[FieldTrip] beamforming pipeline & comparing sources between groups of participants?

[Vladimir Litvak]

As the first thing, I would check whether your grid matches your head model
by plotting the two together (see ft_plot_headmodel, plot3). If you use EEG
BEM you should use cfg.inwardshift option when you make the grid to make
sure that all your grid points are at least 6mm away from the inner skull
surface. If these do not help, there are a few other potential problems
(like it usually makes sense to look at the difference between two
conditions or baseline and activation because of the depth bias) but I
leave it to the FT crowd to guide you further.

Best,

Vladimir

On Wed, May 1, 2019 at 3:48 PM Ioanna Zioga <i.zioga at qmul.ac.uk> wrote:

> Dear Vladimir,
>
>
> For anyone interested, I used SPM to make a template head model which I'm
> going to use to do beamforming in FT.
>
> I have queries with regards to the source analysis pipeline I'm using in
> FT, as the results I get don't seem right.
>
>
> Vladimir, following our previous email exchange (and thanks to your
> suggestions), I have now managed to compute the lead field matrix in FT (by
> removing eeglab and fieldtrip directories from the path, and adding spm's).
>
>
> I want to contrast the sources of two groups of participants (high- vs.
> low-learners) in two frequency bands (low: 2.5-4.5 Hz; high: 12-32 Hz),
> from 0.20-1 sec post stimulus onset.
>
>
> Here is my pipeline:
>
>
> % Calculate the cross spectral density matrix (e.g., for the 12-32 Hz frequency
> band)
>
> cfg                    = [];
> cfg.method     = 'mtmfft';
> cfg.output       = 'powandcsd';
> cfg.foilim         = [22 22];
> cfg.taper          = 'dpss';
> cfg.tapsmofrq = 10;
> cfg.keeptrials   = 'yes';
> cfg.keeptapers = 'no';
> cfg.toi                = 0.6;
> cfg.t_ftimwin   = 0.4;
> freq                    = ft_freqanalysis(cfg, EEGft);
>
> % Source analysis using DICS beamformer
> cfg                      = [];
> cfg.headmodel = vol1;
> cfg.grad             = sens1;
> cfg.senstype     = 'eeg';
> cfg.grid              = grid;
> cfg.method       = 'dics';
> cfg.frequency   = [12 32];
> cfg.latency        = [0.2 1];
> cfg.dics.projectnoise   = 'yes';
> cfg.dics.lambda            = 0;
> cfg.dics.keepfilter        = 'yes';
> cfg.dics.realfilter          = 'yes';
> sourceA                         = ft_sourceanalysis(cfg, freq);
>
> % Plot sources
> cfg                           = [];
> cfg.method            = 'slice';
> cfg.funparameter = 'pow';
> ft_sourceplot(cfg, sourceA);
>
> => The source plots look weird though - they scale from 0 to x10^45, and
> are totally black.
>
>
> 1) Am I doing something wrong in the freqanalysis or the sourceanalysis?
>
> 2) Do I need to do the ft_sourceanalysis separately for each participant?
>
> 3) Is there a way to average the results of the source analysis over
> groups of participants?
>
> 4) Could you give any direction/resource on how to statistically compare
> the sources of different groups?
>
>
> As you all know this is a very exciting but also not trivial analysis..
> so I'd be extremely grateful for any help at this point, it'd be very much
> appreciated! Thanks so much in advance!
>
>
> Best,
>
> Ioanna
>
>
>
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https://doi.org/10.1371/journal.pcbi.1002202