[FieldTrip] volume conduction model missing .mat

[Nathan Weisz]

Hi Akiki,

I am not a headmodel expert. 
but looking at the output message, it seems your segementation did not go too well (see the "intersect" message). my intuition is then then the next temporary file *.ama is not created and ft_prepare_bemmodel then simply says ciao.

perhaps you want to check / redo the segmentation?

good luck,
nathan


On 09.02.2012, at 23:04, Akiko Ikkai wrote:

> Hi,
> 
> I'm trying to create a volume conduction model for my EEG study based on anatomical MRI, and having trouble with ft_prepare_bemmodel
> 
> when I run 
> cfg                = [];
> cfg.tissue         = [7 4 1]; % value for brain, skull, and scalp
> cfg.conductivity   = [1 1/80 1]*.33; % after standard_BEM.zip data
> cfg.isolatedsource = true;
> cfg.method         = 'dipoli'; 
> cfg.sourceunits = 'mm';
> cfg.mriunits = 'mm';
> vol = ft_prepare_bemmodel(cfg, seg4bem);
> 
> I get the following error message while ft_prepare_bemmodel is running: 
> 
> Fatal error in dipoli:  interface /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri and /private/tmp/tp313c9a32_1991_4df6_a404_8efc41b6302e.tri intersect 
>  at vertex 1402 of /private/tmp/tpd8a04422_e19e_4978_9b9b_56d1f2696492.tri
> 
> Warning: an error ocurred while running dipoli 
> > In dipoli at 94
>   In ft_prepare_bemmodel at 112
> Error using ==> fread
> Invalid file identifier.  Use fopen to generate a valid file identifier.
> Warning: File '/private/tmp/tp0c0779e3_a657_4ca5_b9e1_845f41e9574a.ama' not
> found. 
> > In dipoli at 102
>   In ft_prepare_bemmodel at 112
> 
> 
> and the output vol is missing .mat, which causes an error during ft_sourceanalysis. 
> >> vol
> vol = 
>             cond: [0.3300 0.0041 0.3300]
>              bnd: [1x3 struct]
>           source: 3
>     skin_surface: 3
>             skin: 1
>             type: 'dipoli'
> 
> Does anyone know how to correct for "fatal error" so that ft_prepare_bemmodel creates the correct volume conduction model? I opened .tri file and removed line 1402, but got the same results.
> 
> Thanks in advance! Akiko  
> 
> -- 
> Akiko Ikkai, Ph.D. 
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
> 
> 
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