[FieldTrip] Different way of calculating the covariance for LCM
jean-michel.badier at univmed.fr
Thu Mar 24 22:06:03 CET 2011
Thanks all for your explanations,
Le 24/03/11 14:01, jan-mathijs schoffelen a écrit :
> Dear JM et al,
>> see for example in version 20110222 ft_sourceanalysis from line 783
>> elseif Ntrials>1
>> % average the single-trial covariance matrices
>> Cy = reshape(mean(data.cov,1), [Nchans Nchans]);
>> % select the average ERF
>> avg = data.avg;
>> Nrepetitions = 1;
>> of course developers of fieldtrip would be the experts to comment on
> I am not sure what kind of comment you are looking for here. I think
> the previous discussion with much appreciated contributions by Yuval
> and Michael was quite conclusive.
> The difference between keeptrials='yes' and keeptrials='no' is that
> the single replicates are kept in memory when keeptrials='yes' whereas
> the covariance will be averaged (across the single trial covariances)
> if you specify keeptrials='no'. The default behaviour of
> sourceanalysis is to average across single replicate covariances
> before computing the spatial filters. This is done to ensure a
> relatively robust estimate of the covariance matrix. In general,
> covariances estimated from single trials are just very noisy and don't
> lead to good quality source reconstructions.
It is clear.
Part of my misunderstanding comes from a very fast overview of the code
and/or documentation and I did not realize that the option covariance =
'yes' would be enough to calculate the covariance over the wholes trials
and there is no need to specify keeptrials = 'yes'.
> In other words, if you would want to have a single trial estimate of
> the reconstructed source time series, you still need to compute the
> spatial filters based on a covariance averaged across multiple trials.
> Once you have the spatial filter, you can project the single trial
> sensor-level data through them.
> I believe this is most easily achieved by a 2-step procedure.
> tlck = ft_timelockanalysis(cfg, data); (with keeptrials = 'no')
> tlck2 = ft_timelockanalysis(cfg, data); (with keeptrials = 'yes')
> cfg = ;
> source = ft_sourceanalysis(cfg, tlck); (with keepfilters = 'yes')
> cfg.grid.filter = source.avg.filter;
> cfg.rawtrial = 'yes';
> source = ft_sourceanalysis(cfg, tlck2);
> This should (I think) give you the single trial time courses.
Ok it is an other step further
> But perhaps I am totally missing the point and this is not the
> information you were looking for.
I do not think so.
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
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