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<body lang=EN-CA link=blue vlink=purple style='tab-interval:36.0pt;word-wrap: break-word;
-webkit-nbsp-mode: space;-webkit-line-break: after-white-space'>

<div class=Section1>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>Thanks for your response.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>Let me clarify....I have
8 subjects (with 5 channels of data, 2 with 4 channels which I’m not
using at this point)…I used only 2 subjects to test the code (for faster
debugging). <span style='mso-spacerun:yes'>  </span>I do want to do a
within subject statistical test between my conditions (of which I have 3, but I
am only inputting 2 into <span class=SpellE>freqstatistics</span> as I was
unclear whether I could run comparisons across 3 conditions).<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>As you correctly point
out, I did compute coherence across my 5 channels first, resulting in 10
spectra…this is what I inputted into <span class=SpellE>freqstatistics</span>,
which is clearly incorrect.<span style='mso-spacerun:yes'>  </span>This is
what I thought, however I didn’t know exactly what the data input should
look like.<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>So, just to clarify, I’m
running<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span class=SpellE><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D'>freqanalysis</span></span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:
"Times New Roman";color:#1F497D'> – inputting raw data, returning “<span
class=SpellE>powandcsd</span>’<o:p></o:p></span></p>

<p class=MsoNormal><span class=SpellE><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D'>freqdescriptives</span></span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:
"Times New Roman";color:#1F497D'> – inputting data from <span
class=SpellE>freqanalysis</span>, returning ‘<span class=SpellE>coh</span>’<o:p></o:p></span></p>

<p class=MsoNormal><span class=SpellE><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D'>freqgrandaverage</span></span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:
"Times New Roman";color:#1F497D'> (keep individual ‘yes’) –
inputting data from <span class=SpellE>freqdescriptives</span>, returning a <span
class=SpellE>grandaverage</span><o:p></o:p></span></p>

<p class=MsoNormal><span class=SpellE><span style='font-size:11.0pt;font-family:
"Calibri","sans-serif";mso-bidi-font-family:"Times New Roman";color:#1F497D'>freqstatistics</span></span><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";mso-bidi-font-family:
"Times New Roman";color:#1F497D'> – inputting two <span class=SpellE>grandaverages</span>
(for 2 conditions), using the following parameters:<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:forestgreen'>%Compute Permutation Test</span><span style='font-family:
"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = [];</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.parameter</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'<span class=SpellE>cohspctrm</span>'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.method</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'<span class=SpellE>montecarlo</span>'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.frequency</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = [0 50];</span><span style='font-family:"Courier New";
mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.statistic</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'<span class=SpellE>indepsamplesT</span>'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.correctm</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'cluster'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.clusteralpha</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 0.05;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.clusterstatistic</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'<span class=SpellE>maxsum</span>'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.minnbchan</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 2;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.tail</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 0;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.clustertail</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 0;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.alpha</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 0.05;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.numrandomization</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = 100;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.computestat</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = </span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:#A020F0'>'yes'</span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'> </span></span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'> </span></span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>subj</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'> = length(Subjects);</span><span style='font-family:"Courier New";
mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>design=zeros(2,2*<span class=SpellE>subj</span>);</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:blue'>for</span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'> <span class=SpellE>i</span>
= 1:subj</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'>  </span>design(1,i) = <span
class=SpellE>i</span>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:blue'>end</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:blue'>for</span><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'> <span class=SpellE>i</span>
= 1:subj</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'>  </span>design(1,subj+i) = <span
class=SpellE>i</span>;</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:blue'>end</span><span style='font-family:"Courier New";mso-fareast-font-family:
"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>design(2,1:subj)<span
style='mso-spacerun:yes'>        </span>= 1;</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>design(2,subj+1:2*<span class=SpellE>subj</span>) = 2;</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'> </span></span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.design</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'>   </span>= design;</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.uvar</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'>  </span>= 1;</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=SpellE><span style='font-size:10.0pt;font-family:"Courier New";
mso-fareast-font-family:"Times New Roman";color:black'>cfg.ivar</span></span><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'>  </span>= 2;</span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'><span style='mso-spacerun:yes'> </span></span><span
style='font-family:"Courier New";mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
style='font-size:10.0pt;font-family:"Courier New";mso-fareast-font-family:"Times New Roman";
color:black'>[stat] = <span class=SpellE>freqstatistics</span>(<span
class=SpellE>cfg</span>, <span class=SpellE>grandavg</span>{1}, <span
class=SpellE>grandavg</span>{2});</span><span style='font-family:"Courier New";
mso-fareast-font-family:"Times New Roman"'><o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>Are you saying, I should
use the output from <span class=SpellE>freqanalysis</span> (skipping <span
class=SpellE>freqdescriptives</span>) as input to <span class=SpellE>freqgrandaverage</span>?<span
style='mso-spacerun:yes'>  </span>Also, should my “<span
class=SpellE>cfg.parameter</span>” for the <span class=SpellE>freqstatistics</span>
function still be ‘<span class=SpellE>cohspctrm</span>’ or ‘<span
class=SpellE>powspctrm</span>’?<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>Thanks again,<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'>Jamie<o:p></o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-bidi-font-family:"Times New Roman";color:#1F497D'><o:p> </o:p></span></p>

