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<p>Dear Tineke,</p>
<p>thank you very much for your fast answer ! I'm not sure I understand what you mean though... Maybe i did not express myself correctly. I do have individual trial data : I have 26 observations for condition 1 and 26 observations for condition 2. </p>
<p>They appear :</p>
<p>- In my structure "data" (output of ft_preprocessing) : data.trial is a cell {1 x nbtrials} (in my case : {1, 26})</p>
<p>- in my structure "freq" (output of ft_freqanalysis) : freq.powspctrm is a matrix of dimension : nbtrials X nbchannel X nbfreq (in my case 26x2x25)</p>
<p>But I don't have this information anymore in the structure "coh" (output of ft_connectivityanalysis) : coh.cospctrm is a matrix of dimension nbchannelcmb x nbfreq (in my case 1x25) since the coherence is calculated by averaging over trials...</p>
<p> </p>
<p>You may mean I should give the "freq" structures as inputs to the fonction ft_freqstatistics ?</p>
<p>I just tried that : I created a structure data_all by concatenated data1.trial and data2.trial (and every other appropriate attribute). I took the Time Frequency Representation with ft_freqanalysis (with keeptrials='yes') to obtain a structure TFR_all (following this tutorial : <a href="http://www.fieldtriptoolbox.org/tutorial/natmeg/statistics">http://www.fieldtriptoolbox.org/tutorial/natmeg/statistics</a> This is actually how I did the statistics for the Power).</p>
<p>But then, if I give this as an input to ft_freqstatistics, like this : </p>
<p>cfg = [];<br />cfg.statistic = 'diff';<br />cfg.parameter='cohspctrm';<br />cfg.design= [ones(1,nbtrial)) 2*ones(1, nbtrial))]; %same nb of trials for both condition<br />cfg.method = 'montecarlo';<br /> cfg.numrandomization = 1000;<br /> cfg.ivar = 1;<br /> cfg.alpha=0.05;<br /> cfg.tail=0;<br /> cfg.correcttail='alpha';<br />>> stat=ft_freqstatistics(cfg, FR_alltrials);</p>
<p>I have the following error :</p>
<p>Error using getdimord (line 15)<br />field "cohspctrm" not present in data</p>
<p>which makes a lot of sense, since I did not gave coherence as an input... I gave Frequency representations.. I was hoping that maybe the function would calculate the coherence itself for the statistics ? ^^ But it's clearly not the way to go.</p>
<p> </p>
<p>Could you be a bit more explicit about what you meant ?</p>
<p> </p>
<p>Thanks a lot.</p>
<p>Best,</p>
<p style="margin-bottom: 0in; line-height: 100%;">Laetitia Lalla</p>
<p style="margin-bottom: 0in; line-height: 100%;">PhD student in Neurosciences</p>
<p style="margin-bottom: 0in; line-height: 100%;">INMED, Marseille, France</p>
<p> </p>
<p> </p>
<p>On 31-03-2016 13:47, Snijders, T.M. (Tineke) wrote:</p>
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0"><!-- html ignored --><!-- head ignored --><!-- meta ignored -->
<div style="direction: ltr; font-family: Helvetica; color: #000000; font-size: 10pt;"><span style="font-family: Arial,Helvetica,sans-serif; font-size: small;"><span style="font-size: 10pt;"><span style="color: black; font-family: Helvetica;"><span>Hi Laetitia,<br /><br /> If you only have one subject you do need individual trial data, otherwise you can't do statistics like this.<br /> You need multiple observations (either subjects or trials).<br /><br /> Best,<br /> Tineke<br /><br /></span></span></span></span>
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<div id="divRpF533353" style="direction: ltr;"><span style="color: #000000; font-family: Tahoma; font-size: small;"><strong>From:</strong> fieldtrip-bounces@science.ru.nl [fieldtrip-bounces@science.ru.nl] on behalf of laetitia.lalla@inserm.fr [laetitia.lalla@inserm.fr]<br /><strong>Sent:</strong> Thursday, March 31, 2016 1:11 PM<br /><strong>To:</strong> fieldtrip@science.ru.nl<br /><strong>Subject:</strong> [FieldTrip] Question about coherence statistics<br /></span></div>
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<p style="margin-bottom: 0in; line-height: 100%;">Dear FielTrip community,</p>
<p style="margin-bottom: 0in; line-height: 100%;">Sorry to bother you again...</p>
<p style="margin-bottom: 0in; line-height: 100%;">I have a question about the statistical testing to assess coherence differences and the related paper by E Maris, JM Schoffelen and P Fries (Journal of Neuroscience Methods, 2007)</p>
