[FieldTrip] SCD and coherence analysis

Tue Dec 1 15:18:31 CET 2015

Dear Daria,

I did exactly this. 
The problem occurs afterwards, when I want to run ft_mvaranalysis on the data that result from ft_scalpcurrentdensity.
In the fieldtrip document it states, that the output data of  ft_scalpcurrentdensity has the same format as the input data.
When I run ft_mvaranalysis on the original data, everything works fine, but with the SCD data I get this error that the number of channels in sensor description is inconsistent.

Has anyone else experienced this problem?

Best,
Barbara

Am Dienstag, 01. Dezember 2015 12:00 CET, fieldtrip-request at science.ru.nl schrieb: 

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> Today's Topics:
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>    1. Re: power suppression during DICS beamforming ?
>       (Mait? Crespo Garc?a)
>    2. Re: SCD and coherence analysis (Daria Laptinskaya)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Mon, 30 Nov 2015 15:31:20 +0000 (UTC)
> From: Mait? Crespo Garc?a <maity_winky at yahoo.es>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] power suppression during DICS beamforming ?
> Message-ID:
> 	<1881724873.21184223.1448897480847.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Dear Fr?d?ri,
> maybe you have the solution already.
> In case not, could you explain how did you get the last two plots? Are spectra computed after averaging across all virtual channel spectra or you are representing the spectrum of the source with maximal power?
> Best,Maite
> 
> 
> 
>     El Jueves 26 de noviembre de 2015 13:55, Fr?d?ric Roux <f.roux at bcbl.eu> escribi?:
>  
> 
>  Dear all,
> 
> I am observing a counter-intuitive result after applying the spatial filters obtained from DICS beamforming to my MEG data.
> 
> The plot in the attachment summarizes the issue: The raw data shows a clear peak of activity at 10 Hz, however, after applying the spatial filter to the MEG data the spectrum of the virtual channels shows that power in this frequency band is reduced. The same also happens when I apply a spatial filter in the gamma range for power at 70 Hz to the raw MEG signals.
> 
> Is this something that falls out of the beamformer math due to the fact how the algorithm suppresses power at all locations by minimizing the noise level, or is there something wrong with my code? I (maybe naively) assumed that the results should come out the opposite. On the other hand, when plotting the noise normalized maps (NAI) of both the alpha and gamma beamformers the sources look quite accurate. Should I normalize with the level of noise first before plotting the spectrum to see the expected results (ie an upregulation of power instead of a downregulation of power)?
>  
> The code that I use to generate the figures is:
> 
> % 1) compute CSD matrix
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.output = 'powandcsd';
> cfg.foilim = [10 10];
> cfg.tapsmofrq = 2;
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> 
> [csd] = ft_freqanalysis(cfg,meg_data);
> 
> 
> % 2) compute DICS filter
> cfg = [];
> cfg.method = 'dics';
> cfg.grad = meg_data.grad;
> cfg.headmodel = vol;
> cfg.frequency = csd.freq;
> 
> cfg.dics.realfiter = 'yes';
> cfg.dics.fixedori = 'yes';
> 
> [alpha_filter]= ft_sourceanalysis(cfg,csd);
> 
> % 3) compute the virtual channel data
> 
> VC = meg_data;
> VC.trial = cell(1,length(meg_data.trial));
> VC.label = cell(1,length(alpha_filter.avg.pow));
> 
> for i = 1:length(VC.trial)
> ? for j = 1:length(VC.label)
> 
> ? ? ? VC.trial{i}(j,:) = alpha_filter{j}*meg_data.trial{i};
> ? ? ? VC.label(j) = {['virtual_channel',num2str(j)]};
> ? end;
> end;
> 
> % 4) compute the spectrum of the virtual channel data
> cfg = [];
> cfg.method = 'mtmfft';
> cfg.pad = 'maxperlen';
> cfg.taper = 'dpss';
> cfg.tapsmofrq = 1;
> cfg.foi = 0.1:100;
> 
> [pow] = ft_freqanalysis(cfg,VC);
> 
> 
> Any help or suggestions would be greatly appreciated.
> 
> Fred
> 
> --
> Fr?d?ric Roux
> Postdoctoral Scientist, Marie-Curie fellow
> BCBL. Basque Center on Cognition, Brain & Language.
> 
> f.roux at bcbl.eu
> Tel: +34 943 309 300 Ext 211
> Fax: +34 943 309 052
> 
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
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> ------------------------------
> 
> Message: 2
> Date: Tue, 1 Dec 2015 09:58:46 +0100
> From: Daria Laptinskaya <daria.laptinskaya at googlemail.com>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] SCD and coherence analysis
> Message-ID:
> 	<CADcxnnMJHQLRjginYZs4T5Mh5_1hdfW8qrs3HMwk=kq7jUGvfQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Barbara,
> 
> try this:
>  sens=ft_read_sens('GSN-HydroCel-257.sfp');
>  cfg=[];
>  cfg.elec=sens;
> 
> Hope it helps :-)
> Daria
> 
> 
> 
> 
> 
> 
> 2015-11-30 10:52 GMT+01:00 Barbara Schorr <barbara.schorr at uni-ulm.de>:
> 
> > Dear Fieltripers,
> >
> > I would like to do coherence analysis. I did a SCD analysis on my data
> > first ('finite' method), and want to run ft_mvaranalysis now. I get
> > the error
> >
> > Error using ft_datatype_sens (line 186)
> > inconsistent number of channels in sensor description
> >
> > As cfg.elec I use the GSN-HydroCel-257.sfp file which is included in
> > fieldtrip (my raw data set has 257 channels), but there are only 256
> > channels left after the SCD analysis. Can this cause the problem?
> >
> > Has anyone had this problem before and can provide a solution? I only
> > found one prior entry with this topic, but there was no final solution for
> > it.
> >
> >
> > Thanks and all the best,
> > Barbara
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
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