[FieldTrip] volume conduction model missing .mat

patrick cox phc5 at georgetown.edu
Thu Feb 9 23:15:30 CET 2012


Hi Akiko,

I had that same problem and also tried using the 'bemcp' which gave me a
vol.mat file that was all NaNs. I did not figure out how to solve the
problem in FT directly, but have been having some success creating the head
model in SPM and loading that into FeildTrip. The SPM manual helped me.

Hope that is somewhat helpful,
Pat

Patrick Cox
Prethesis Student
Lab For Computational Cognitive Science
Georgetown University Medical Center
3970 Reservoir Rd. NW
Washington, DC 20007

On Thu, Feb 9, 2012 at 5:04 PM, Akiko Ikkai <akiko.ikkai at gmail.com> 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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>
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