<p style="margin-bottom: 0in; line-height: 100%;">I believe I am exactly in the framework described in this paper, but I guess there is still some crucial information that I don't understand...</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">This is my story :</p>
<p style="margin-bottom: 0in; line-height: 100%;">- It's a single-subject study</p>
<p style="margin-bottom: 0in; line-height: 100%;">- I want to compare two sets of trials observed in different conditions.</p>
<p style="margin-bottom: 0in; line-height: 100%;">- The 2 sets of trials are exactly the same size, so my coherence estimate won't be biased by the "unequal sample size problem".</p>
<p style="margin-bottom: 0in; line-height: 100%;">- I just want to compare for 1 channel pair, for 1 frequency bin [6Hz 10Hz], so I guess the Multiple Comparison problem won't affect my analysis too much (either in the spatial or the spectral dimension).</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">Based on the paper, I could refer myself to the point "2.7.1. A non parametric satistical test for a single signal pair and a single frequency bin".</p>
<p style="margin-bottom: 0in; line-height: 100%;">- Since my interest is in the coherence difference for a single signal pair, I can choose [|C1(f)|-|C2(f)|] as a test statistic.</p>
<p style="margin-bottom: 0in; line-height: 100%;">- And I can perform the montecarlo simulation.</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">My question is the following : How can I implement the nonparametric test of the coherence difference between my 2 conditions with the fieldtrip functions ?</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">This is what I did :</p>
<p style="margin-bottom: 0in; line-height: 100%;">1) Extract and preprocess the signal from my condition 1.</p>
<p style="margin-bottom: 0in; line-height: 100%;">2) freq1= ft_freqanalysis(cfg, signal1) (with cfg.method='mtmfft', cfg.output='powandcsd') →</p>
<p style="margin-bottom: 0in; line-height: 100%;">3) coh1= ft_connectivityanalysis(cfg, freq1)</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">I did the same thing for the other condition → coh2.</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">And then for the statistics :</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg = [];</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.statistic = 'diff'; (% because the statistic test than I chose is the difference [|C1(f)|-|C2(f)|])</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.parameter='cohspctrm';</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.method = 'montecarlo';</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.numrandomization = 1000;</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.ivar = 1;</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.alpha=0.05;</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.tail=0;</p>
<p style="margin-bottom: 0in; line-height: 100%;">cfg.correcttail='alpha';</p>
<p style="margin-bottom: 0in; line-height: 100%;">stat=ft_freqstatistics(cfg, coh1, coh2);</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">And it gives me the following error :</p>
<p style="margin-bottom: 0in; line-height: 100%;">Error using ft_checkconfig (line 153)</p>
<p style="margin-bottom: 0in; line-height: 100%;">The field cfg.design is required.</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">Here, I really don't understand why I'm asked for the design matrix... When doing the statistics for the Power, I understood that the design matrix was telling which trial belonged to the condition 1 and which trial belonged to the condition 2. But here, it doesn't make any sense because my coherence was calculated by averaging on the trials...</p>
<p style="margin-bottom: 0in; line-height: 100%;">Does the design matrix mean something differently here ? Or maybe I forgot one parameter to put in the cfg ?</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">Any help will be appreciated !</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">Thanks a lot for your time,</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;">Laetitia Lalla</p>
<p style="margin-bottom: 0in; line-height: 100%;">PhD student in Neurosciences</p>
<p style="margin-bottom: 0in; line-height: 100%;">INMED, Marseille, France</p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
<p style="margin-bottom: 0in; line-height: 100%;"> </p>
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