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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Hi Nathan,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>I have implemented the biascorrect option in one of the older
versions of freqdescriptives. With this option, the Jacknife was used to
calculate a bias-corrected version of coherence. Actually, there is a very nice
theorem about the fact that Jacknife-based bias correction effectively removes the
first order bias. Surprisingly, the Jacknife is mainly used to calculate a
proxy for the standard error, and for this application a similar theorem does
not exist. I learned this from a nice chapter by John Tukey in a book called “(Exploratory)
Data Analysis” (or something like that).<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Best,<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Eric<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>dr. Eric Maris<br>
Donders Institute for Brain, Cognition and Behavior<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Center for Cognition and F.C. Donders Center for Cognitive
Neuroimaging<o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>Radboud University</span><span lang=EN-US style='font-size:11.0pt;
font-family:"Verdana","sans-serif";color:#1F497D'><br>
</span><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>P.O. Box 9104</span><span lang=EN-US style='font-size:11.0pt;
font-family:"Verdana","sans-serif";color:#1F497D'><br>
</span><span lang=EN-GB style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>6500 HE Nijmegen<br>
The Netherlands<br>
T:+31 24 3612651<br>
Mobile: 06 39584581<o:p></o:p></span></p>
<p class=MsoNormal><span lang=DE style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'>F:+31 24 3616066<br>
E: e.</span><span style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><a href="mailto:e.maris@donders.ru.nl"
title="blocked::mailto:maris@nici.kun.nl"><span lang=DE>maris@donders.ru.nl</span></a></span><span
lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Verdana","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> FieldTrip discussion list
[mailto:FIELDTRIP@NIC.SURFNET.NL] <b>On Behalf Of </b>Nathan Killian<br>
<b>Sent:</b> woensdag 24 maart 2010 21:21<br>
<b>To:</b> FIELDTRIP@NIC.SURFNET.NL<br>
<b>Subject:</b> Re: [FIELDTRIP] freqdescriptives/statistics<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Arial","sans-serif"'>Hi
Fieldtrip Users,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Arial","sans-serif"'>I'm
curious about the "bias correct" for coherence existing in past
versions of fieldtrip (old discussion thread below) but I couldn't locate in
the FT code (October 14 2009 version) what this is actually doing and what bias
it was addressing (e.g. bias from number of trials used in an average). Can
anyone explain what this was meant to do? Also is there any other sort of bias
correction done in the more recent versions of FT?<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Arial","sans-serif"'>Thanks
for any help!<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:8.0pt;font-family:"Arial","sans-serif"'>Nathan<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<p class=MsoNormal>On Tue, Sep 1, 2009 at 6:40 PM, Dahlia Sharon <<a
href="mailto:dahliash@stanford.edu">dahliash@stanford.edu</a>> wrote:<o:p></o:p></p>
<p class=MsoNormal>Thanks Jan-Mathijs for that useful reply.<br>
<br>
Regarding permutation analysis, we're running into some difficulty<br>
understanding what the code does. Could you clarify these points?<br>
<br>
1. We're using Neuromag (Vectorview 306) data, and giving the appropriate<br>
layout file (all channels). Does fieldtrip take into account which channels<br>
are gradiometers and which magnetometers when it calculates adjacency for<br>
clustering?<br>
<br>
2. How does fieldtrip calculate adjacency for channels? (time and frequency<br>
are obvious...)<br>
<br>
3. How is the clustering performed?<br>
<br>
We're getting a significant cluster but it doesn't look like a single blob<br>
in the time-frequency domain (averaging over sensors) but like two very<br>
distant blobs, which is very strange...<o:p></o:p></p>
<div>
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<p class=MsoNormal><br>
On Tue, 1 Sep 2009 09:09:53 +0000, Jan-Mathijs Schoffelen<br>
<<a href="mailto:j.schoffelen@PSY.GLA.AC.UK">j.schoffelen@PSY.GLA.AC.UK</a>>
wrote:<br>
<br>
>Dear Dahlia,<br>
><br>
>Hemant Bokil indeed uses the jackknife to obtain variance estimates of<br>
>power (and coherence), see also for example his 2007 paper in<br>
>J.Neurosci.Methods. More specifically, if your data is 'well-behaved',<br>
>he has shown that by applying a specific correction to the power<br>
>estimate, in combination of the jackknife, generates a test-statistic<br>
