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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Feng,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I see that you use the following
configuration for your frequency-analysis: channels with the dics method,
following is my script:</span></font><o:p></o:p></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg = [];</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.method='mtmfft';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.ouput='powandcsd';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.keeptrials='yes';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.taper='dpss';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.tapsmofrq=4;</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.foilim =[8 12];</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.sgncmb =
channelcombination({'MEG','MEG'},bldata.label);</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>blfreq =
freqanalysis(cfg,bldata);</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>clear bldata</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>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).<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>For the
sourceanalysis you use the following configuration:<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg = [];</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.grid =
source2sparse(ldf); % Only consider gridpoints within head volume </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.method = 'power'; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.refdip=refdip; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.numrandomization = 100; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.randomization = 'yes'; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.projectnoise = 'yes'; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.lambda = 0; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.hdmfile = headmodel; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.frequency =
(foi(1)+foi(2))/2; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.keepleadfield = 'no';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.feedback = 'none'; </span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>[sourceRand] =
sourceanalysis(cfg, eoifreq, blfreq);</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>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). <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Either
way, you betray yourself using an old version of fieldtrip by specifying
cfg.method = ‘power’, which should be cfg.method = ‘dics’.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg=[];</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.comparestat =
'relchange' ;</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.method = 'randomization'
;</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.parameter = 'coh'
;</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>cfg.approach = 'parametric';</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>sourcestat =
sourcestatistics(cfg,sourceRand);</span></font><o:p></o:p></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face="Courier New"><span style='font-size:10.0pt;font-family:"Courier New";
color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>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. <o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New"'>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?<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Indeed,
pow stands for the power at the specified voxels. This shouldn’t change
when you use a reference channel.<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Yours,<o:p></o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='text-autospace:none'><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Jan-Mathijs<o:p></o:p></span></font></p>
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_______________________________________________
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/
<p>----------------------------------</p>
<p>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.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>