[FieldTrip] volume conduction model missing .mat

Gio Piantoni g.piantoni at nin.knaw.nl
Fri Feb 10 10:36:20 CET 2012


Hi Akiki and Patrick,

I agree with Nathan about segmentation problems. I had the same
problem when two of the three meshes intersected each other. Before
you run the forward model, you should check the segmentation (bnd)
using ft_plot_mesh.
ft_plot_mesh(bnd(1), 'facealpha', .5)
hold on
ft_plot_mesh(bnd(2), 'facecolor', 'r')
You will see that the two meshes intersect with each other. Depending
on how you created the meshes, you should fix the parameters in such a
way that they don't intersect. For example, ft_volumesegment has a
cfg.threshold option (you can check how the segmentation went with
ft_sourceplot) and ft_prepare_mesh_new has cfg.thresholdseg and
cfg.smoothseg.

I think that the meshes in SPM are computed on an (affine-transformed)
template and not on the anatomically derived meshes. The template is
more robust and that's why the two surfaces do not intersect.

In general, the segmentation depends on the quality of your MRIs and
you should really visually check the segmentation and meshes. When
those look ok, the BEM forward model usually works. Hope this helps.

Cheers,

Gio

On Fri, Feb 10, 2012 at 09:00, Nathan Weisz <nathanweisz at mac.com> wrote:
> 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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