[FieldTrip] FEM using Simbio

Carsten Wolters carsten.wolters at uni-muenster.de
Thu Apr 7 09:22:10 CEST 2016


Dear Rajat,

if you want to use another meshing tool than VGRID, the 
element-node-ordering of SimBio-NeuroFEM
can be downloaded here:
http://www.sci.utah.edu/~wolters/SimBio/SimBioNeuroFEMElementNodeOrdering0001.pdf

For regular cubic elements and geometry-adapted cubic elements, please 
see the ordering
of x23.

I hope this will finally fully answer your question.

Best regards
     Carsten

Am 06.04.2016 um 16:03 schrieb Carsten Wolters:
> Dear Rajat,
>
> the element-node cards of SimBio-NeuroFEM need to follow certain 
> orientations (see www.simbio.de).
>
> If you do not want to struggle with meshing/ordering, use the 
> SimBio-VGRID mesher
> http://vgrid.simbio.de/
> that follows the required ordering of nodes. You might use this mesher 
> to produce 1mm geometry-adapted FEM meshes
> that show good overall performance, see
> http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf
> and
> http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf
> (latter was just accepted by NeuroImage).
>
> Best regards
>       Carsten
>
> Am 06.04.2016 um 15:10 schrieb Rajat Thomas:
>>
>> Dear all,
>>
>>
>> Has anyone used the FEM approach to Headmodels using Simbio recently?
>>
>>
>> If so, I get this error:
>>
>> "Elements have wrong orientation or are degenerated"
>>
>> Any ideas?
>>
>> cfg        = [];
>>
>> cfg.method ='simbio';
>>
>> cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows 
>> mesh.tissyelabel
>>
>> vol        = ft_prepare_headmodel(cfg, mesh);
>>
>>
>> And;
>>
>> ‚Äč
>>
>> disp(mesh)
>>             hex: [545883x8 double]
>>             pnt: [569722x3 double]
>>          labels: [545883x1 double]
>>          tissue: [545883x1 double]
>>     tissuelabel: {'csf'  'gray'  'scalp'  'skull'  'white'}
>>            unit: 'mm'
>>             cfg: [1x1 struct]
>>
>>
>> Any help would be highly appreciated.
>>
>> Rajat
>>
>>
>>
>>
>>
>>
>> Rajat Mani Thomas
>> Social Brain Lab
>> Netherlands Institute for Neuroscience
>> Amsterdam
>>
>>
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>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
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