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<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Hi Stephen,</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Thanks again for the reply and reassurance.
<font size="2"><span style="font-size:11pt;">ft_neighbourplot</span></font> is looking fine.
<br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">I didn't expect the t-stats to look exactly the same but I'd have thought the occipital difference might have been more prominent in the t-stat. That said, my hypothesis is
a central-parietal difference so perhaps I shouldn't worry about it! I'll double check the means and variance.
<br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Thanks for your help.</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Jac<br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;"><br>
</span></font></p>
<p style="margin-top:0;margin-bottom:0"><font size="2"><span style="font-size:11pt;">Hi Jac,<br>
<br>
To my eyes all looks fine to me!<br>
<br>
- Your stat output seems to fit your raw difference rather well, I would<br>
say! Why do you think otherwise? Sure, the t-stats are not the same as<br>
absolute differences, but that's to be expected - the general topography<br>
looks rather similar. If you don't trust the calculation you can perhaps<br>
just do a MATLAB ttest on one electrode and compare that to the<br>
freqstatistics output.<br>
- Yes, you seem to be plotting the average over time ([5 5] in the plot)<br>
and frequency ([10 10] in the plot). As I said earlier, I can't track the<br>
clusterplot at the point (it also has no parameters in the image). Without<br>
the code that you use, I can't see if anything else is going on.<br>
- The significant cluster/electrodes you see in the clusterplot seems to<br>
correspond to that blue central blog on the stats left of it in the same<br>
image file just fine.<br>
- You can check your neighbours with ft_neighbourplot<br>
<br>
Since you are probably doing your statistics on average time and freq, the<br>
only dimension that your cluster extends to is 'space', i.e. electrodes, so<br>
for now you don't need to use clusterplot, but just highlight the<br>
electrodes in ft_topoplotXX based on your stats. This is just to not make<br>
it more confusing than it is - clusters that span time/freq/space are just<br>
very hard to plot.<br>
<br>
Cheers,<br>
Stephen<br>
</span></font><br>
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<p class="MsoNormal"><i><span style="color:#7F7F7F">Dr Jac Billington</span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F">Lecturer in Cognitive Neuroscience</span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F">School of Psychology, Rm G.06A</span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F">University of Leeds</span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F">Leeds, LS2 9JT</span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F">Tel: +44(0)113 343 6686</span></i></p>
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<p class="MsoNormal"><i><span style="color:#7F7F7F"><a href="http://medhealth.leeds.ac.uk/profile/1300/983/jac_billington" id="LPNoLP">Jac Billington</a></span></i></p>
<p class="MsoNormal"><i><span style="color:#7F7F7F"><a href="http://www.leeds.ac.uk/coni/index.html" id="LPNoLP">CoNi Lab</a></span></i></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Jac Billington<br>
<b>Sent:</b> 21 January 2019 12:51:26<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> Re: ft_clusterplot error?</font>
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<p style="margin-top:0; margin-bottom:0">Dear Stephen,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">Thank you for the useful reply, I've been doing some trouble shooting and it seems the output of
<span>ft_freqstatistics doesn't seem to be reflecting my raw data. See "stat_discrepency.jpg" in dropbox link.</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>This plots condition 1 and 2 and the raw difference (as per your suggestion
<font size="2"><span style="font-size:11pt">data_diff.powspctrm = data1.powspctrm - data2.powspctrm</span></font>). I then plot stat.stat and the clusterplot output, clusterplot is representing my stat output.
<br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>In general I want to look at all channels, time 4-6seconds, for frequencies 8-12. The latter 2 parameters I want averaged.
<br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>I noticed that the T-stat plot (of stat.stat) reports only one time and frequency. I presumed this was the average for display purposes (- double checked by plotting only that time and frequency in "<span>stat_discrepency_onetimefreq</span>.jpg"
and it is different).</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>I think my design matrix is correct (following
<a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/" class="x_OWAAutoLink" id="LPlnk220108">
http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/</a>). I have 28 trials in con1 and 25 in con2, my design matrix is 1x53 reflecting the trials for the two conditions. I don't think I need to specify anything further until I move on to
group analysis (this is just a single subject). <br>
</span></p>
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</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>The only other issue I can think of is in the parameter:</span></p>
<p style="margin-top:0; margin-bottom:0"><span><span> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, elec);</span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>I create 'elec' by using <span>ft_read_sens</span> to read the preprocessing output from EEGlab.</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span></span></p>
<div> filenameA=strcat([det.subjects{s} '_postPreProICA_epoched_' det.epochs{1} '.set'])<br>
elec = ft_read_sens(filenameA)</div>
<div><br>
</div>
<div><br>
Again, I'd be grateful for any pointers. My computation of <span>ft_freqstatistics</span> has not changed from the original post.
