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<p class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">
Hi Jan-Mathijs,</p>
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I would like to follow up on the below message exchange between you and Bushra regarding using indepsamplesZcoh.</p>
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Your suggestions works well for method ‘mtmfft’ when computing frequency. However when using ‘mtmconvol’ to get time-freq representation of coherence, the code ends up with an error. Please see below.</p>
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There seems to be an issue in line 210 Clusterstat.m that it is unable to reshape the statistics to original dimension. cfg.origdim option doesn’t seem to work.</p>
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Any help us much appreciated.</p>
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</p>
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% computing Frequency</p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf = [];</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.output =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'fourier'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.method =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'mtmconvol'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.foi = 5:1:40;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.t_ftimwin = 3 ./ cfgf.foi;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">%length of the sliding time window in seconds</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.toi = 0:0.01:1;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.trials = find(data_preproc.trialinfo(:,1)==284);</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.taper =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'hanning'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">freq1 = ft_freqanalysis(cfgf, data_preproc);</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfgf.trials = find(data_preproc.trialinfo(:,1)==280);</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">freq2 = ft_freqanalysis(cfgf, data_preproc);</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfga=[];</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfga.appenddim=</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'rpt'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">comb_freq = ft_appendfreq(cfga,freq1,freq2);</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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%Permutation</p>
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</p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg = [];</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.method =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'montecarlo'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% use the Monte Carlo Method to calculate the significance probability</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.statistic =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'indepsamplesZcoh'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% use the independent samples T-statistic as a measure to evaluate the effect at the sample level</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.correctm =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'cluster'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.clusteralpha = 0.05;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% alpha level of the sample-specific test statistic that will be used for thresholding</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.clustertail = 0;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.clusterstatistic =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'maxsum'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% test statistic that will be evaluated under the permutation distribution.</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.tail = 0;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% -1, 1 or 0 (default = 0); one-sided or two-sided test</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.correcttail =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'prob'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% the two-sided test implies that we do non-parametric two tests</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.alpha = 0.05;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% alpha level of the permutation test</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.numrandomization = 50;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% number of draws from the permutation distribution</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.design = [comb_freq.trialinfo(:,1)'];
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% design matrix, note the transpose</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.ivar = 1;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% the index of the independent variable in the design matrix</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.neighbours = [];
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% there are no spatial neighbours, only in time and frequency</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.channel = {‘FC1’
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'mean*'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">};</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.parameter =
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#AA04F9">'fourierspctrm'</span><span style="font-size:13.0pt; font-family:"Courier New"; color:black">;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.clustercritval = 0.05;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.origdim = [1 numel(comb_freq.freq)];</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.connectivity = false;</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black"></span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.design=[];</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">trlblk=unique(comb_freq.trialinfo(:,1));
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">%trlblk=trlblk(logical(trlblk>10));</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.design(comb_freq.trialinfo(:,1)== trlblk(1)) = 1;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% OFF condition</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">cfg.design(comb_freq.trialinfo(:,1)==trlblk(2)) = 2;
</span><span style="font-size:13.0pt; font-family:"Courier New"; color:#028009">% ON condition</span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:#028009"></span><span style="font-size:12.0pt; font-family:"Courier New""></span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black">stat = ft_freqstatistics(cfg, comb_freq);</span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black"> </span></p>
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<span style="font-size:13.0pt; font-family:"Courier New"; color:black"> </span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Error using reshape</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Number of elements must not change. Use [] as one of the</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">size inputs to automatically calculate the appropriate</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">size for that dimension.</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> </span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Error in clusterstat (line 210)</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> tmp = reshape(postailobs, [cfg.dim 1]);</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> </span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Error in ft_statistics_montecarlo (line 364)</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> [stat, cfg] = clusterstat(cfg, statrand, statobs);</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> </span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Error in ft_freqstatistics (line 194)</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> [stat, cfg] = statmethod(cfg, dat, design);</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red"> </span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">Error in Priming_task_permutation (line 68)</span></p>
