[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;
>>
>>
>>
>> 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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>
>
>
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