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<p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif">I am still struggling with this. I’m now trying to use F-statistics for my cluster analysis as Jan-Mathijs recommended, and my code is as follows:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.method =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'template'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% try 'distance' as well</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.template =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'actiCapSnap-64ch-standard_neighb.mat'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% specify type of template</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.layout =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'actiCapSnap-64ch-standard.mat'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% specify layout of channels</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">neighbours = ft_prepare_neighbours(cfg, GA_R_alpha_visinvis);
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% define neighbouring channels</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:12.95pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.channel =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'EEG'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.neighbours = neighbours;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% defined as above</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.latency = [2 3];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.avgovertime =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'no'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.parameter =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'alpha'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.method =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'montecarlo'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.statistic =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'ft_statfun_depsamplesFunivariate'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.alpha = 0.05;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.correctm =
</span><span style="font-size:10.5pt;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'cluster'</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.numrandomization = 5000;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.minnbchan = 2;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% minimal number of neighbouring channels</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:12.95pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">Nsub = 30;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.design(1,1:2*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub)];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.design(2,1:2*Nsub) = [1:Nsub 1:Nsub];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.ivar = 1;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% the 1st row in cfg.design contains the independent variable</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.uvar = 2;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% the 2nd row in cfg.design contains the subject number</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt;line-height:12.95pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:7.5pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">RL_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_visinvis{:}, L_alpha_visinvis{:});<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">But I get the following error:<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-family:"Arial",sans-serif">Error using ft_statistics_montecarlo<o:p></o:p></span></i></p>
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-family:"Arial",sans-serif">could not determine the parametric critical value for clustering<o:p></o:p></span></i></p>
<p class="MsoNormal" style="text-indent:36.0pt"><i><span style="font-family:"Arial",sans-serif">Error in ft_timelockstatistics (line 182)<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span style="font-family:"Arial",sans-serif"> [stat, cfg] = statmethod(cfg, dat, design);<o:p></o:p></span></i></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I imagine this is referring to cfg.alpha, which I am specifying? Or is there something I am missing?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Also, sorry to repeat this from my previous message but I am still a bit confused as to how to proceed. Should I be doing fine-grained pairwise comparisons as above? Or
</span>should I just compare both main effects, of cycling (averaging across vis and invis, and comparing R, L, H) and of perception (averaging across R/L/H and comparing vis versus invis)?<span style="font-family:"Arial",sans-serif"> Is a design like this
possible:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">Nsub = 30;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.design(1,1:3*Nsub) = [ones(1,Nsub) 2*ones(1,Nsub) 3*ones(1,Nsub)];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.design(2,1:3*Nsub) = [1:Nsub 1:Nsub 1:Nsub];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:13.5pt;background:whitesmoke">
<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.ivar = 1;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% the 1st row in cfg.design contains the independent variable</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">cfg.uvar = 2;
</span><span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% the 2nd row in cfg.design contains the subject number</span><span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
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<span style="font-size:10.5pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% Main effect of cycling<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:Consolas;color:#212121;mso-fareast-language:EN-GB">RLH_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_visinvis{:}, L_alpha_visinvis{:}, H_alpha_visinvis{:});<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I actually tried this out but I got the same error as above.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Also, I am also trying out TFCE correction and I’ve still not found the answer to my question from my previous post, so I am going to post it again here:<o:p></o:p></span></p>
<p class="MsoNormal">The TFCE example on the FieldTrip website is only for on one channel (<a href="https://www.fieldtriptoolbox.org/example/threshold_free_cluster_enhancement/">https://www.fieldtriptoolbox.org/example/threshold_free_cluster_enhancement/</a>)
and I was wondering what it looks like scaled up for multiple channels. How would I evaluate any effects and possibly even visualise them?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m sorry about repeating my questions and I would really appreciate any help addressing them, thanks!<o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Ash <o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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<b><span lang="EN-US" style="font-family:"Calibri",sans-serif;mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="font-family:"Calibri",sans-serif;mso-fareast-language:EN-GB"> Bhonsle, Aishwarya
<br>
<b>Sent:</b> 29 April 2024 17:39<br>
<b>To:</b> 'fieldtrip@science.ru.nl' <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] Threshold free cluster enhancement for a Repeated Measures design<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Jan-Mathijs,<o:p></o:p></p>
<p class="MsoNormal">Thank you so much for your response! I have some follow-up questions:<o:p></o:p></p>
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<![if !supportLists]><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>True, using F-statistics makes more sense for my design. But to clarify, you are recommending using F-statistics (ft_statfun_depsamplesFunivariate) and then doing pairwise tests for the main effects to get around the fact that the depsamplesF
functions only take 1xN factorial design? Or do you mean I should continue using T-statistics, and do the pairwise tests?
