[FieldTrip] FEM using Simbio

Johannes Vorwerk j.vorwerk at uni-muenster.de
Thu Apr 7 14:25:42 CEST 2016


Hi,

this question was already answered in this thread

http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html <http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html>

If ft_volumereslice is not applied before the mesh generation, the afterwards applied transformation might flip the directions of the mesh, leading to the described error.

Best,
	Johannes

> Am 06.04.2016 um 16:03 schrieb Carsten Wolters <carsten.wolters at uni-muenster.de>:
> 
> Dear Rajat,
> 
> the element-node cards of SimBio-NeuroFEM need to follow certain orientations (see www.simbio.de <http://www.simbio.de/>).
> 
> If you do not want to struggle with meshing/ordering, use the SimBio-VGRID mesher 
> http://vgrid.simbio.de/ <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 <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 <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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