[FieldTrip] LCMV beamformer source reconstruction

["Jörn M. Horschig"]

Dear Alistair,

I am not quite sure whether I understand your request correctly, but you 
are looking for help to get the maximum activity per trial in your 
source reconstructed data? I guess your confusion arises because of the 
different subfields, so here a short explanation:

Every dipole has strengths in 3 directions (think of it as magnetic 
field strength in the x,y and z direction), this is stored in .mom
In order to get it down to one number instead of three, there are 
different possibilities, but what's roughly happening by default is that 
an SVD is computed then the principal direction is taken, i.e. the 
strongest of these three vectors. This is what you find back in .pow.  
The filter matrix is the filter per grid position to get from your 
sensor data to the source data. Noise is an approximation of the noise 
level per trial.

So, if you want to get the maximum activity, I would suggest to take [~, 
idx] = max(sourceDiff.avg.pow{i}), where idx then is the the grid 
position of maximal power. If you are interested in the maximum over 
e.g. the posterior part of the brain, you should limit your search. You 
can best do that by using sourceDiff.pos and an atlas.

If that does not answer your question, feel free to clarify your request ;)

Best,
Jörn

On 10/25/2012 10:40 PM, Alistair Vardy - 3ME wrote:
>
> Hi all,
>
> I trying to reconstruct the activity in a source using the LCMV 
> beamformer with EEG data. My code follows several examples that stop 
> at the source localization. Unfortunately, I am unable to reconstruct 
> the source.
>
> The data is a series of 198 button presses, self-paced. The two time 
> locked data sets are pre- and post-event windows. The data is filtered 
> in the beta band (13-30 Hz). There are 128 EEG channels, three of 
> which are excluded due to excessive noise. The data was re-referenced 
> to the common average. The source that provides the normalized 
> difference in power between the two time windows has a field avg with 
> subfields, filter, noise, pow, and mom:
>
> sourceDiff =
>
>         dim: [17 13 14]
>
>        time: [1x819 double]
>
>         pos: [3094x3 double]
>
>      inside: [1x1567 double]
>
>     outside: [1x1527 double]
>
>      method: 'average'
>
>         avg: [1x1 struct]
>
>         cfg: [1x1 struct]
>
> sourceDiff.avg
>
> ans =
>
>        pow: [1x3094 double]
>
>        mom: {1x3094 cell}
>
>      noise: [1x3094 double]
>
>     filter: {1x3094 cell}
>
> The moment entries are sized  3 x 819, the filter 3 x 65.
>
> I hope someone can help me with the code required to reconstruct the 
> source at the voxel with the largest power during the entire duration 
> of each trial. The code used to determine the source is below. MRI, 
> head model and leadfield were computed as well but are not included in 
> the code below.
>
> Kind regards,
>
> Alistair
>
> channel         = {'EEG', '-AFF1', '-AFZ', '-AF1'};
>
> cfg1                 = [];
>
> cfg1.keeptrials      = 'yes';
>
> cfg1.covariance      = 'yes';
>
> cfg1.channel         = channel;
>
> dataPre             = ft_redefinetrial(cfg1, data1FIC);
>
> timelock1           = ft_timelockanalysis(cfg1, dataPre);
>
> cfg2                 = [];
>
> cfg2.keeptrials      = 'yes';
>
> cfg2.covariance      = 'yes';
>
> cfg2.channel         = channel;
>
> dataPost            = ft_redefinetrial(cfg2, data2FIC);
>
> timelock2           = ft_timelockanalysis(cfg2, dataPost);
>
> %% Source analysis
>
> cfg = [];
>
> cfg.grid = grid;
>
> cfg.hdmfile = volname;
>
> cfg.elec = sens;
>
> cfg.vol = vol;
>
> cfg.method = 'lcmv';
>
> cfg.channel = channel;
>
> cfg.lcmv.keeptrials = 'yes';
>
> % cfg.lcmv.projectnoise = 'yes';
>
> cfg.lmvc.lambda     = '5%';
>
> cfg.lcmv.keepfilter = 'yes';
>
> [source1] = ft_sourceanalysis(cfg, timelock1);
>
> [source2] = ft_sourceanalysis(cfg, timelock2);
>
> sourceDiff = source2;
>
> sourceDiff.avg.pow = (source2.avg.pow - source1.avg.pow) ./ 
> source1.avg.pow;
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

Contact:
E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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