dics method for coherence analysis
Rong, Feng (NIH/NIDCD) [V]
rongf at NIDCD.NIH.GOV
Mon Apr 30 18:47:16 CEST 2007
Jan-Mathijs,
Thanks for the comprehensive feedback. It is really helpful. I have
downloaded the new version and will try.
As you have predicted, this procedure is time-consuming. May I know what
can I do to revise the script so that I can save some time?
Best,
Feng
-----Original Message-----
From: Jan Mathijs Schoffelen [mailto:Jan.Schoffelen at FCDONDERS.RU.NL]
Sent: Saturday, April 28, 2007 11:32 AM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] dics method for coherence analysis
Dear Feng,
I see that you use the following configuration for your
frequency-analysis: channels with the dics method, following is my
script:
cfg = [];
cfg.method='mtmfft';
cfg.ouput='powandcsd';
cfg.keeptrials='yes';
cfg.taper='dpss';
cfg.tapsmofrq=4;
cfg.foilim =[8 12];
cfg.sgncmb = channelcombination({'MEG','MEG'},bldata.label);
blfreq = freqanalysis(cfg,bldata);
clear bldata
This in itself is OK, but given the fact that you use cfg.sgncmb instead
of cfg.channelcmb, you seem to use an old version of the freqanalysis
function (with old syntax, but newer versions are backward-compatible
with respect to these formulations). I'm not sure, but the tutorial
documentation on the fieldtrip-website, as well as the help content of
the respective m-file should contain the most up-to-date info about the
proper configuration terminology (provided you have the most up-to-date
version of fieldtrip). I would advise anyhow to get the latest version
(see below as well).
For the sourceanalysis you use the following configuration:
cfg = [];
cfg.grid = source2sparse(ldf); % Only consider gridpoints within head
volume
cfg.method = 'power';
cfg.refdip=refdip;
cfg.numrandomization = 100;
cfg.randomization = 'yes';
cfg.projectnoise = 'yes';
cfg.lambda = 0;
cfg.hdmfile = headmodel;
cfg.frequency = (foi(1)+foi(2))/2;
cfg.keepleadfield = 'no';
cfg.feedback = 'none';
[sourceRand] = sourceanalysis(cfg, eoifreq, blfreq);
I don't see why this shouldn't work but it is computationally very
demanding (as you might have noticed), because you recompute for each
randomization two volumes based on two sets of newly computed spatial
filters (for each of the shuffled conditions). Moreover, in your
comparison between the baseline and your epoch of interest (of your
observed data), you compute two sets of spatial filters as well. Our
experience however is, that source reconstruction is more robust (and
computationally less expensive, and interpretation-wise less
complicated) when you use common filters, i.e. collapsing the
cross-spectral densities for the baseline and the active condition (even
though there might be a clear difference between the conditions, e.g.
dipoles switching on or off).
Either way, you betray yourself using an old version of fieldtrip by
specifying cfg.method = 'power', which should be cfg.method = 'dics'.
cfg=[];
cfg.comparestat = 'relchange' ;
cfg.method = 'randomization' ;
cfg.parameter = 'coh' ;
cfg.approach = 'parametric';
sourcestat = sourcestatistics(cfg,sourceRand);
Again, this configuration is a relic from old times, and you should use
the function sourcedescriptives to get what you want (given your
preceding steps). I guess, that your variable sourceRand contains the
fields avgA, avgB, and trialA, and trialB. If you look into the code (of
the latest sourcedescriptives.m) you should be able to get an idea of
what's going on there.
I found in the output variable sourceRand subfield 'pow' and 'coh',
which one shall I use for statistical analysis? I assume it should be
'coh', then what does 'pow' stand for? Is it the psd with the target
frequency range for each virtual channel? Then will the 'pow' values be
different from the computation without specifying reference virtual
channel in the script?
Indeed, pow stands for the power at the specified voxels. This shouldn't
change when you use a reference channel.
Yours,
Jan-Mathijs
_______________________________________________ The aim of this list is
to facilitate the discussion between users of the FieldTrip toolbox, to
share experiences and to discuss new ideas for MEG and EEG analysis.
http://listserv.surfnet.nl/archives/fieldtrip.html
http://www.ru.nl/fcdonders/fieldtrip/
----------------------------------
The aim of this list is to facilitate the discussion between users of
the FieldTrip toolbox, to share experiences and to discuss new ideas for
MEG and EEG analysis.
http://listserv.surfnet.nl/archives/fieldtrip.html
http://www.ru.nl/fcdonders/fieldtrip/
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.
http://listserv.surfnet.nl/archives/fieldtrip.html
http://www.ru.nl/fcdonders/fieldtrip/
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