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<span style="font-size:12.0pt; font-family:"Courier New"; color:red">stat = ft_freqstatistics(cfg, comb_freq);</span></p>
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<b><span style="font-size:13.5pt; color:black">Schoffelen, J.M. (Jan Mathijs)</span></b><span style="font-size:13.5pt; color:black; background:white"> </span><a href="mailto:fieldtrip%40science.ru.nl?Subject=Re%3A%20%5BFieldTrip%5D%20Error%20using%20indepsamplesZcoh%20function%20for%0A%20calculating%20coherence%20differences&In-Reply-To=%3CA525165A-72A2-4EBE-98A4-A709C95B137A%40donders.ru.nl%3E" title="[FieldTrip] Error using indepsamplesZcoh function for calculating coherence differences"><span style="font-size:13.5pt">jan.schoffelen
at donders.ru.nl</span></a><span style="font-size:13.5pt; color:black"><br>
<i>Tue May 18 16:21:58 CEST 2021</i></span></p>
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<span style="font-size:13.5pt">Previous message (by thread): <a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2021-May/040872.html">[FieldTrip] Error using indepsamplesZcoh function for calculating coherence differences</a></span></li><li class="MsoNormal" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;color:black">
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<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";white-space:pre-wrap; font-variant-ligatures:normal; font-variant-caps:normal; orphans:2; text-align:start; widows:2; text-decoration-style:initial; text-decoration-color:initial; word-spacing:0px"><span style="color:black">Hi Bushra,</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Thank you for your reply. I am stuck with this for couple of days now.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Welcome to science.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> >Can you please specify the cfg to ft_freqstatistics as well? Otherwise, we don’t know what you did exactly.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg = [];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.method = 'montecarlo';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.statistic = 'indepsamplesZcoh';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.design(1,1:148)=1;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.design(1,149:296)=2;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.numrandomization = 1000;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.correctm = 'cluster';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.neighbours=[];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.parameter='crsspctrm';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.alpha = 0.05;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.clusteralpha = 0.05;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">stat=ft_freqstatistics(cfg,freq_coh);</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Sorry I didnt follow this point. I am calling freqstatistics with above cfg parameters</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">To reiterate, you need to use cfg.parameter = ‘fourierspctrm’, and (cfg.output = ‘fourier’ when calling ft_freqanalysis). The low-level ft_statfun_indepsamplesZcoh assumes that the input data are fourier coefficients.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Next, as a disclaimer: I think that indepsamplesZcoh has hardly been used recently, so it could very well be that it’s functional behavior has not been kept up-to-date with the state of the rest of the toolbox.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">><i>Also, ft_freqstatistics with cfg.statistic = ’indepsamplesZcoh’ requires frequency data that has been computed with >‘fourier’ rather than ‘powandcsd’ as cfg.method for ft_freqanalysis</i></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">when freq_coh is calculated with fourier method, then above code give following error</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Error using ft_freqstatistics (line 177)</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">the length of the design matrix (1) does not match the number of observations in the data (2072)</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">It seems as if the dimord for fourier data is not read correctly, rpttap_chan_freq is getting confused with rpt_chan_freq as 2072 are rpttap , number of repetitions are only 296</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">If you use multitaper spectral analysis, each ’trial’ (aka rpt) gets more than one taper assigned, in your case about 7. These are the number of columns in your data matrix, so that needs to be reflected in the design. Therefore, the design have 2072 columns. In addition, for the randomization to be done correctly, you need to specify in the design, which columns belong to the same trial. So you need to define a second column consisting of [1 1 … 1 2 2 .. 2 …296] coding the individual trials. Then you need to appropriately set the cfg.ivar=1, and cfg.wvar=2 -> please consult the documentation on the fieldtrip website for this.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">In addition you may need to specify cfg.origdim = [1 numel(freq_coh.freq)], and cfg.connectivity = false; before calling ft_freqstatistics.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Moreover, you may need to comment out lines 127 and 150 in ft_statfun_indepsamplesZcoh.m</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">I hope that this will help you on your way, to get it resolved for you. Perhaps you could filie a Pull Request on our github repository with the required change to ft_statfun_indepsamplesZcoh. Also it would be superhelpful for the rest of the community, if your experiences will be solidified in an example script that can be hosted on: <a href="https://www.fieldtriptoolbox.org/example/">https://www.fieldtriptoolbox.org/example/</a></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Best wishes,</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Jan-Mathijs</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">The error can be reproduced by running following script</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"><a href="https://www.dropbox.com/s/7bupsr8gkdmy28c/testcode.m?dl=0%3Chttps://urldefense.com/v3/__https://www.dropbox.com/s/7bupsr8gkdmy28c/testcode.m?dl=0__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDb85XDPxE$">https://www.dropbox.com/s/7bupsr8gkdmy28c/testcode.m?dl=0<https://urldefense.com/v3/__https://www.dropbox.com/s/7bupsr8gkdmy28c/testcode.m?dl=0__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDb85XDPxE$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">with this data</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"><a