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<div class=Section1 dir=RTL>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Dear Eric and Jan-Mathijs,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>My reference channel is indeed EMG. I thought
about this trial shuffling idea myself over night. It can actually be combined
with clustering in channel/frequency space. Is there a way to do it with the
current version of statistics routines or should it be programmed by hand?<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><st1:City w:st="on"><st1:place w:st="on"><font size=2 color=navy
face=Arial><span style='font-size:10.0pt;font-family:Arial;color:navy'>Vladimir</span></font></st1:place></st1:City><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center;direction:
ltr;unicode-bidi:embed'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>
<hr size=3 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:
Tahoma;font-weight:bold'>From:</span></font></b><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'> <st1:PersonName w:st="on">FieldTrip
discussion list</st1:PersonName> [mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Jan Mathijs Schoffelen<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, November 28, 2006
10:24 PM<br>
<b><span style='font-weight:bold'>To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [FIELDTRIP] Some
issues in freqanalysis</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Dear Vladimir,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Regarding the missing functions: you are
absolutely right. The functions will be added to the latest release.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Regarding the crash: I don’t know what is
happening there, and I do not have any experience with the option biascorrect.
You’ll have to ask Eric about this.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Does it still crash when you use cfg.biascorrect
= ‘no’? This might already solve your problem. <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>cfg.combinechan is a rather obscure option (and
is set to ‘no’ by default) in freqdescriptives which is (as far as
I know) undocumented. It has to do with combining planar gradiometer
representation back into an axial gradiometer representation in order to be
able to compute coherence between sensor-combinations (in their original axial
representation). As a matter of fact, it is an option which has a high
‘don’t try this at home’-content. At least a correct behavior
is not guaranteed. Anyhow, it should run through even when it is not specified.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>If you want to test coherence against 0, the
jack-knife estimate of the variance is not going to help you too much. Rather,
you could use some kind of Z-transformation as proposed by Jarvis & Mitra
Neural computation 2001, or the Z-transformation that is described in James
Kilner’s papers, or from the <st1:place w:st="on"><st1:City w:st="on">Rosenberg</st1:City></st1:place>
group. In this context, the coherence can be parametrically evaluated.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Another possibility is using a
‘shiftpredictor’ to estimate the bias, meaning that you shuffle the
trial order of one of the two channels in your channel-combination (only works
when taking fourier as an output of freqanalysis). In my experience this only
works if you use an external reference signal, such as the EMG.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 color=navy face=Arial><span style='font-size:10.0pt;
font-family:Arial;color:navy'>Hope this gives some handles,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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 dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><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>
<div>
<div class=MsoNormal align=center dir=LTR style='text-align:center;direction:
ltr;unicode-bidi:embed'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><b><font size=2 face=Tahoma><span style='font-size:10.0pt;font-family:
Tahoma;font-weight:bold'>From:</span></font></b><font size=2 face=Tahoma><span
style='font-size:10.0pt;font-family:Tahoma'> <st1:PersonName w:st="on">FieldTrip
discussion list</st1:PersonName> [mailto:FIELDTRIP@NIC.SURFNET.NL] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Vladimir Litvak<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, November 28, 2006
8:33 PM<br>
<b><span style='font-weight:bold'>To:</span></b> FIELDTRIP@NIC.SURFNET.NL<br>
<b><span style='font-weight:bold'>Subject:</span></b> [FIELDTRIP] Some issues
in freqanalysis</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Dear
Robert and all,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>I'm
writing a new script for analysis of MEG data and I encountered some problems
with FT (I'm using 20061029 version):<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='text-align:left;direction:ltr;unicode-bidi:
embed'><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:36.0pt;text-align:left;
text-indent:-18.0pt;mso-list:l0 level1 lfo2;direction:ltr;unicode-bidi:embed'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>1)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><span
dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>In
freqdescriptives the lines 494 and 515 seem to be redundant and also don't work
and cause a crash.<o:p></o:p></span></font></span></p>
<p class=MsoNormal dir=LTR style='margin-left:36.0pt;text-align:left;
text-indent:-18.0pt;mso-list:l0 level1 lfo2;direction:ltr;unicode-bidi:embed'><![if !supportLists]><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><span
style='mso-list:Ignore'>2)<font size=1 face="Times New Roman"><span
style='font:7.0pt "Times New Roman"'> </span></font></span></span></font><![endif]><span
dir=LTR><font size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>there
are some missing functions: <o:p></o:p></span></font></span></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>
inputlabel2outputlabel called by freqdescriptives, line 234<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>
fourier2crsspctrm called by freqdescriptives, line 290<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Can you please explain to me what cfg.combinechan
in freqdescriptives does (I'm new to MEG which might explain my ignorance)?<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Finally, I would like to compute
coherence from data of a single subject with 300 trials and check whether it is
significant (i.e. not random). I don't think I can use any of the nonparametric
stuff because I don't have a baseline. It seems to me that I should use the
jackknife SEMs. How exactly? Should I use the bias correction? Should I take
2*SEM as the threshold?<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Thanks,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR style='margin-left:18.0pt;text-align:left;
direction:ltr;unicode-bidi:embed'><st1:place w:st="on"><st1:City w:st="on"><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'>Vladimir</span></font></st1:City></st1:place><font
size=2 face=Arial><span style='font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p>
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