Thank you for the dataset. I could reproduce the error with subject BCH008_copy. More precisely:
- When using only the "scalp" interface: it works.
- When using only the "brain" interface: it crashes with the error your reported.
The main difference is that some cortex vertices are outside the inner skull surface, but they are all inside the scalp. You have a warning telling you this at the beginning:
Another major problem is that there is at least one sensor that is outside the inner skull (PIN10), but this was not captured before calling OpenMEEG. I added an extra test in this commit: OpenMEEG: Add check for sensors outside the BEM layers · brainstorm-tools/brainstorm3@e419e0d · GitHub
Update Brainstorm, and it will show one more warning:
Now if we look at the log file $HOME/.brainstorm/tmp/openmeeg_log.txt, it indicates that there are things that OpenMEEG really doesn't like in input (see full report below).
I'm not sure which of the two problems causes this weird behavior, but I suggest you fix both, by following the recommendations in the messages.
@Alexandre The openmeeg files and logs are available here: Dropbox - File Deleted - Simplify your life
Do you think something needs to be addressed on your end?
om_assemble version 2.4.1 compiled at Aug 22 2018 19:47:28 using OpenMP
Executing using 4 threads.
| ------ om_assemble
| -HM
| C:\Users\franc\.brainstorm\tmp\openmeeg.geom
| C:\Users\franc\.brainstorm\tmp\openmeeg.cond
| C:\Users\franc\.brainstorm\tmp\openmeeg_hm.mat
| -----------------------
(DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): C:\Users\franc\.brainstorm\tmp\openmeeg.geom
This geometry is a NESTED geometry.
Info:: Mesh name/ID : 1
# vertices : 272
# triangles : 540
Euler characteristic : 2
Min Area : 7.02964e-05
Max Area : 0.000281747
Info:: Domain name : Brain
Conductivity : 1
Composed by interfaces : -1
Interface "1"= { mesh "1"(outermost), }
Info:: Domain name : Air
Conductivity : 0
Composed by interfaces : +1
Considered as the outermost domain.
Interface "1"= { mesh "1"(outermost), }
OPERATOR N ... (arg : mesh 1 , mesh 1 )
[*...................][**..................][***.................][****................][*****...............][******..............][*******.............][********............][*********...........][**********..........][***********.........][************........][*************.......][**************......][***************.....][****************....][*****************...][******************..][*******************.][********************]
[*...................][**..................][***.................][****................][*****...............][******..............][*******.............][********............][*********...........][**********..........][***********.........][************........][*************.......][**************......][***************.....][****************....][*****************...][******************..][*******************.][********************]
-------------------------------------------
| Elapsed Time: 0.230908 s.
-------------------------------------------
om_minverser version 2.4.1 compiled at Aug 22 2018 19:48:24 using OpenMP
Executing using 4 threads.
| ------ om_minverser
| C:\Users\franc\.brainstorm\tmp\openmeeg_hm.mat
| C:\Users\franc\.brainstorm\tmp\openmeeg_hminv.mat
| -----------------------
-------------------------------------------
| Elapsed Time: 0.0436095 s.
-------------------------------------------
om_assemble version 2.4.1 compiled at Aug 22 2018 19:47:28 using OpenMP
Executing using 4 threads.
| ------ om_assemble
| -DSM
| C:\Users\franc\.brainstorm\tmp\openmeeg.geom
| C:\Users\franc\.brainstorm\tmp\openmeeg.cond
| C:\Users\franc\.brainstorm\tmp\openmeeg_dipoles.txt
| C:\Users\franc\.brainstorm\tmp\openmeeg_dsm.mat
| -----------------------
(DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): C:\Users\franc\.brainstorm\tmp\openmeeg.geom
This geometry is a NESTED geometry.
Info:: Mesh name/ID : 1
# vertices : 272
# triangles : 540
Euler characteristic : 2
Min Area : 7.02964e-05
Max Area : 0.000281747
Info:: Domain name : Brain
Conductivity : 1
Composed by interfaces : -1
Interface "1"= { mesh "1"(outermost), }
Info:: Domain name : Air
Conductivity : 0
Composed by interfaces : +1
Considered as the outermost domain.
Interface "1"= { mesh "1"(outermost), }
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
[*...................][**..................][***.................][****................][*****...............][******..............][*******.............][********............]Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
Interface::contains_point(0.0231385 0.0381451 0.00442699) Error. Are you sure the interface "1" is closed? Solid angle: 8.106e-16*PI.
[*********...........]Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0201097 0.0332053 0.00358853) Error. Are you sure the interface "1" is closed? Solid angle: 8.07287e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0254921 0.0338826 0.00354881) Error. Are you sure the interface "1" is closed? Solid angle: 4.46713e-16*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
Interface::contains_point(0.0226149 0.0308357 0.00318497) Error. Are you sure the interface "1" is closed? Solid angle: 2.00607e-15*PI.
[**********..........]Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
Interface::contains_point(0.0220865 0.035996 0.00350139) Error. Are you sure the interface "1" is closed? Solid angle: 1.14853e-16*PI.
