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<font size="+1">Dear Monika,<br>
<br>
Indeed, Coh cannot be calculated on single trials, it requires
averaging of the cross-spectrum over (some) trials. Customarily,
people average ALL trials recorded in a subject and end up with
just only one coherence measurement for this subject. Then
obviously stats cannot be run on the individual level and only a
group analysis can be done (e.g., you have 20 subjects, they give
you 20 coherence values and you run your stats on those 20
values). Does this mean that coherence can be analyzed only on a
group level? Perhaps not. <br>
<br>
I suggest the following approach. Coherence can be considered as a
'sample', or 'population', statistic (similar to means, medians,
variances etc, which are calculated from a set of data points).
Methods of estimating statistical properties of those 'population'
measures are well known, they are based on resampling, jackknifing
and bootstrapping. Simply put, you can take a SUBSET of your
trials (e.g., selecting randomly 50 trials from all 100 trials in
a particular subject) and calculate coherence over those 50
selected trials. Then repeat the process of random selection (with
replacement, as in jackknifing) a certain number of times (N) and
you would have a set of N 'sample' coherences for this subject.
Then you can run your stats on those 'sample' coherences for this
particular subject thus achieving your goal of the individual
subject analysis.<br>
<br>
Any feedback from the fellows Fieldtripers about this approach?<br>
<br>
Thank you,<br>
<br>
Andrei Medvedev<br>
Georgetown University.<br>
<br>
</font><br>
On 11/27/2012 6:49 AM, jan-mathijs schoffelen wrote:
<blockquote
cite="mid:D33AD4F1-279E-40F0-AACF-34E3A4D9A5AB@donders.ru.nl"
type="cite">Dear Monika,
<div><br>
</div>
<div>It may have escaped your attention while digging to the
previous posts, but the question has been raised (and answered
;-) ) before. Just for the very very last time I will make the
following statement:</div>
<div><br>
</div>
<div><font class="Apple-style-span" face="Chalkboard"><span
class="Apple-style-span" style="font-size: 36px;"><b><font
class="Apple-style-span" color="#ce71fe">Single </font><font
class="Apple-style-span" color="#e04b3e">trial</font><font
class="Apple-style-span" color="#ce71fe"> </font><font
class="Apple-style-span" color="#667cfd">coherence</font><font
class="Apple-style-span" color="#ce71fe"> </font><font
class="Apple-style-span" color="#9afa67">estimates</font><font
class="Apple-style-span" color="#ce71fe"> </font><font
class="Apple-style-span" color="#df3c73">cannot</font><font
class="Apple-style-span" color="#ce71fe"> </font><font
class="Apple-style-span" color="#0d0103">be</font><font
class="Apple-style-span" color="#ce71fe"> computed!</font></b></span></font></div>
<div><font class="Apple-style-span" color="#ce71fe"
face="Chalkboard"><span class="Apple-style-span"
style="font-size: 36px;"><b><br>
</b></span></font></div>
<div>Perhaps the font size and color will make it memorable ;-).
This is due to the simple fact that coherence is defined across
observations. If you have just a single observation, due to the
mathematics involved, the coherence value will be 1.</div>
<div>Since you want to do group analysis, I think you really
should compute the coherence per condition, where each condition
should consist of a sufficient number of trials. Assuming that
the time domain data is organised such that you have all trials
(irrespective of the condition) in a single structure, do
something like this.</div>
<div><br>
</div>
<div>for each subject</div>
<div> cfg = [];</div>
<div> cfg.output = 'fourier';</div>
<div> cfg.method = 'mtmfft'/'mtmconvol'</div>
<div> cfg.keeptrials = 'yes';</div>
<div> ...</div>
<div> freq = ft_freqanalysis(cfg, data);</div>
<div><br>
</div>
<div> cfg = [];</div>
<div> cfg.channelcmb = {something here}</div>
<div> cfg.trials = [indices of trials belonging to condition 1];</div>
<div> coh1 = ft_connectivityanalysis(cfg, freq); % compute
coherence across the trials for condition 1</div>
<div> cfg.trials = [indices of trials belonging to condition 2];</div>
<div> coh2 = ft_connectivityanalysis(cfg, freq); % compute
coherence across the trials for condition 2</div>
<div>end</div>
<div><br>
</div>
<div><br>
</div>
<div>Good luck,</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
<div>
<div>On Nov 27, 2012, at 12:25 PM, Monika Mellem wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Thank you Sheraz and Jan-Mathijs for
your help! <br>
Sheraz, if you do have the code to keep single-trial
coherence estimates, I would much appreciate it if you could
pass it along (<a moz-do-not-send="true"
href="mailto:monikamellem@gmail.com">monikamellem@gmail.com</a>).
