[FieldTrip] spatial and temporal ICA after beamformer
kousik sarathy
sarathykousik at gmail.com
Sun Apr 6 11:09:24 CEST 2014
Hey Tyler,
Check out the "Computation of virtual MEG channels in source-space" in this
page (http://fieldtrip.fcdonders.nl/tutorial/connectivityextended).
It gives some hints on what x-y-z components are, how to collapse it and
use the filters.
--
Regards,
Kousik Sarathy, S
On Sun, Apr 6, 2014 at 7:43 AM, Tyler Grummett <
tyler.grummett at flinders.edu.au> wrote:
> Hi Jorn,
>
> I think the fundamental issue with this is that the spatial filter has
> three dimensions, each corresponding to either x y or z.
>
> I must admit I am confused at this point, because I dont know whether to
> choose x, y or z or somehow combine them or have them as additional
> channels.
>
> >> source_inside.avg.filter
>
> ans =
>
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> [3x123 double]
> etc....
>
> Currently I am chosing only the first dimension ie
> source_inside.avg.filter{ 1}( 1, :) and then multiplying that by the data.
>
> for j = 1:numel( source_inside.avg.filter),
> temp{ j} = source_inside.avg.filter{ j}( 1, :) *
> data.trial{ 1}(chans,:);
> virtual_chans.trial( j, :) = temp{ j};
> end
>
> to end up with:
>
> virtual_chans =
>
> label: {1x642 cell}
> time: {[1x19767 double]}
> trial: [642x19767 double]
>
> Like I said, I dont know what to with the 2nd and 3rd dimension filters.
>
> 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 "Jörn M. Horschig" <jm.horschig at donders.ru.nl>
> Sent: Saturday, 5 April 2014 7:21 PM
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] spatial and temporal ICA after beamformer
>
> Hi Tyler,
>
> > 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).
>
> Yep, you will (should) get 642 virtual channels, where each of these
> virtual channels correspond to the activity at the grid-point you
> specified when computing the spatial filter.
>
>
> Best,
> Jörn
>
>
> On 4/4/2014 4:19 PM, Tyler Grummett wrote:
> >
> > 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/
> >>>
> >>>
> >>> _______________________________________________
> >>> fieldtrip mailing list
> >>> fieldtrip at donders.ru.nl <mailto: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 <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
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > 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
> >
> >
> >
> > _______________________________________________
> > 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
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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