[FieldTrip] head model mat contains only NaN values

[gj]

Thanks for your reply, Simon.

I had plotted the segmentation and it seems to look fine (see attached), 
which makes me think that it's the meshing, but I tried a slew of 
methods and number of vertices but I can't get rid of the scalp planes 
internal to the brain.

Any advice on what to try greatly appreciated!
Gina

 > Dear Gina,
 >
 >  I see that the "scalp" has vertices that connect planes
 > internal to the brain (see images attached).
 >
 > I guess this is the reason why you get the NaN values. BEM needs
 > nested and sufficiently distant surfaces.

 > As I don't know the quality and sequence (T1, T2?) of your MRI I
 > suggest you to look at the segmentation to be sure that this is well 
done. With a good segmentation preparing the mesh is not a problem.

 > Bests,

 > Simon Homölle
 > PhD Candidate
 > Donders Institute for Brain, Cognition and Behaviour
 > Centre for Cognitive Neuroimaging
 > Radboud University Nijmegen
 > Phone: +31-(0)24-36-65059
 >
 > On 20/05/2016 10:51, gj wrote:
 >
 >
 > On 19/05/2016 18:36, gj wrote:
 >> Hi FieldTrippers,
 >>
 >> While trying to calculate a head model (FT ver.20160309), the head model
 >> contains only NaNs, and I get the following errors:
 >>
 >> ------------- beg error ------------
 >> Warning: NaN detected, trying once more with slightly different vertex
 >> positions
 >>  > In ft_prepare_headmodel (line 280)
 >> Warning: No conductivity is declared, assuming standard values
 >>  > In ft_headmodel_bemcp (line 79)
 >> In ft_prepare_headmodel (line 281)
 >>
 >> Warning: Matrix is singular, close to singular or badly scaled. Results
 >> may be inaccurate. RCOND = NaN.
 >>  > In ft_headmodel_bemcp (line 185)
 >>    In ft_prepare_headmodel (line 281)
 >> ------------- end error ------------
 >>
 >>
 >>
 >> This was what I ran:
 >>
 >> -----------
 >> smri = ft_read_mri(smrifn); % subject's own structural MRI
 >>
 >> cfg = [];
 >> mri.coordsys = 'MNI';
 >> cfg.brainthreshold = 0.5;
 >> cfg.output = {'brain','skull','scalp'};
 >> smri_seg = ft_volumesegment(cfg, smri);
 >>
 >> cfg=[];
 >> cfg.tissue={'brain','skull','scalp'};
 >> cfg.method = 'projectmesh';
 >> cfg.numvertices = [2400 1600 800];
 >> mesh_hd=ft_prepare_mesh(cfg,smri_seg);
 >>
 >> cfg = [];
 >> cfg.method = 'bemcp';
 >> headmodel = ft_prepare_headmodel(cfg, mesh_hd);
 >> -----------
 >>
 >> Not sure if this might be related, but we have head+neck MRIs and when I
 >> plot the meshes, I see that the "scalp" has vertices that connect planes
 >> internal to the brain (see images attached). I've tried different
 >> ft_prepare_mesh methods, different number of vertices....
 >>
 >> Thanks in advance for any advice!
 >> Gina
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