[FieldTrip] spatial and temporal ICA after beamformer

[Tyler Grummett]

Hello All,


So once I have calculated the preprocessing data, timelock data, headmodel, lead field and source.


I have the following code to create virtual EEG channels of data (similar to the tutorial):

            % find sensor names and indices
            chans = ft_channelselection( 'EEG', data.label);
            chans = match_str( data.label, chans);

            % compute virtual channels
            virtual_chans = [];
            virtual_chans.label = data.label;
            virtual_chans.time = data.time;
            virtual_chans.trial = source.avg.filter{ 1} * timelock.trial{ 1}(chans,:);

However as I have 642 source.avg.filter, which filter do I chose? Or do I calculate EEG channels for each voxel I landed with (I only had one trial).

Btw, the source was calculated with the following code:

            cfg              = [];
            cfg.method       = 'lcmv';
            cfg.grid.inside  = grid.inside;
            cfg.grid.outside = [];
            cfg.vol          = vol;
            cfg.keepfilter = 'yes';
            source = ft_sourceanalysis( cfg, timelock);

Thankyou for all the help you have provided me thus far.

tyler







*************************

Tyler Grummett ( BBSc, BSc(Hons I))
PhD Candidate
Brain Signals Laboratory
Flinders University
Rm 5A301
Ext 66124
________________________________
From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl> on behalf of jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
Sent: Friday, 4 April 2014 7:02 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] spatial and temporal ICA after beamformer

Hi all,

Allow me to chime in here. As I understand it Tyler wants to do ICA on the output of an LCMV beamformer. This is in general allowed, and can be done if you know how to handle the data. In Fieldtrip there is no pre-cooked way of doing it. What you need is to fool ft_componentanalysis into believing that your source reconstructed data is of the type 'raw'. To get started, you can have a look at http://fieldtrip.fcdonders.nl/tutorial/shared/virtual_sensors. In this particular tutorial, only a few 'virtual channels' are created. You probably want many of those, defined on a 3D grid. The only constraint there is probably the amount of RAM on your computer. Note that you want to do (and will do) temporal ICA in this case. Also, note that you probably should pre-PCA your data (this will be a parameter in the specs for the options for the ICA algorithm you are going to use). If you want to apply the ICA algorithm on amplitude envelope timeseries of band-limited activity, rumour has it that the fastica method works quite well.

Cheers,
Jan-Mathijs

On Apr 4, 2014, at 10:17 AM, Jörn M. Horschig wrote:

Hi Tyler,

sorry, I realized too late that you want to use LCMV on ICA components - mostly because your approach resulted in many different erros ;). Afaik, it is not possible to use beamforming on ICA components. On Wednesday we talked about this in our weekly FieldTrip meeting and identified some occasions where FieldTrip is not handling IC-data well. This can lead to unexpected results and missing warnings or errors. However, you can use dipole modelling (like EEGlab does) or MNE if you want to. These should work with ICs.

Any reason why you want to use LCMV on ICs? In theory, both steps constitute a spatial filter, so you can try to be smart and first to LCMV on all your channel level data, and then apply the LCMV spatial filter on the individual backprojected ICs. Somewhat a complicated procedure, but I think it would work?

Best,
Jörn



On 4/4/2014 7:23 AM, Tyler Grummett wrote:

Hello fieldtrip,


I was wondering whether it was possible in the fieldtrip toolbox to run a spatial and temporal ICA on data after it has been run through ft_sourceanalysis (We can a LCMV beamformer on EEG data that had been timelocked).


Currently it is saying that I need raw data for it to be processed.


Tyler


*************************

/Tyler Grummett ( BBSc, BSc(Hons I))/
/PhD Candidate/
/Brain Signals Laboratory/
/Flinders University/
/Rm 5A301/
/Ext 66124/


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--
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<mailto: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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Jan-Mathijs Schoffelen, MD PhD

Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl<mailto:J.Schoffelen at donders.ru.nl>
Telephone: +31-24-3614793

http://www.hettaligebrein.nl

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