[FieldTrip] Question on bemcp's and openmeeg's vol.mat

[Lilla.Magyari at mpi.nl]

Hi Kidist,

Have you checked if the segmentation is OK? The segmentation for a BEM
model should contain binary masks of the brain, skull and skin tissues.
But these tissues should not overlap and they should form a closed shape
without empty space between. One way to check this, if you plot the
different tissue-types in the same image. For this, you can convert your
binary segmentation to an indexed type segmentation.

Here is a FAQ which explains how to do that:

http://fieldtrip.fcdonders.nl/faq/how_is_the_segmentation_defined#conversion_between_probabilistic_and_indexed_representations

Best,
Lilla


> Hi Lilla,
>
> Thank you for your reply.
>
> The openmeeg works well for the mri (subject01.mri) that is used in the
> fieldtrip tutorial.
>
> But the error comes when I use my subject's mri whose anatomy is
> 256*256*192. I have also tried to use mri = ft_volumereslice(cfg,mri)
> thinking that the error might be due to the inequality of the size of the
> anatomical volume into each direction.
>
> Kidist
>
>
>> hi Kidist,
>>
>> I am wondering if you have installed openmeeg properly. Here is a site
>> to
>> explain it:
>> http://fieldtrip.fcdonders.nl/faq/how_can_i_use_openmeeg_for_forward_modelling
>>
>> Have you followed this?
>>
>> Lilla
>>
>>
>>
>>> Hi,
>>>
>>> I am working with the combined EEG and MEG recording and would like to
>>> do
>>> the forward model for the EEG.
>>>
>>> So I was trying to use the 'bemcp' and 'openmeeg' as am working on
>>> windows
>>> platform. I have the anatomy of my subject (DICOM file stacked and
>>> cleaned
>>> using SPM).
>>>
>>> When I try to use openmeeg, vol.mat is missing from the vol structure
>>> giving an error message om_minverser.exe doesn't function anymore.
>>>
>>> When I try to use 'bemcp', vol.mat contains all NaNs which resulted
>>> from
>>> the c12 and c21 matrices being not a square matrix which makes the
>>> inverse
>>> to be non-existent and also those matrices consists a large number of
>>> 'Inf' entries.
>>>
>>> Like it was mentioned on one of the forums, the error might come when
>>> the
>>> meshes are generated. I was able to find the index of the vertices from
>>> the Cij matrix, but I couldn't find the actual relation to the
>>> vol.bnd(i).pnt and vol.bnd(i).tri matrices, 'i' representing either
>>> brain,
>>> skull or scalp.
>>>
>>> Here are all the steps that I have followed.
>>>
>>> % reading MRI
>>> mri = ft_read_mri('msGAP724534-0002-00001-000192-01.img');
>>>
>>> % segment the brain
>>> cfg = [];
>>> cfg.output = {'brain', 'skull', 'scalp'};
>>> cfg.coordsys = ''; % here I use the RAS coordsys and for the origin
>>> 'i'-
>>> interauricular
>>> segmentedmri = ft_volumesegment(cfg, mri);
>>> segmentedmri.anatomy = mri.anatomy;
>>>
>>> % prepare mesh
>>> cfg = [];
>>> cfg.tissue = {'brain','skull', 'scalp'};
>>> cfg.numvertices = [3000 2000 1000];
>>> cfg.transform = segmentedmri.transform;
>>> bnd = ft_prepare_mesh(cfg, segmentedmri);
>>>
>>> % create head model
>>> cfg = [];
>>> cfg.method = 'openmeeg';
>>> cfg.conductivity = [0.33 0.0041 0.33];
>>> vol = ft_prepare_headmodel(cfg, bnd);
>>>
>>> figure;
>>> ft_plot_mesh(vol.bnd(1),'facecolor','none'); %brain
>>> figure;
>>> ft_plot_mesh(vol.bnd(2),'facecolor','none'); %skull
>>> figure;
>>> ft_plot_mesh(vol.bnd(3),'facecolor','none'); %scalp
>>>
>>> Any help?
>>>
>>> Thanks.
>>> Kidist
>>>
>>>
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>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
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>>>
>>
>>
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>
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