<br>
And Jan-Mathijs, okay, the necessary statistics make sense,
and I will z-transform the data too. But as far as you
know, is there no implementation already in Fieldtrip to
keep the single-trial coherence estimates? I assumed
setting cfg.keeptrials = 'yes' would do this, but is there
something else I'm missing as this doesn't seem to work? I
would prefer to try what Fieldtrip has implemented first
before integrating Sheraz's code into my version of
Fieldtrip.<br>
<br>
Thank you very much!<br>
Monika<br>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Nov 27, 2012 at 3:14 AM,
jan-mathijs schoffelen <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jan.schoffelen@donders.ru.nl"
target="_blank">jan.schoffelen@donders.ru.nl</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt
0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div style="word-wrap: break-word;">Hi Monika,
<div><br>
</div>
<div>If you want to test across subjects in a
paired fashion, you can use depsamplesT. Your
dependent variable then should contain for each
subject and condition the coherence (which of
course should be estimated across all trials
belonging to that condition). Even better would be
to perform a so-called Z-transformation to the
data. For some inspiration you could have a look
at the following paper: <a moz-do-not-send="true"
href="http://www.jneurosci.org/content/31/18/6750.long" target="_blank">http://www.jneurosci.org/content/31/18/6750.long</a></div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
<div>
<div>
<div class="h5">
<div>On Nov 27, 2012, at 12:22 AM, Monika
Mellem wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
Dear Fieldtrippers,<br>
<br>
I am trying to calculate coherence
estimates on individual trials of our EEG
data and then want to perform a
within-subjects statistical test, but so
far I have not been able to figure out how
to do this. I am able to calculate
coherence for our 22 subjects and then
perform statistics on the grand average,
so I understand the basic usage of these
functions (ft_freqanalysis,
ft_connectivityanalysis,
ft_freqgrandaverage, ft_freqstatistics).
But now we want to do statistical testing
on individual subjects. Is it possible to
keep coherence for individual trials in
Fieldtrip as they seem necessary for this
statistical analysis?<br>
<br>
I am setting cfg.keeptrials = 'yes' as an
input to ft_freqanalysis, and get the
cross-spectra of individual trials (I also
tried computing the fourier spectra but it
made no difference in the following
step). However, when computing the
coherence in ft_connectivityanalysis,
Fieldtrip averages over the trials. Is
there a way to output coherence for
individual trials instead? Please see the
full cfg structure settings below.<br>
<br>
Also, I did look into the option of
cfg.statistic = 'indepsamplesZcoh' as an
input to ft_freqstatistics since previous
posts suggested this was for single
subject coherence statistics, but our data
is paired as the same stimulus appears in
the 2 conditions we are comparing. Is
there a paired test for single subject
coherence testing, or should we use
cfg.statistic = 'depsamplesT'?<br>
<br>
Many thanks for any suggestions you may
have!<br>
Monika<br>
________________
<div>
<div><img moz-do-not-send="true"
src="https://mail.google.com/mail/u/0/images/cleardot.gif">Monika
Mellem<br>
</div>
</div>
<span><font color="#888888"><span><font
color="#888888">PhD Candidate<br>
Interdisciplinary Program in
Neuroscience<br>
Georgetown University<br>
Washington, DC<br>
<a moz-do-not-send="true"
href="mailto:msm79@georgetown.edu"
target="_blank">msm79@georgetown.edu</a><br>
<a moz-do-not-send="true"
href="tel:202-687-2687"
value="+12026872687"
target="_blank">202-687-2687</a></font></span>
</font></span><br>
<br>
***********************************************************************<br>
cfg settings for ft_freqanalysis and
ft_connectivityanalysis<br>
***********************************************************************<br>
cfg = [];<br>
cfg.prestim = -0.5; <br>
cfg.poststim = 1.5; <br>
cfg.foilim = [2 30];<br>
cfg.freqrange = 'low';<br>
% cfg.output = 'fourier';<br>
cfg.output = 'powandcsd';<br>
cfg.method = 'mtmconvol';<br>
cfg.keeptrials = 'yes'; <br>
cfg.channel = {'all'}; <br>
cfg.channelcmb = {refchan 'all'}; <br>
<br>
cfgcoh=[];<br>
cfgcoh.channelcmb = cfg.channelcmb;<br>
cfgcoh.method = 'coh';<br>
<br>
v = genvarname(['CRSP_' condition
'_low']);<br>
eval([v '= ft_multitaper_powcoh_EGI(cfg,
data);']); %Wrapper around
ft_freqanalysis <br>
<br>
w = genvarname(['COH_' condition '_low']);<br>
eval([w '= ft_connectivityanalysis(cfgcoh,
' v ');']);<br>
<br>
<br>
</div>
</div>
<div class="im">
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</blockquote>
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<br>
<div>
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<div style="word-wrap: break-word;">
<span style="text-indent: 0px;
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<div>Jan-Mathijs
Schoffelen, MD PhD </div>
<div><br>
</div>
<div>Donders Institute for
Brain, Cognition and
Behaviour, <br>
Centre for Cognitive
Neuroimaging,<br>
Radboud University
Nijmegen, The
Netherlands</div>
<div><br>
</div>
<div>Max Planck Institute
for Psycholinguistics,</div>
<div>Nijmegen, The
Netherlands</div>
<div><br>
</div>
<div><a
moz-do-not-send="true"
href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a></div>
<div>Telephone: <a
moz-do-not-send="true"
href="tel:%2B31-24-3614793" value="+31243614793" target="_blank">+31-24-3614793</a></div>
</div>
</span></div>
</span></div>
</span></div>
</span></div>
</span></span>
</div>
<br>
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<div style="word-wrap: break-word;">
<div>Jan-Mathijs Schoffelen, MD PhD </div>
<div><br>
</div>
<div>Donders Institute for Brain,
Cognition and Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The
Netherlands</div>
<div><br>
</div>
<div>Max Planck Institute for
Psycholinguistics,</div>
<div>Nijmegen, The Netherlands</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div>
<div>Telephone: +31-24-3614793</div>
</div>
</span></div>
</span></div>
</span></div>
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<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Andrei Medvedev, PhD
Assistant Professor,
Center for Functional and Molecular Imaging
Georgetown University
Building D, Room 154
4000 Reservoir Rd, NW
Washington DC, 20057
Tel.: 202-687-5126
</pre>
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