[Eeglablist] Fieldtrip Source-localization issues

[Makoto Miyakoshi]

Dear Ugo,

In this Wiki article, you see my past simulation reports using Fieldtrip.
https://sccn.ucsd.edu/wiki/Makoto's_preprocessing_pipeline#Does_a_broad_dipole_layer_produce_a_depth_bias_when_fitted_with_a_single_dipole.3F_.28For_190.2C000_page_views.2C_02.2F22.2F2022_added.2C_07.2F18.2F2022_updated.29
In separate email, I will send you all Matlab code to replicate it. I
cannot provide the completely detailed support on this, but I hope you can
find the tricks I used to make it work.

Makoto

On Sat, Apr 1, 2023 at 5:42 PM Bruzadin Nunes, Ugo via eeglablist <
eeglablist at sccn.ucsd.edu> wrote:

> Dear EEGLAB community,
>
> I know this is a fieldtrip problem, but I’m using the dipfit settings to
> source-localize frequency activity. I hope anyone can help me! I have two
> issues and one question.
>
>   1.  When I plot the source localization, the orientation is 90 degrees
> wrong. When using dipfit, the activity is correctly localized, but after
> doing all the dipfit processes – altered to plot frequency – frontal
> activity is being plot in the right ear. I thought something was wrong, so
> I artificially increased the activity at channel 12 (the anterior-most
> channel in my channel model, and the activity is coming from the ear in the
> eloreta.
>   2.  For some reason, fieldtrip won’t accept the atlas. The error says my
> axis are 10mm in diameter, and the atlas is 150mm in each direction. I’m
> reading the ROI_MNI_V4 atlas in.
>   3.  I am not sure the following code is localizing and plotting the
> correct frequencies. I don’t think it’s working, but I haven’t tested the
> frequencies yet since I haven’t fixed the headmodel orientation issue.
>
> Below is my code! Any feedback is welcome. Thank you so much in advance,
>
> Ugo
>
>
>
> Ugo Bruzadin Nunes, Ph.D. Candidate (he/him)
>
> Visiting Assistant Professor, Psychology
>
> Webster University
>
>
>
>
> Script/Code:
>
> EEG = pop_dipfit_settings( EEG, 'hdmfile',...
>
> 'C:\\GitHub\\eeglab\\plugins\\dipfit3.7\\standard_BEM\\standard_vol.mat','coordformat','MNI','mrifile',...
>
> 'C:\\GitHub\\eeglab\\plugins\\dipfit3.7\\standard_BEM\\standard_mri.mat','chanfile',...
>
> ['C:\\GitHub\\eeglab\\plugins\\dipfit3.7\\standard_BEM\\elec\\standard_1005.elc
> ' ],...
>     'coord_transform',...
>     [0.05476 -17.3653 -8.1318 0.075502 0.0031836 -1.5696 11.7138 12.7933
> 12.213] ,'chansel',[1:EEG.nbchan] );
>
>
> atlas = ft_read_atlas('ROI_MNI_V4.nii');
> %% compute spectral params (only need to be done once to get the right
> structures)
>
> EEGdata = eeglab2fieldtrip(EEG, 'preprocessing', 'none');
>
> cfg = [];
> cfg.method    = 'mtmfft';
> cfg.output    = 'powandcsd';
> cfg.tapsmofrq = 10;
> cfg.foilim    = range;
> cfg.pad = 'nextpow2';
> cfg.gpu = 'yes';
> fftdata = ft_freqanalysis(cfg, EEGdata);
>
> if ~isfield(EEG,'lor')
>     EEG.lor = struct();
> end
>
> EEG.fftdata = fftdata;
> %% read headmodel
>
> p = fileparts(which('eeglab'));
> if ~isfield(EEG.lor,'HM')
>     headmodel = load('-mat', EEG.dipfit.hdmfile);
>     headmodel = headmodel.vol;
>     EEG.lor.HM = headmodel;
> else
>     headmodel  = EEG.lor.HM;
> end
>
>     cfg                 = [];
>     cfg.elec            = fftdata.elec;
>     cfg.headmodel       = headmodel;
>     cfg.reducerank      = 2;
>     cfg.grid.resolution = 10;   % use a 3-D grid with a 1 cm resolution
>     cfg.grid.unit       = 'mm';
>     cfg.channel         = { 'all' };
>     cfg.parallel = 'yes';
>     cfg.solver = 'cg';
>
>     [grid] = ft_prepare_leadfield(cfg);
>     EEG.lor.grid = grid;
>
>
>     mri = load('-mat', EEG.dipfit.mrifile);
>     mri = ft_volumereslice([], mri.mri);
>     EEG.lor.mri = mri;
>
> %% loops per frequency then plots
> counter = 0;
>
> numfreq = size(frequencies,2);
>
> EEGlor = EEG;
>
> vol = load('-mat', EEG.dipfit.hdmfile);
>
> for i = 1:numfreq
>
>     atlas = ft_read_atlas('ROI_MNI_V4.nii');
>
>     freq = frequencies(i);
>
>     cfg              = struct(g.ft_sourceanalysis_params{:});
>     cfg.frequency    = freq;
>     cfg.grid         = grid;
>     cfg.headmodel    = headmodel;
>     cfg.method       = 'eloreta';
>     cfg.atlas        = atlas;
>     cfg.roi          = atlas.tissuelabel;
>     cfg.eloreta.projectnoise = 'yes';
>     cfg.eloreta.lambda   = 5;
>     cfg.gpu           = 'yes';
>
>     sourcemodel = ft_sourceanalysis(cfg, fftdata);
>
>     EEGlor.lor.cfg(numfreq) = cfg;
>     EEGlor.lor.freq(numfreq) = fftdata;
>     EEGlor.lor.source(numfreq) = sourcemodel;
> %% load MRI and INTERPOLATE
>
>     cfg                 = [];
>     cfg.downsample      = 2;
>     cfg.parameter       = 'avg.pow';
>     sourcemodel.oridimord = 'pos';
>     sourcemodel.momdimord = 'pos';
>     sourcemodel_int        = ft_sourceinterpolate(cfg2, sourcemodel , mri);
>     EEGlor.lor.source_int(numfreq) = sourcemodel_int;
>
> %% plot
>     cfg                 = [];
>     cfg.method          = 'ortho';
>     cfg.funparameter    = 'pow';
>     ft_sourceplot(cfg2,sourcemodel_int);
>     textsc(sprintf('eLoreta source localization of %d frequency
> power',freq), 'title');
>
> %
> end
>
>
>
>
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