[Mne_analysis] error creating geometry file

Matti Hamalainen msh at nmr.mgh.harvard.edu
Mon Aug 16 08:59:24 EDT 2010
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Hello Ricky,

On Aug 15, 2010, at 1:12 PM, rsachdev at nmr.mgh.harvard.edu wrote:

> Hello,
>
> I am getting this error for one of my subjects when I run the
> mne_setup_forward_model(mne_setup_forward_model --subject --surf -- 
> ico 4).
>
>
> Going from 5th to 4th subdivision of an icosahedron (ntri: 20480 ->  
> 5120)
>
> outer skin  CM is   1.26  -5.30   7.83 mm
> outer skull CM is   1.28  -5.09   7.35 mm
> inner skull CM is   0.84  -9.45  16.70 mm
> Checking that outer skull surface is inside outer skin  surface...[ok]
> Checking that inner skull surface is inside outer skull surface... 
> [failed]
> Surface outer skull is not completely inside surface inner skull(sum  
> of
> solid angles = -4.31123e-16 * 4*PI).
> Could't create the geometry file
>
>
> Any idea why the outer skull might not be completely inside the inner
> skull?  Should I run the outershift or innershift with the command?

First of all your error message reveals a bug in the MNE code: the  
surface names are swapped. The message should say: "Surface inner  
skull is not completel inside surface outer skull...". I have fixed  
this.
The reason for this is that the automatic segmentation procedure  
produced surfaces which intersect. You can try whether shifting the  
outer skull surface slightly helps.

- Matti

-------------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Building 149, 13th Street, Mailcode 149-2301
Charlestown, MA 02129-2060
USA

e-mail          msh at nmr.mgh.harvard.edu
Tel             +1 617 726 0323
FAX             +1 617 726 7422



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