[FieldTrip] spatial and temporal ICA after beamformer
Tyler Grummett
tyler.grummett at flinders.edu.au
Mon Apr 7 07:49:23 CEST 2014
Hello all,
Im really interested in calculating granger causality using method in connectivity extended (last bit of the document).
Specifically, I would like to compute the spectrally resolved granger connectivity.
How would one go about doing that?
Is it just be
cfg = [];
cfg.output = 'fourier';
cfg.method = 'mtmfft';
cfg.foilim = [5 100];
cfg.tapsmofrq = 5;
cfg.keeptrials = 'yes';
cfg.channel = {'visual' 'motor' 'EMGlft' 'EMGrgt'};
freq = ft_freqanalysis(cfg, combineddata);
cfg = [];
cfg.method = 'granger';
coherence = ft_connectivityanalysis(cfg, freq);
or would you need to calculate multivariate autoregressive coefficients.
Because my data keeps crashing when I try to running it.
cfg = [];
cfg.order = 5;
cfg.toolbox = 'bsmart';
mdata = ft_mvaranalysis( cfg, comp);
With an error of:
Index exceeds matrix dimensions.
Error in ft_mvaranalysis (line 321)
tmpcfg.toilim = [timeaxis(sample-floor(tfwin/2)) timeaxis(sample+ceil(tfwin/2)-1)];
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 kousik sarathy <sarathykousik at gmail.com>
Sent: Sunday, 6 April 2014 6:39 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] spatial and temporal ICA after beamformer
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<mailto: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<mailto:fieldtrip-bounces at science.ru.nl> <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of "Jörn M. Horschig" <jm.horschig at donders.ru.nl<mailto: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<mailto:fieldtrip-bounces at science.ru.nl>
> <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of jan-mathijs schoffelen
> <jan.schoffelen at donders.ru.nl<mailto: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> <mailto: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> <mailto:jm.horschig at donders.ru.nl<mailto:jm.horschig at donders.ru.nl>>
>> Tel: +31-(0)24-36-68493<tel:%2B31-%280%2924-36-68493>
>> 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> <mailto: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> <mailto:J.Schoffelen at donders.ru.nl<mailto:J.Schoffelen at donders.ru.nl>>
> Telephone: +31-24-3614793<tel:%2B31-24-3614793>
>
> http://www.hettaligebrein.nl
>
>
>
> _______________________________________________
> 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<tel:%2B31-%280%2924-36-68493>
Web: http://www.ru.nl/donders
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands
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fieldtrip at donders.ru.nl<mailto:fieldtrip at donders.ru.nl>
http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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