[Mne_analysis] again mne_surf2_bem problem

[Matti Hamalainen]

Hi Elisabeth,

On Mar 10, 2009, at 7:39 AM, Elisabeth Fonteneau wrote:

>
> Dear all,
>
> I am in the process of aligning MRI-MEG, and for some of my  
> participants (3 out of 22), I failed to create the output file with  
> mne_surf2bem
>
> below is the message error
>
> *****************
> Running mne_surf2bem on l18
> mne_surf2bem version 1.4 compiled at Apr  5 2007 16:04:15
> input  file #   1 : /imaging/ef02/lexpro/subject/0327/surf/ 
> lh.smseghead / id = 4 / sigma N/A
> output file       : /imaging/ef02/lexpro/subject/0327/bem/0327- 
> head.fif
> New quad file : nvert = 193696 nquad = 193927
>       Triangle and vertex normals and neighboring triangles...[done]
>       Vertex neighbors...Too many neighbors for vertex 94524.
> ******************
>
> One of my colleague here told me that it happened also for her and  
> then she tried to re-run the mkheadsurf command
> and then the mne_surf2_bem
>
> I tryied that with no luck
> I also try to re-run the last step of recon-all -autorecon3 on  
> freesurfer to be sure that the output was not corrupted, again no  
> success
>
> Any advices would be appreciated

MNE software is much quite picky about the correct topology of the  
surfaces and the mkheadsurf script is not so careful about it because  
tksurfer can work around these defects much better than MNE can.

A solution to this problem is to get the latest MNE Matlab toolbox  
from the download web site. There is a function mne_reduce_surface,  
which can reduce the number of triangles on a surface and in the  
process the topology defects are (often) fixed. I have used 20000  
triangles on the reduced surface with good results:

mne_reduce_surface('lh.smseghead',20000,'lh.smseghead.red');

Naturally, you need to be in the surf directory of the subject to do  
this and use the 'red' surface as input to mne_reduce_surface.

- 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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