<div>

<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>

<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:
EN-US'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";mso-fareast-font-family:"Times New Roman";mso-ansi-language:
EN-US'> <span class=SpellE>FieldTrip</span> discussion list
[mailto:FIELDTRIP@NIC.SURFNET.NL] <b>On Behalf Of </b><span class=SpellE>jan-mathijs</span>
<span class=SpellE>schoffelen</span><br>
<b>Sent:</b> May 3, 2009 1:34 PM<br>
<b>To:</b> FIELDTRIP@NIC.SURFNET.NL<br>
<b>Subject:</b> Re: [FIELDTRIP] <span class=SpellE>independsamplesZcoh</span><o:p></o:p></span></p>

</div>

</div>

<p class=MsoNormal><o:p> </o:p></p>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Dear
Jamie,<o:p></o:p></span></p>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>For
me it is not exactly clear what you want to do. In an earlier message you
referred to our paper using a permutation test to test for a significant
difference in coherence between conditions (Maris et al 2007). Essentially, as
described, this is a test which is performed within each subject allowing you
to do statistical inference about the potential difference between two
conditions. As such this is the type of test <span class=SpellE>indepsamplesZcoh</span>
can perform, if properly used (see below). Yet, you describe using two subjects
as an input. This to me sounds rather that you would like to do statistics
across subjects (although 2 subjects of course is a rather low number). This is
NOT something <span class=SpellE>indepsamplesZcoh</span> can do  for you.
In general it is possible to test for a significant difference between two
conditions across a population of subjects, but this would require a different
approach. Rather than shuffling single observations across conditions PRIOR TO
COMPUTING THE COHERENCE DIFFERENCE (sorry about the capitals but this is
essential for what is to follow below), one would swap the sign of the
Z-transformed coherence difference for a random subset of subjects prior to
averaging.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>It
seems as if you computed coherence spectra between all unique pairs of channels
(4x5)/2 and used this as an input to <span class=SpellE>freqstatistics</span>.
Yet, for single subject statistics this does not make sense, because <span
class=SpellE>indepsamplesZcoh</span> expects <span class=SpellE>fourier</span>-spectra
in the input. Within the function Z-transformed coherence difference will be
computed between all pairs of input channels (in your case this would be
(9x10)/2 (even though the function does not know you provide it with the wrong
input), and multiplying this number with 52 would give your 'magical' 2340).<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>So,
indeed you should either format your data in a different way using single
subject <span class=SpellE>fourier</span> spectra in two conditions as an input
to <span class=SpellE>freqstatistics</span>, or using a different statistical
test to test for differences across subjects.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Yours,<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>Jan-<span
class=SpellE>Mathijs</span><o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'> <o:p></o:p></span></p>

<div>

<div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'>On
May 3, 2009, at 7:00 PM, Jamie Johnston wrote:<o:p></o:p></span></p>

</div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><br
style='mso-special-character:line-break'>
<![if !supportLineBreakNewLine]><br style='mso-special-character:line-break'>
<![endif]><o:p></o:p></span></p>

