[FieldTrip] Antw: Creating a head model using OPENMEEG - Intersecting mesh error

[Roey Schurr]

Dear Gregor,

Thank you so much for your helpful advice!
I will try this soon and report back to you all.

Best regards,
roey




On Mon, Jan 20, 2014 at 1:21 PM, Gregor Volberg <
Gregor.Volberg at psychologie.uni-regensburg.de> wrote:

>  Dear Roey,
>
> just two or three hints that might be helpful:
>
> I assume that the segmentation itself was successful; you can check this
> with ft_plot_vol for each of your tissues. Given that the segmentation is
> correct and the tissue borders are not intersecting, the error occurred
> during the mesh construction. I experienced that the number of triangles
> used for the mesh is often critical, with large numbers producing
> self-intersections. You could play around a bit with the number of
> triangles used for each compartement as specified in cfg.numvertices. Then,
> check the effect on the resulting volume. You do not need to call the
> ft_sourceanalysis for that; there is the funktion om_check_vol  in the
> external/openmeeg folder that checks the integrity of the volumes and
> reports intersections or self-intersections.
> During the leadfield computation, OpenMEEG writes some files to the hard
> disk for later use. If the meshes are incorrect, then the leadfield fails
> and no file can be written to the disk. So the error warning on the file
> identifiers is presumably secondary to the mesh issue.
>
> Kind regards,
> Gregor
>
>
>
>
> --
> Dr. rer. nat. Gregor Volberg <gregor.volberg at psychologie.uni-regensburg.de>
> ( mailto:gregor.volberg at psychologie.uni-regensburg.de<gregor.volberg at psychologie.uni-regensburg.de>)
> University of Regensburg
> Institute for Experimental Psychology
> 93040 Regensburg, Germany
> Tel: +49 941 943 3862
> Fax: +49 941 943 3233
> http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
> >>> Roey Schurr <roeysc at gmail.com> 19.01.2014 12:21 >>>
> Dear fieldtrippers,
>
> I am writing you after encountering an error using the OPENMEEG method for
> creating a head model, which I need for source reconstruction of EEG data
> (using 19 electrodes), e.g.:
>  ...
>  triangles 5018 and 5129 are intersecting
> triangles 5305 and 5781 are intersecting
> triangles 5879 and 5907 are intersecting
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!! WARNING !!!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> Mesh is self intersecting !
> ...
> 2 meshes are intersecting !
>
> It seems to be the same problem reported by Olivia about two years ago:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2012-March/004881.html
>
> In what follows I will describe the main steps in my script:
>
> 1) I create a segmented 'brain','skull','scalp' mri structure of the
> subject:
> cfg.output = {'brain','skull','scalp'};
> [bss_segmentedmri] = ft_volumesegment(cfg, mri);
>
> 2) I try using ft_sourceanalysis
>
> 3) which in turn tries to compute the leadfield using ft_compute_leadfield
> through ft_leadfield_openmeeg.
>
> yes this doesn't work, and I get the following error:
>  Error using fprintf
> Invalid file identifier. Use fopen to generate a valid file identifier.
>
> Error in ft_leadfield_openmeeg (line 112)
> fprintf(fid,'%s\t%.15f\t%.15f\t%.15f\n', sens.label{ii},
> sens.chanpos(ii,:));
>
>
> Since it is crucial that I use a realistic head model, do you have any
> suggestions?
>
> Any advice would be greatly appreciated!
> Thank you, and have a nice week,
>
> roey
>
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