[FieldTrip] Source analysis of EEG oscillatory activity/ NaN values in the leadfield matrices

[Tyler Grummett]

I don't know if this advice is at all correct but I usually get that error if I've got a relatively small number of electrodes (~29) or a small data set (30 seconds of data).

Does that sound familiar?

I usually clear all and run it again and it will work eventually haha

Sent from my iPad

On 19 Jul 2014, at 8:01 am, "Azadeh Hajihosseini" <azadehh at uvic.ca<mailto:azadehh at uvic.ca>> wrote:

Hello FieldTrip members,

I am trying to source localize EEG oscillatory activity and have a few problems in constructing the forward model and eventually running the source analysis. I think the problems are related to each other. Here is what happens:

1- When I run the source analysis, I get this error message:

??? Error using ==> svd
Input to SVD must not contain NaN or Inf.

Error in ==> beamformer_dics>pinv at 650
  [U,S,V] = svd(A,0);

Error in ==> beamformer_dics at 339
        filt = pinv(lf' * invCf * lf) * lf' * invCf;              % Gross eqn. 3, use PINV/SVD to cover rank
        deficient leadfield

Error in ==> ft_sourceanalysis at 572
      dip(i) = beamformer_dics(grid, sens, vol, [],  squeeze(Cf(i,:,:)), optarg{:});

Error in ==> test_sourceanalysis at 12
sourceTF = ft_sourceanalysis(cfg, data_TF);

2- Checking the leadfiled matrices, I see there are a lot of NaN values.
3- When I visualize the head model I have created, the plots don't look right. The third field, vol.bnd(3), which is supposed to be the brain tissue, looks like a cube.

And here are my code lines:

% CONSTRUCT A HEAD MODEL from the template mri in FT's template/anatomy
mri = ft_read_mri('template\anatomy\single_subj_T1.nii');
mri.coordsys = 'spm';

%SEGMENTATION:
cfg           = [];
cfg.output    = {'brain','skull','scalp'};
segmentedmri_template  = ft_volumesegment(cfg, mri); % Using NOT resliced data
save segmentedmri_template segmentedmri_template


%CREATE THE HEAD MODEL (VOLUME CONDUCTION MODEL)
cfg        = [];
cfg.method ='bemcp';
cfg.tissue ={'brain','skull','scalp'};
% cfg.outputfile = 'template_';
vol        = ft_prepare_headmodel(cfg, segmentedmri_template);
save vol vol

%Visualization of the head model
figure;
ft_plot_mesh(vol.bnd(1),'facecolor','none'); %scalp
figure;
ft_plot_mesh(vol.bnd(2),'facecolor','none'); %skull
figure;
ft_plot_mesh(vol.bnd(3),'facecolor','none'); %brain This one looks like a cube

% Align electrodes
elec = ft_read_sens('template\electrode\standard_1020.elc');
% load volume conduction model
% load vol;

%interactive allignment
cfg           = [];
cfg.method    = 'interactive';
cfg.elec      = elec;
cfg.headshape = vol.bnd(1);
elec_aligned  = ft_electroderealign(cfg);

save elec_aligned elec_aligned

% Prepare leadfield
load data_TF
cfg=[];
cfg.vol           = vol; %structure with volume conduction model
cfg.elec          = elec_aligned;%structure with electrode positions
[grid] = ft_prepare_leadfield(cfg, data_TF);

% Find source
cfg              = [];
cfg.method       = 'dics';
cfg.frequency    = 25;
cfg.grid         = grid;
cfg.vol          = vol;
cfg.latency       = .4;%single number in seconds, for time-frequency analysis
cfg.dics.projectnoise = 'yes';
cfg.dics.lambda       = 0;
cfg.elec          = elec_aligned;%structure with electrode positions

sourceTF = ft_sourceanalysis(cfg, data_TF);

I am using wavelet with a fourier output for the time-frequency analysis (data_TF). Do you have any idea what might be wrong here?

I also have a more general question. What type of time-frequency data can be input to source analysis? ft_freqanalysis provides power, power and cross-spectra, and complex fourier outputs. But is source-localization based on only power data correct? I couldn't find any explanations regarding this issue in the tutorial.

I look forward to hearing from anyone who might have ideas about any of these issues!

Many thanks,

--
Azadeh HajiHosseini

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