<div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Hi all –<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>I am trying to run a<span class=apple-converted-space> </span><span
class=SpellE><span class=spelle>monte</span></span><span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>carlo</span></span><span
class=apple-converted-space> </span>–<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>indepsamplesZcoh</span></span><span
class=apple-converted-space> </span>– cluster on my data using<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>freqstatistics</span></span>.<span
class=apple-converted-space> </span> I input two data files into<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>freqstatistics</span></span><span
class=apple-converted-space> </span>with the<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>cohspctrm</span></span><span
class=apple-converted-space> </span>having dimensions 2 (subjects) x 10
(channels, # of coherence spectra) x 52 (frequencies). <span
class=apple-converted-space> </span>I run into a dimension mismatch in the
function<span class=apple-converted-space> </span><span class=SpellE><span
class=spelle>clusterstat</span></span>. <span class=apple-converted-space> </span>If
I run any other statistic (i.e.,<span class=apple-converted-space> </span><span
class=SpellE><span class=spelle>indepsamplesT</span></span>) it runs fine.<span
class=apple-converted-space> </span> When running the<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>indepsamplesT</span></span>,<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>clusterstat</span></span><span
class=apple-converted-space> </span>receives two inputs:<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>statobs</span></span><span
class=apple-converted-space> </span>(520x1) and<span
class=apple-converted-space> </span><span class=SpellE><span class=spelle>statrnd</span></span><span
class=apple-converted-space> </span>(520x100). These dimensions make sense
to me. <span class=apple-converted-space> </span>However, when
running<span class=apple-converted-space> </span><span class=SpellE><span
class=spelle>indepsamplesZcoh</span>these</span> two variables have dimensions
2340x1 and 2340x100, respectively. <span class=apple-converted-space> </span>This
happens around lines 104-108 in<span class=apple-converted-space> </span><span
class=SpellE><span class=spelle>indepsamplesZcoh.m</span></span><span
class=apple-converted-space> </span>with computation of the variables
“<span class=SpellE><span class=spelle>chancmbsel</span></span>”
and “<span class=SpellE><span class=spelle>nnewsamples</span></span>.” <span
class=apple-converted-space> </span>I’m not understanding what these
variables do, but my guess is that I need to setup my data files differently in
the beginning. <span class=apple-converted-space> </span>My
understanding of what this analysis protocol does is compute the z-statistic on
each channel of coherence data (10 for each data file) and then find the
difference between the z-statistic for each channel across the data
files. Once this is complete it runs the permutations to determine the
significance.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Please verify that what I have done is correct and any help with
the error I am getting would be greatly appreciated.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Thanks,<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Jamie<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>_______________<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Jamie Johnston, Ph.D.<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Assistant Professor<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Faculty of Kinesiology<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>University of Calgary<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>2500 University Dr. NW<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Calgary, AB<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>T2N 1N4<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Phone: +1 (403) 220-3649<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>Fax: +1 (403) 284-3553<o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>email: <a href="mailto:johnston@kin.ucalgary.ca">johnston@kin.ucalgary.ca</a><o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'>website: <a
href="http://www.kin.ucalgary.ca/wcm/knes/johnston.html">http://www.kin.ucalgary.ca/wcm/knes/johnston.html</a><o:p></o:p></span></p>

</div>

<div>

<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:Helvetica;
color:black'> <o:p></o:p></span></p>

</div>

</div>

<p><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>----------------------------------<o:p></o:p></span></p>

<p><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'>The aim of this list is to facilitate the discussion between users
of the <span class=SpellE>FieldTrip</span> toolbox, to share experiences and to
discuss new ideas for MEG and EEG analysis.<o:p></o:p></span></p>

<p><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><a href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a><o:p></o:p></span></p>

<p><span style='font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black'><a href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a><o:p></o:p></span></p>

</div>

<p class=MsoNormal><span style='mso-fareast-font-family:"Times New Roman"'><o:p> </o:p></span></p>

</div>

<p>----------------------------------<o:p></o:p></p>

<p>The aim of this list is to facilitate the discussion between users of the <span
class=SpellE>FieldTrip</span> 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>

</div>

</body>

</html>
<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>