OpenMEEG error when attempting to compute head model with ICBM152 template and CAT12 segmentation

[pdhami]

Dear Brainstorm community,

I tried computing the head model using the default anatomy of the ICBM152 template, but I am running into the following error. I follow the steps outline here for CAT12 segmentation prior to computing the head model:

CAT12 Missing Files

Regarding all your missing files: make sure you do not start another instance of Brainstorm while you run CAT. Starting Brainstorm empties the temporary folder $HOME/.brainstorm/tmp, which includes the temporary folder for cat12, causing the process to fail. I updated the CAT segmentation and import in Brainstorm, it may help as well: https://github.com/brainstorm-tools/brainstorm3/commit/5212b573192212cc661caf9661b459323ae7f469 https://github.com/brainstorm-tools/brainstorm3/commit/7528573c8…

This issue seems to be new, as I was able to follow the same steps I am doing now with success last week. I did go back to using the ICBM152 template (without CAT12 segmentation), and OpenMEEG worked. Since it worked before with CAT12 segmentation, should I just follow the instructions provided at the end of the error and increase the number of vertices? Thank you.

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** Error: OpenMEEG call: om_assemble -HM
** "/Users/prabhjotdhami/.brainstorm/tmp/openmeeg.geom"
** "/Users/prabhjotdhami/.brainstorm/tmp/openmeeg.cond"
** "/Users/prabhjotdhami/.brainstorm/tmp/openmeeg_hm.mat"
** OpenMEEG error #1:
** ./om_assemble version 2.4.1 compiled at Aug 29 2018 08:19:07
**
** | ------ ./om_assemble
** | -HM
** | /Users/prabhjotdhami/.brainstorm/tmp/openmeeg.geom
** | /Users/prabhjotdhami/.brainstorm/tmp/openmeeg.cond
** | /Users/prabhjotdhami/.brainstorm/tmp/openmeeg_hm.mat
** | -----------------------
** (DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): /Users/prabhjotdhami/.brainstorm/tmp/openmeeg.geom
** This geometry is a NESTED geometry.
** Info:: Mesh name/ID : 1
** # vertices : 1922
** # triangles : 3840
** Euler characteristic : 2
** Min Area : 9.70682e-06
** Max Area : 9.09576e-05
** Info:: Mesh name/ID : 2
** # vertices : 1922
** # triangles : 3840
** Euler characteristic : 2
** Min Area : 8.7222e-06
** Max Area : 8.55674e-05
** Info:: Mesh name/ID : 3
** # vertices : 1922
** # triangles : 3840
** Euler characteristic : 2
** Min Area : 1.45854e-05
** Max Area : 0.000148821
** 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 : 9.70682e-06
** Max Area : 9.09576e-05
** Info:: Mesh name/ID : 3
** # vertices : 1922
** # triangles : 3840
** Euler characteristic : 2
** Min Area : 1.45854e-05
** Max Area : 0.000148821
**
** For help with OpenMEEG errors, please refer to the online tutorial:
** https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#Errors

---

[Francois]

The problem is not coming from the CAT12 segmentation, it's coming from the BEM surfaces generated by Brainstorm on top of the CAT12 surfaces. The BEM meshes (inner skull, outer skull, head) are considered as intersecting by OpenMEEG at least in one place.

You could try to recompute BEM surfaces using slightly different parameters:
https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem#BEM_surfaces

Just to make sure that there is no obvious error in your selection of default surfaces (the ones in green in your database explorer), please post a screen capture showing all the layers and the cortex in the same 3D figure, with different colors, as in the tutorial.

You can also try to play with transparencies and colors to identify where the different surfaces are intersecting (using the surface tab: https://neuroimage.usc.edu/brainstorm/Tutorials/ExploreAnatomy#Surfaces).

[pdhami]

Hi Francois,

thank you for the reply. Everything here looks normal to me.

I recomputed the BEM surfaces using the 2432 vertices (for head, outerskull, and innerskull) and computing of the head model worked fine.

Thank you again,
Paul