[***********.........][************........][*************.......][**************......][***************.....][****************....][*****************...][******************..][*******************.]Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0198306 -0.0381092 -0.00124464) Error. Are you sure the interface "1" is closed? Solid angle: 3.18055e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0216417 -0.0397103 -0.000318682) Error. Are you sure the interface "1" is closed? Solid angle: 3.07012e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0207651 -0.0349274 -0.00171846) Error. Are you sure the interface "1" is closed? Solid angle: 2.16454e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0162744 -0.0277205 -0.00162265) Error. Are you sure the interface "1" is closed? Solid angle: 4.81501e-16*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0242262 -0.0370155 -0.000978272) Error. Are you sure the interface "1" is closed? Solid angle: 2.65709e-15*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0199149 -0.0238616 -0.00267197) Error. Are you sure the interface "1" is closed? Solid angle: 2.87133e-17*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
Interface::contains_point(0.0267551 -0.0386204 0.000704918) Error. Are you sure the interface "1" is closed? Solid angle: 2.65046e-16*PI.
[********************]Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0797685 -0.0358122 0.0344163) Error. Are you sure the interface "1" is closed? Solid angle: 1.02705e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0759468 -0.0358923 0.0274783) Error. Are you sure the interface "1" is closed? Solid angle: 9.32079e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0748948 -0.0356139 0.0251042) Error. Are you sure the interface "1" is closed? Solid angle: 1.75869e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
Interface::contains_point(0.0805199 -0.0358809 0.0367387) Error. Are you sure the interface "1" is closed? Solid angle: 4.8012e-16*PI.
-------------------------------------------
| Elapsed Time: 132.318 s.
-------------------------------------------
om_assemble version 2.4.1 compiled at Aug 22 2018 19:47:28 using OpenMP
Executing using 4 threads.
| ------ om_assemble
| -H2IPM
| C:\Users\franc\.brainstorm\tmp\openmeeg.geom
| C:\Users\franc\.brainstorm\tmp\openmeeg.cond
| C:\Users\franc\.brainstorm\tmp\openmeeg_loc_seeg.txt
| C:\Users\franc\.brainstorm\tmp\openmeeg_h2ipm.mat
| -----------------------
(DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): C:\Users\franc\.brainstorm\tmp\openmeeg.geom
This geometry is a NESTED geometry.
Info:: Mesh name/ID : 1
# vertices : 272
# triangles : 540
Euler characteristic : 2
Min Area : 7.02964e-05
Max Area : 0.000281747
Info:: Domain name : Brain
Conductivity : 1
Composed by interfaces : -1
Interface "1"= { mesh "1"(outermost), }
Info:: Domain name : Air
Conductivity : 0
Composed by interfaces : +1
Considered as the outermost domain.
Interface "1"= { mesh "1"(outermost), }
Interface::contains_point(0.00571985 0.0703522 0.052212) Error. Are you sure the interface "1" is closed? Solid angle: 1.35229e-15*PI.
Interface::contains_point(0.00571985 0.0703522 0.052212) Error. Are you sure the interface "1" is closed? Solid angle: 1.35229e-15*PI.
Surf2Vol: Point [ 0.00571985 0.0703522 0.052212 ] is inside a nonconductive domain. Point is dropped.
INTERNAL OPERATOR D...
-------------------------------------------
| Elapsed Time: 0.0622965 s.
-------------------------------------------
om_assemble version 2.4.1 compiled at Aug 22 2018 19:47:28 using OpenMP
Executing using 4 threads.
| ------ om_assemble
| -DS2IPM
| C:\Users\franc\.brainstorm\tmp\openmeeg.geom
| C:\Users\franc\.brainstorm\tmp\openmeeg.cond
| C:\Users\franc\.brainstorm\tmp\openmeeg_dipoles.txt
| C:\Users\franc\.brainstorm\tmp\openmeeg_loc_seeg.txt
| C:\Users\franc\.brainstorm\tmp\openmeeg_ds2ipm.mat
| -----------------------
(DEPRECATED) Please consider updating your geometry file to the new format 1.1 (see data/README.rst): C:\Users\franc\.brainstorm\tmp\openmeeg.geom
This geometry is a NESTED geometry.
Info:: Mesh name/ID : 1
# vertices : 272
# triangles : 540
Euler characteristic : 2
Min Area : 7.02964e-05
Max Area : 0.000281747
Info:: Domain name : Brain
Conductivity : 1
Composed by interfaces : -1
Interface "1"= { mesh "1"(outermost), }
Info:: Domain name : Air
Conductivity : 0
Composed by interfaces : +1
Considered as the outermost domain.
Interface "1"= { mesh "1"(outermost), }
Interface::contains_point(0.00571985 0.0703522 0.052212) Error. Are you sure the interface "1" is closed? Solid angle: 1.35229e-15*PI.
Interface::contains_point(0.00571985 0.0703522 0.052212) Error. Are you sure the interface "1" is closed? Solid angle: 1.35229e-15*PI.
DipSource2InternalPot: Point [ 0.00571985 0.0703522 0.052212 ] is outside the head. Point is dropped.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
Interface::contains_point(-0.0671907 0.0232617 0.0514932) Error. Are you sure the interface "1" is closed? Solid angle: 9.58584e-16*PI.
[TRUNCATED]