<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=us-ascii">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
h1
{margin-top:12.0pt;
margin-right:0in;
margin-bottom:3.0pt;
margin-left:0in;
page-break-after:avoid;
font-size:12.0pt;
font-family:"Times New Roman";
font-weight:bold;}
h2
{margin-top:12.0pt;
margin-right:0in;
margin-bottom:3.0pt;
margin-left:0in;
page-break-after:avoid;
font-size:12.0pt;
font-family:"Times New Roman";
font-weight:bold;
font-style:italic;}
p.MsoBodyText, li.MsoBodyText, div.MsoBodyText
{margin-top:0in;
margin-right:0in;
margin-bottom:6.0pt;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
p.JMsstyle01, li.JMsstyle01, div.JMsstyle01
{margin:0in;
margin-bottom:.0001pt;
line-height:200%;
font-size:12.0pt;
font-family:"Times New Roman";
font-weight:bold;}
p.JMsstyle02, li.JMsstyle02, div.JMsstyle02
{margin:0in;
margin-bottom:.0001pt;
line-height:200%;
font-size:12.0pt;
font-family:"Times New Roman";
font-style:italic;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=purple>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Dear Lorina,<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'>For the time being, I assume that you have
your data imported into a fieldtrip-like format, using besa2fieldtrip. I am not
familiar with this function, but when I read the help of besa2fieldtrip I guess
that your besa file was a .tfc file. So probably your data-object looks like
what fieldtrip considers to be a frequency-structure, containing a TFR for each
ROI. I guess you have two data-objects for each subject. <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'>What you would like to do is possible
within fieldtrip, but I would advise you not to use clusterrandanalysis to get
there. Quite some correspondence has been devoted to the new statistical
interface, you can read about it on the discussion list’s website (follow
the appropriate links on the fieldtrip website), concerning <a
href="https://listserv.surfnet.nl/scripts/wa.exe?A2=ind0610&L=fieldtrip&P=4074">Re:
clusterrandanalysis on scalar values + problem with topoplotER</a> during the
past month, but which started in August.<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'>In a nutshell: instead of using
clusterrandanalysis you could use freqstatistics (under the above assumption
that your data resembles a fieldtrip-frequency structure) with the appropriate
settings to get your statistics done. Freqstatistics relies on
statistics_montecarlo, when you specify cfg.method = ‘montecarlo’.<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'>Please have a try following the thread on
the discussion list, and the following configuration settings, as well as the
information in statistics_montecarlo and other dependent functions. You’ll
probably need the attached function as well, which computes your statistic of
interest.<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'>Cfg = [];<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'>Cfg.method = ‘montecarlo’;<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'>Cfg.statistic = ‘diff’;<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'>Cfg.parameter = ‘cohspctrm’;
%This is at least what I expect your data objects to contain!<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'>Cfg.numrandomization = a number;<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'>Cfg.design = [1 1 2 2 3 3 with all the
numbers in between 14 14; …<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'>
1 2 1 2 1 2 with all the numbers in between 1 2]; %this specifies how the data
has to be interpreted<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'>Cfg.ivar = 2; %row-index of independent
variable, which is the condition in your case<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'>Cfg.uvar = 1; %row-index of the ‘unit’-variable,
your unit of observation, which are your individual subjects.<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'> %the design-matrix will be
shuffled, by swapping the 1 and 2’s in the ivar-row, while keeping the
uvar-doublets together.<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'>Cfg.correctm = ‘yes’; %keep it
at this for the time being, we have to develop a cunning strategy to
incorporate something about the neighbourhood structure of your ROIs<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'> %as soon as you get your script
running, you can try to incorporate fancy multiple-comparison correction
strategies, such as clustering in time and frequency.<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'>Stat = freqstatistics(cfg, subj1cond1,
subj1cond2, subj2cond1, subj2cond2 ….); %take care that this corresponds
with how you specified your design.<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'>Subjxconx should then be the
data-structure containing your TFRs in a field called cohspctrm.<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 hope this puts you on track,<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'>Yours,<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'>Jan-Mathijs<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>
<div>
<div class=MsoNormal align=center style='text-align:center'><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><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>Lorina Naci<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, October 23, 2006
7:18 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]
Within-subject coherence statististics for virtual sources</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>Dear FIELDTRIP
members,</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>I have used BESA
to perform source coherence <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>calculations for
a multiple-subject/multiple-condition experiment. I have 14 subjects, and 2
conditions for which I’d like to compare coherence values. I have calculated
coherence values in the Time-Frequency domain for each person.</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> </span></font><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>Given that
BESA cannot calculate statistics in a multiple-subject study, their
support personnel directed me towards FieldTrip.</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span
style='font-size:10.0pt;font-family:"Courier New";color:black'>I would like to
use your existing script ‘</span></font><font size=2 color=black
face="Courier New"><span lang=EN style='font-size:10.0pt;font-family:"Courier New";
color:black'>clusterrandanalysis on TFRs of power that were computed with
BESA,’ but I cannot relate this to my data as <u>the coherence values
have been calculated for ROI sources, (8 per hemisphere - 16 sources total),
and not for electrodes (I had 128).<o:p></o:p></u></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span lang=EN
style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span lang=EN
style='font-size:10.0pt;font-family:"Courier New";color:black'>Do you have any
advice regarding how I may adopt the script to for source coherence as opposed
to electrode coherence? How do I import the source locations?<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span lang=EN
style='font-size:10.0pt;font-family:"Courier New";color:black'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span lang=EN
style='font-size:10.0pt;font-family:"Courier New";color:black'>Many thanks is
advance for your help,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=2 color=black face="Courier New"><span lang=EN
style='font-size:10.0pt;font-family:"Courier New";color:black'>Lorina</span></font><font
size=2 color=black face="Courier New"><span style='font-size:10.0pt;font-family:
"Courier New";color:black'><o:p></o:p></span></font></p>
</div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> Send
instant messages to your online friends http://uk.messenger.yahoo.com <o:p></o:p></span></font></p>
</div>
</body>
</html>