Area : 0.00189509
** 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 : 998
** # triangles : 2000
** Euler characteristic : -2
** Min Area : 2.55657e-06
** Max Area : 0.000798526
** Info:: Mesh name/ID : 2
** # vertices : 1001
** # triangles : 1998
** Euler characteristic : 2
** Min Area : 2.57178e-06
** Max Area : 0.000409643
** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
** !!!!!!!!!!! WARNING !!!!!!!!!!!
** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
** 2 meshes are intersecting !
** Info:: Mesh name/ID : 1
** # vertices : 998
** # triangles : 2000
** Euler characteristic : -2
** Min Area : 2.55657e-06
** Max Area : 0.000798526
** Info:: Mesh name/ID : 3
** # vertices : 1090
** # triangles : 2176
** Euler characteristic : 2
** Min Area : 3.34257e-06
** Max Area : 0.00189509
** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
** !!!!!!!!!!! WARNING !!!!!!!!!!!
** !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
** 2 meshes are intersecting !
** Info:: Mesh name/ID : 2
** # vertices : 1001
** # triangles : 1998
** Euler characteristic : 2
** Min Area : 2.57178e-06
** Max Area : 0.000409643
** Info:: Mesh name/ID : 3
** # vertices : 1090
** # triangles : 2176
** Euler characteristic : 2
** Min Area : 3.34257e-06
** Max Area : 0.00189509
**
** For help with OpenMEEG errors, please refer to the online tutorial:
** https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#Errors

---

[Monalisa]

Hi Corinne,

I got this error before and found several previous discussions on that if that helps to solve your problem quickly. Based on your operating system there have been several solutions suggested, so it is better to have a look at those if any applies to your case. In the meantime I am sure they will help you with your problem.

Isil

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Hi! , i got a recent problem with OpenMEEG. Never have any problem before and i am using the same method in the last year. any idea? here the error message! Thank a lot! ** Error: OpenMEEG call: om_assemble -HM ** "/home/mdesjardins/.brainstorm/tmp/openmeeg.geom" ** "/home/mdesjardins/.brainstorm/tmp/openmeeg.cond" ** "/home/mdesjardins/.brainstorm/tmp/openmeeg_hm.mat" ** OpenMEEG error #1: ** ./om_assemble: /usr/local/MATLAB/R2013b/sys/os/glnxa64/libstdc++.so.6: versi…

BEM error nested geometry

Hello There is a similar discussion started last week: Can you see if changing the number of points on the various layers helps? Or recomputing a new head surface, or trying the menu "Remesh" on the head"...

https://lists.gforge.inria.fr/pipermail/openmeeg-info/2018/000255.html

[Francois]

Hi Corinne,

Two of the BEM surfaces you generated are intersecting.
Start by making sure the all the surfaces look good, by displaying the inner skull, outer skull, head and cortex surfaces in the same figure. From the surface tab, you can change the color of the different layers to help with the visibility. Set the smoothing to 0% for all of them. Please post the results if you're not sure this is what it should look like.

If your surfaces look good, you could try to get rid of this problem by computing BEM layers with different numbers of vertices (prefer keeping the same number for the inner and outer skull layers).

[barehaco]

Hi Francois,

Thank you for coming back to me so quickly!
The surfaces look pretty terrible -
3D_Subject001.tif (265.1 KB)

I used Brainsuite software and the automatic pipeline to segment the structural MRI, then imported the brainsuite folder into Brainstorm. Any ideas how I can improve these surfaces?

Thank you
Corinne

[Francois]

The inner and outer skull surfaces produced by BrainSuite are actually much more accurate than the ones generated by Brainstorm, but unfortunately they are too irregular in order to be used for computing a forward model with OpenMEEG.
You can generate smoother surfaces with the menu "Generate BEM surfaces" as illustrated in this tutorial: https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem

FYI: @aajoshi @Anand_Joshi @tmedani @juangpc @Alexandre @papadop @mclerc