<br>
</div>
<div><br>
</div>
<div>Thank you. Jac<br>
</div>
<a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/" class="x_OWAAutoLink" id="LPlnk137825"></a><br>
<p></p>
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</span></p>
<p style="margin-top:0; margin-bottom:0"><span><a href="https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0" class="x_OWAAutoLink" id="LPlnk495425">https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0</a></span></p>
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<font size="2"><span style="font-size:11pt">FieldTrip discussion list <fieldtrip@science.ru.nl><br>
Subject: Re: [FieldTrip] ft_clusterplot error?<br>
Message-ID:<br>
<CAFrxm=zMQuaKsyyBxOewfS5GgBYDMrXoUpHMk674WYFWXSfA+w@mail.gmail.com><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Jac,<br>
<br>
I would start by plotting your (t)stats, and for simplicity doing that with<br>
ft_singleplotER (cfg.param = 'stat') rather than ft_clusterplot.<br>
Then try plotting the power-difference. This should not be more than a<br>
subtraction of data_diff.powspctrm = data1.powspctrm - data2.powspctrm, .<br>
No reshaping should be needed.<br>
The problem is probably a mistake somewhere keeping track of<br>
dimensions/latencies etc. which is tricky with clusters.<br>
Also, make sure to clear your cfg before every function so you don't carry<br>
the cfg of a previous function into the next. That will also help<br>
readability and debugging.<br>
<br>
HTH,<br>
Stephen<br>
</span></font>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Jac Billington<br>
<b>Sent:</b> 18 January 2019 18:07:04<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> ft_clusterplot error?</font>
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<p style="margin-top:0; margin-bottom:0">Dear experts,</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I've recently begun using fieldtrip and have been following tutorials well. however, I have perhaps run into a problem with ft_clusterplot.
<br>
</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">An example output is located in dropbox here:
<a href="https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0" class="x_x_OWAAutoLink" id="LPlnk961654">
https://www.dropbox.com/sh/64m3xpgco2uavky/AADT6-rXEdylVzHN1lY-q7SNa?dl=0</a></p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">My negative cluster labels don't seem to be located in a cluster per se, or in regions with a greater raw effect. This seems at odds with tutorial examples and papers. Apologies if I'm missing something, but can this
be correct? <br>
</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0">I did have earlier errors ('<span> ft_error('unsupported dimord %s', dimord);</span>') but I realised this was because dimensions of my
<span>stat.raweffect (64 5 200) were in conflict with collapsing time and frequency when running
<span>ft_freqstatistics</span>. Reducing stat.raweefect to 64 1 solved this error, but I'm wondering if I have done something wrong.
<br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>My code is posted below and I'd happily be poited to some papers if I'm misunderstanding this. </span></p>
<p style="margin-top:0; margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span>Thank you in advance. Jac</span><br>
</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0"><br>
</p>
<p style="margin-top:0; margin-bottom:0"></p>
<div> % load data (from ft_freqanalysis) <br>
load(filename1);<br>
con1= freqScaling<br>
load(filename2);<br>
con2=freqScaling;<br>
<br>
%%%% run the stats: <br>
cfg = [];<br>
cfg.channel = 'all';<br>
cfg.latency = [4 6];<br>
cfg.frequency = [8 12];<br>
cfg.method = 'montecarlo';<br>
cfg.statistic = 'ft_statfun_indepsamplesT';<br>
cfg.correctm = 'cluster';<br>
cfg.clusteralpha = 0.05;<br>
cfg.clusterstatistic = 'maxsum';<br>
cfg.minnbchan = 2;<br>
cfg.tail = 0;<br>
cfg.clustertail = 0;<br>
cfg.alpha = 0.025;<br>
cfg.numrandomization = 500; <br>
cfg.avgoverchan = 'no' <br>
cfg.avgovertime = 'yes' <br>
cfg.avgoverfreq = 'yes' <br>
% prepare_neighbours determines what sensors may form clusters<br>
cfg_neighb.method = 'distance';<br>
cfg.neighbours = ft_prepare_neighbours(cfg_neighb, elec);</div>
<div><br>
design = zeros(1,size(con1.powspctrm,1) + size(con2.powspctrm,1));<br>
design(1,1:size(con1.powspctrm,1)) = 1;<br>
design(1,(size(con1.powspctrm,1)+1):(size(con1.powspctrm,1)+ size(con2.powspctrm,1))) = 2;<br>
cfg.design = design;<br>
cfg.ivar = 1;<br>
<br>
<br>
[stat] = ft_freqstatistics(cfg, con1, con2);<br>
<br>
<br>
<br>
cfg=[]<br>
cfg.keeptrials = 'no'<br>
cfg.latency = [4 6];<br>
cfg.frequency = [8 12];<br>
con1 = ft_freqdescriptives(cfg, con1);<br>
con2 = ft_freqdescriptives(cfg, con2);<br>
<br>
%%%% resize powerspec to avoid dimord error. Collapse freq/ time<br>
con1rs=mean(con1.powspctrm,3) %%% collapse time dim<br>
con2rs=mean(con2.powspctrm,3) %%% collapse time dim<br>
con1rs=mean(con1rs,2) %%% collapse freq<br>
con2rs=mean(con2rs,2) <br>
stat.raweffect = con1rs-con2rs<br>
<br>
cfg.alpha = 0.025;<br>
cfg.zparam = 'raweffect';<br>
cfg.zlim = [-1 3];<br>
cfg.layout = 'biosemi64.lay';<br>
cfg.subplotsize = ([1 1]);<br>
ft_clusterplot(cfg, stat);</div>
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