<o:p></o:p></p>
<p class="MsoListParagraphCxSpMiddle"><o:p> </o:p></p>
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<![if !supportLists]><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>Thank you for pointing out that bit of documentation about testing interactions effects, I totally missed that before. All things considered now I am leaning towards not getting into interaction effects, since it doesn’t seem to be recommended
for my design and especially if I end up using F-statistics, these will not inform me about the pattern in the data responsible for the interaction effect. But I am still a bit uncertain as to what I should do for the main effects - should I just compare both
main effects, of cycling (averaging across vis and invis, and comparing R, L, H) and of perception (averaging across R/L/H and comparing vis versus invis), just like in a two-way RM-ANOVA and leave it at that? What would you recommend?<o:p></o:p></p>
<p class="MsoListParagraphCxSpMiddle"><o:p> </o:p></p>
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<![if !supportLists]><span style="mso-list:Ignore">3)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>I was clearly confusing cluster based and TFCE approaches. Also, I apologise for my poor choice of wording – I have read Benedikt Ehinger’s post of TFCE as well as the FieldTrip page on how not to interpret results from cluster-based
permutation tests, so I do understand it doesn’t make sense to talk about significant clusters. But one thing I am uncertain about – will I be able to plot an effect topographically using ft_clusterplot when I run an analysis with TFCE? Or is that only possible
for other methods of correcting for multiple comparisons in cluster based permutation analyses? I am asking this because the TFCE example on the FieldTrip website is only for on one channel (<a href="https://www.fieldtriptoolbox.org/example/threshold_free_cluster_enhancement/">https://www.fieldtriptoolbox.org/example/threshold_free_cluster_enhancement/</a>)
and I was wondering what it looks like scaled up for multiple channels. I actually tried running the TFCE analysis for all channels on the dataset used in the example but I couldn’t plot the effect using ft_clusterplot. But maybe, this is something that doesn’t
even make sense to attempt? <o:p></o:p></p>
<p class="MsoListParagraphCxSpMiddle"><o:p> </o:p></p>
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<![if !supportLists]><span style="mso-list:Ignore">4)<span style="font:7.0pt "Times New Roman"">
</span></span><![endif]>The reason I was asking about this analysis without a prior constraints was also to further my understanding about these analyses. I am puzzled by the fact the same test in not significant on data obtained for very similar paradigms
with a very similar number of subjects. So in essence, if in the previous experiment, the cluster-based tests were not significant and we didn’t have a prior constraints to limit our analysis then, we would have likely missed the effect in the time window
and channels that we are now using as a prior constraints in the current experiment.
<o:p></o:p></p>
<p class="MsoListParagraphCxSpMiddle"><o:p> </o:p></p>
<p class="MsoListParagraphCxSpLast">This is also relevant to me because I will also be performing a similar cluster based analysis for other parameters (e.g. heart-evoked potential amplitudes) on the same dataset, where I don’t have any a priori topographical
constraints, and I am wondering if there are additional tests I should perform for fear of missing out on some effect that is not evident in cluster based tests?
<o:p></o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Ash<o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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