>from a differential (i.e. contrast) power spectrum which has a<br>
>standard normal distribution (i.e. the jackknife estimate of the<br>
>variance is expected to be 1 and the estimate of the mean 0).<br>
>Unfortunately, MEG data is hardly ever well-behaved, so we prefer to<br>
>use non-parametric techniques to do statistical inference.<br>
>Freqdescriptives in this respect still historically has the option of<br>
>computing a jackknife estimate of the SEM of the powerspectrum/<br>
>coherencespectrum, which can be used to compute a T-statistic across<br>
>two conditions for example. However, I you would choose this path, you<br>
>have to write some code which does this, because it is not in<br>
>fieldtrip. The biascorrect option has been taken out altogether as far<br>
>as I can see, (and had been designed only to correct the bias in the<br>
>coherence spectra, and not in the power spectra if I remember<br>
>correctly), and any reference in the documentation should be removed.<br>
>Unfortunately, we did not yet have time to considerably clean up<br>
>freqdescriptives, but this is quite high on the developer's to do list.<br>
>The bottom line is: ignore biascorrect, and if you use the jackknife<br>
>estimate of the SEM, you have to come up with some code of your own.<br>
>Alternatively, you could look into freqstatistics and use<br>
>cfg.statistic = 'indepsamplesT' / 'depsamplesT' if you want to do<br>
>statistical inference.<br>
><br>
>Best,<br>
><br>
>Jan-Mathijs<br>
><br>
><br>
>On 28 Aug 2009, at 06:34, Dahlia Sharon wrote:<br>
><br>
>> Hi all,<br>
>><br>
>> Is there a more detailed explanation of usage for the jackknife and<br>
>> biascorrect options for freqdescriptives than the one in the<br>
>> freqdescriptives reference<br>
page(<a href="http://fieldtrip.fcdonders.nl/reference/freqdescriptives"
target="_blank">http://fieldtrip.fcdonders.nl/reference/freqdescriptives</a>)?<br>
>><br>
>> More specifically, are these options related to Bokil et al NeuroIm<br>
>> 2007? How should they be employed to determine significance of<br>
>> difference between conditions? (Is there somewhere a tutorial for<br>
>> the use of these options analogous to the one about cluster-based<br>
>> permutation testing?)<br>
>><br>
>> Also, for the permutation analysis of TFRs<br>
(<a href="http://fieldtrip.fcdonders.nl/tutorial/statistics?s" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/statistics?s</a><br>
>> []=freqstatistics), if I don't want to employ the planar gradient<br>
>> step (what exactly IS combineplanar? sorry I couldn't find it), can<br>
>> I simply skip it and calculate the TFRs of the raw sensor data?<br>
>><br>
>> Many thanks!<br>
>> Dahlia.<br>
>> ----------------------------------<br>
>> The aim of this list is to facilitate the discussion between users<br>
>> of the FieldTrip toolbox, to share experiences and to discuss new<br>
>> ideas for MEG and EEG analysis.<br>
>> <a href="http://listserv.surfnet.nl/archives/fieldtrip.html"
target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a><br>
>> <a href="http://www.ru.nl/fcdonders/fieldtrip/" target="_blank">http://www.ru.nl/fcdonders/fieldtrip/</a><br>
><br>
>----------------------------------<br>
><br>
>The aim of this list is to facilitate the discussion between users of<br>
>the FieldTrip toolbox, to share experiences and to discuss new ideas<br>
>for MEG and EEG analysis.<br>
><br>
><a href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a><br>
><br>
><a href="http://www.ru.nl/fcdonders/fieldtrip/" target="_blank">http://www.ru.nl/fcdonders/fieldtrip/</a><br>
><br>
><br>
><br>
><br>
><br>
>----------------------------------<br>
>The aim of this list is to facilitate the discussion between users of the<br>
FieldTrip toolbox, to share experiences and to discuss new ideas for MEG<o:p></o:p></p>
</div>
</div>
<p class=MsoNormal>and EEG analysis. See also<br>
<a href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a>
and<br>
<a href="http://www.ru.nl/neuroimaging/fieldtrip" target="_blank">http://www.ru.nl/neuroimaging/fieldtrip</a>.<br>
><br>
<br>
----------------------------------<br>
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. See also <a
href="http://listserv.surfnet.nl/archives/fieldtrip.html" target="_blank">http://listserv.surfnet.nl/archives/fieldtrip.html</a>
and <a href="http://www.ru.nl/neuroimaging/fieldtrip" target="_blank">http://www.ru.nl/neuroimaging/fieldtrip</a>.<o:p></o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p>----------------------------------<o:p></o: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.<o:p></o:p></p>
<p>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></p>
<p>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></p>
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<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>