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<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" size="2">Dear Stephen</font></span></div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" size="2"></font></span> </div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" size="2">Thank you, It now perfectly works, but I always get this warning I'm not sure how to handle that:</font></span></div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" color="#0000ff" size="2"></font></span> </div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" color="#0000ff" size="2"><font color="#ff0000">Warning: doing a two-sided test without correcting p-values or alpha-level,<br>
p-values and alpha-level will reflect one-sided tests per tail</font> </font></span></div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Arial" color="#ff0000" size="2"></font></span> </div>
<div dir="ltr" align="left"><span class="287305807-13112012"><font face="Courier New" size="2">
<p>cfg.clusteralpha = 0.05;</p>
<p>cfg.alpha = 0.05;</p>
<p>cfg.clustertail = 0; </p>
</font></span></div>
<div><span class="287305807-13112012"></span><font face="Arial" size="2">When I want to test whet<span class="287305807-13112012">h</span>er my data is significant different<span class="287305807-13112012"> (direction not known, therefore two sided)</span> with an alpha level <0.05 d<span class="287305807-13112012">o</span> I have to adjust my level to 0.<span class="287305807-13112012">0</span>25?</font></div>
<div><font face="Arial" size="2"></font> </div>
<div><font size="2"><font face="Arial"><span class="287305807-13112012">All the </span>
B<span class="287305807-13112012">est, Caroline</span></font></font></div>
<div><br>
</div>
<div class="OutlookMessageHeader" lang="de" dir="ltr" align="left">
<hr tabindex="-1">
<font face="Tahoma" size="2"><b>Von:</b> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>Im Auftrag von </b>Stephen Whitmarsh<br>
<b>Gesendet:</b> Montag, 12. November 2012 17:08<br>
<b>An:</b> FieldTrip discussion list<br>
<b>Betreff:</b> Re: [FieldTrip] Cluster statistics<br>
</font><br>
</div>
<div></div>
Dear Caroline,
<div><br>
</div>
<div>Just to be sure - are you working on a recent version of FieldTrip (your pathname suggests otherwise)? The error seems to suggest you are just missing the mexfile which updating your version might solve.</div>
<div><br>
</div>
<div>You can take a look at the specific statfun_* functions for details about their output. A very generic overview is giving in the Fieldtrup Walkthrough (see the left dropdown documentation menu on the website) in which the output input-output structure
is explained. That might help as well.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Stephen </div>
<div><br>
</div>
<div><br>
<br>
<div class="gmail_quote">On 12 November 2012 16:55, Lustenberger Caroline <span dir="ltr">
<<a href="mailto:Caroline.Lustenberger@kispi.uzh.ch" target="_blank">Caroline.Lustenberger@kispi.uzh.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<u></u>
<div>
<div dir="ltr" align="left"><span><font face="Arial">Dear Steve</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial"></font></span> </div>
<div dir="ltr" align="left"><span><font face="Arial">It seems to work now. However, when I have NaN values in my powerspectrum array, I recieve the following error:</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff"></font></span> </div>
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000">??? Invalid MEX-file<br>
'C:\Users\Caroline\MATLAB_PhD\fieldtrip-20110927\fieldtrip-20110927\statfun\private\nanmean.mexw64':<br>
The specified module could not be found.</font></span></div>
<div><font color="#ff0000"></font> </div>
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000">Error in ==> statfun_depsamplesT at 98<br>
avgdiff = nanmean(diffmat,2);</font></span></div>
<div><font color="#ff0000"></font> </div>
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000">Error in ==> statistics_montecarlo at 240<br>
[statobs, cfg] = statfun(cfg, dat, design);</font></span></div>
<div><font color="#ff0000"></font> </div>
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000">Error in ==> ft_freqstatistics at 279<br>
[stat, cfg] = statmethod(cfg, dat, cfg.design);</font></span></div>
<div class="im">
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000"></font></span> </div>
<div dir="ltr" align="left"><span><font face="Arial">What might be the problem?</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial"></font></span> </div>
</div>
<div dir="ltr" align="left"><span><font face="Arial">Is there a detailed documentation about the command ft_freqstatistics, especially about the meanings of the stats output and what kind of input is possible (e.g. t-test, ...)</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial"></font></span> </div>