href="https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0%3Chttps://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDb1di9xyl$">https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0<https://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDb1di9xyl$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Thank you</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Kind regards</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Bushra Riaz</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">________________________________</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">From: fieldtrip <<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">fieldtrip-bounces at science.ru.nl</a><mailto:<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">fieldtrip-bounces at science.ru.nl</a>>> on behalf of Schoffelen, J.M. (Jan Mathijs) <<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">jan.schoffelen at donders.ru.nl</a><mailto:<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">jan.schoffelen at donders.ru.nl</a>>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Sent: 18 May 2021 14:05</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">To: FieldTrip discussion list <<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">fieldtrip at science.ru.nl</a><mailto:<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">fieldtrip at science.ru.nl</a>>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Subject: Re: [FieldTrip] Error using indepsamplesZcoh function for calculating coherence differences</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Hi Bushra,</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Can you please specify the cfg to ft_freqstatistics as well? Otherwise, we don’t know what you did exactly.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Also, ft_freqstatistics with cfg.statistic = ’indepsamplesZcoh’ requires frequency data that has been computed with ‘fourier’ rather than ‘powandcsd’ as cfg.method for ft_freqanalysis</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Best wishes,</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Jan_Mathijs</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">On 14 May 2021, at 13:36, Bushra Riaz Syeda <<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">bushra.riaz at gu.se</a><mailto:<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">bushra.riaz at gu.se</a>>> wrote:</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Hello,</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">I am trying to do the analysis based on the paper "nonparametric statistical testing of coherence differences" in fieldtrip for comparing differences between two conditions on single subject level.</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">I am using the following code</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg = [];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.method = 'montecarlo';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.statistic = 'indepsamplesZcoh';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.design(1,1:148)=1;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.design(1,149:296)=2;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.numrandomization = 1000;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.correctm = 'cluster';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.neighbours=[];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.parameter='crsspctrm';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.alpha = 0.05;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.clusteralpha = 0.05;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">stat=ft_freqstatistics(cfg,freq_coh);</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Where freq_coh is calculated as</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg = [];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.output = 'powandcsd';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.method = 'mtmfft';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.foilim = [1 40];</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.tapsmofrq = 2;</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.pad = 'nextpow2';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">cfg.keeptrials = 'yes';</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">freq_coh = ft_freqanalysis(cfg, Coh_data);</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">I am getting the following error</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Error using ft_statistics_montecarlo (line 250)</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">could not determine the parametric critical value for clustering</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Error in ft_freqstatistics (line 194)</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> [stat, cfg] = statmethod(cfg, dat, design);</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Sample data can be found at the following link</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"><a href="https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0%3Chttps://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$">https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0<https://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">[<a href="https://www.dropbox.com/static/images/spectrum-icons/generated/content/content-unknown-large.png">https://www.dropbox.com/static/images/spectrum-icons/generated/content/content-unknown-large.png</a>]<<a href="https://urldefense.com/v3/__https:/www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$">https://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Coh_data.mat<<a href="https://urldefense.com/v3/__https:/www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$">https://urldefense.com/v3/__https://www.dropbox.com/s/6gfj97srttteawy/Coh_data.mat?dl=0__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA-cj5upg$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Shared with Dropbox</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">www.dropbox.com<<a href="https://urldefense.com/v3/__http:/www.dropbox.com__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA7PXFKq_$">https://urldefense.com/v3/__http://www.dropbox.com__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA7PXFKq_$</a>></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">any help would be highly appreciated</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Kind regards</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">Bushra Riaz</span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">_______________________________________________</span></pre>
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<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"><a href="https://urldefense.com/v3/__https:/doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA0G39K1J$">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!rzdciE12ryfrSpIQp-4LAZj3EK_9U0i1XJby6k79PqsvZKuG4jrCMN-qjHXKDzonA0G39K1J$</a></span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"> </span></pre>
<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black">_______________________________________________</span></pre>
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<pre style="margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: "Courier New";"><span style="color:black"><a href="https://urldefense.com/v3/__https:/doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDbwSy0ZCd$">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!og3YlDTnQJXpbwiNKFrIAwklgaHzW9Gkdlv-WeCI05whozlcD9pwXXXbKggQyxNDbwSy0ZCd$</a></span></pre>
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