<div dir="ltr" align="left"><span><font face="Arial">Thanks again for all your help and best wishes</font></span></div>
<div class="im">
<div dir="ltr" align="left"><span><font face="Arial">Caroline</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial" color="#ff0000"></font></span> </div>
<br>
<div lang="de" dir="ltr" align="left">
<hr>
<font face="Tahoma"><b>Von:</b> <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">
fieldtrip-bounces@science.ru.nl</a> [mailto:<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>]
<b>Im Auftrag von </b>Stephen Politzer-Ahles<br>
<b>Gesendet:</b> Montag, 12. November 2012 14:30<br>
<b>An:</b> <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>
<b>Betreff:</b> Re: [FieldTrip] Cluster statistics<br>
</font><br>
</div>
<div></div>
</div>
<div>
<div class="h5">Hi Caroline,<br>
<br>
It looks to me like your grand averages don't have any EEG data in them; here is what mine look like:<br>
<br>
<span style="FONT-FAMILY: courier new,monospace"> label: {60x1 cell}<br>
time: [1x601 double]<br>
individual: [19x60x601 double]<br>
dimord: 'subj_chan_time'<br>
cfg: [1x1 struct]<br>
elec: [1x1 struct]</span><br>
<br>
To run cluster statistics your structure has to have that "individual" field, which has the ERPs for each subject (for instance, from mine you can see I had 19 subjects with a 60-channel cap, and 601 samples in the epoch). I got mine by importing each subject's
data into FieldTrip, and then using ft_timelockgrandaverage() with cfg.keepindividual='yes'.<br>
<br>
That is my guess about what your problem is, but I could be wrong. After you ran it, did you check stat.posclusters and stat.negclusters? I think those are more important than stat.stat and stat.prob; they tell you which clusters are actually significant (and
stat.posclusterslabelmat and stat.negclusterslabelmat tell you where/when the clusters are).<br>
<br>
Best,<br>
Steve<br>
<br>
<br>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
Message: 1<br>
Date: Sun, 11 Nov 2012 13:25:31 +0000<br>
From: Lustenberger Caroline <<a href="mailto:Caroline.Lustenberger@kispi.uzh.ch" target="_blank">Caroline.Lustenberger@kispi.uzh.ch</a>><br>
To: "<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>
Subject: [FieldTrip] Cluster statistics<br>
Message-ID: <<a href="mailto:2B94F80C-7331-45B9-86BF-2ED1123B680A@kispi.uzh.ch" target="_blank">2B94F80C-7331-45B9-86BF-2ED1123B680A@kispi.uzh.ch</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear fieldtrip users<br>
<br>
I tried to perform cluster analysis with fieldtrip. Since I've performed preprocessing/frequency analysis before using fieldtrip, I had to form the specific<br>
data structure to use for ft_freqstatistics by myself.<br>
<br>
I made a a structur as follows:<br>
Condition 1 'EEGa':<br>
--> 10 subjects:<br>
EEGa{1:10}<br>
label: {128x1 cell} %128 egi elec.<br>
dimord: 'chan_freq'<br>
freq: 1<br>
powspctrm: [128x1 double]<br>
cumtapcnt: 1<br>
cfg: [1x1 struct]<br>
<br>
Condition 2 'EEGm':<br>
EEGm{1:10}<br>
label: {128x1 cell}<br>
dimord: 'chan_freq'<br>
freq: 1<br>
powspctrm: [128x1 double]<br>
cumtapcnt: 1<br>
cfg: [1x1 struct]<br>
<br>
<br>
Then I performed the following steps:<br>
<br>
cfg = [];<br>
<br>
cfg.elec = elec; %was defined before EGI 128 electrodes<br>
<br>
cfg.neighbours = neighbours; %also successfully defined before<br>
<br>
cfg.latency = 'all';<br>
<br>
%cfg.frequency = 'all';<br>
<br>
cfg.channel = 'all';%eleselection % see CHANNELSELECTION<br>
<br>
cfg.avgovertime = 'no';<br>
<br>
%cfg.avgoverfreq = 'no';<br>
<br>
cfg.avgoverchan = 'no';<br>
<br>
cfg.statistic = 'depsamplesT';<br>
<br>
cfg.numrandomization = 2^10;<br>
<br>
cfg.correctm = 'cluster';<br>
<br>
cfg.method = 'montecarlo';<br>
<br>
cfg.clusteralpha = 0.05;<br>
<br>
cfg.alpha = 0.05;<br>
<br>
cfg.alpha = 0.05;<br>
<br>
cfg.clustertail = 0;<br>
<br>
cfg.feedback = 'gui';<br>
<br>
cfg.parameter = 'powspctrm';<br>
<br>
cfg.design = [<br>
<br>
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9<tel:9%2010%201%202%203%204%205%206%207%208%209> 10 % subject number<br>
<br>
1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 ]; % condition number<br>
<br>
cfg.uvar = 1; % "subject" is unit of observation<br>
<br>
cfg.ivar = 2; % "condition" is the independent variable<br>
<br>
stat = ft_freqstatistics(cfg, EEGa{:}, EEGm{:});<br>
<br>
<br>
<br>
<br>
The function ft_freqstatistics runs but the stats results are strange.<br>
My stats.stat is always -inf<br>
and stats.prob always 0<br>
<br>
What might be the problem?<br>
<br>
<br>
Thanks and all the best<br>
Caroline<br>
</blockquote>
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