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<p class="MsoNormal"><span style="font-size:10.0pt;line-height:106%">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;line-height:106%">I am a little lost with cluster-based analyses for my data. My experiment is a within-subjects design, with 30 subjects performing a perceptual task where they report on whether they see a
given target or not (factor, perception; 2 levels – visible, invisible), and they perform the task either at rest or while cycling at low-resistance or at high-resistance (factor, cycling; 3 levels: rest, low-resistance, high-resistance).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;line-height:106%">I am using Fieldtrip to analyse alpha (8-12 Hz) amplitudes in a specific time window of interest. I do this by calculating the average absolute value of the 8-12 Hz filtered Hilbert transform
for each channel separately. I am trying to find time points and channels that differ between my experimental conditions in my time window of interest by running a threshold free cluster enhancement, requiring a minimum number of two neighbouring channels
and consecutive time points and employing a Monte Carlo permutation with 5000 iterations in order to obtain cluster-corrected p-values as follows:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg = [];<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.channel =
<span style="color:#A709F5">'EEG'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.avgovertime =
<span style="color:#A709F5">'no'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.parameter =
<span style="color:#A709F5">'alpha'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.method =
<span style="color:#A709F5">'montecarlo'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.statistic =
<span style="color:#A709F5">'ft_statfun_depsamplesT'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.correctm =
<span style="color:#A709F5">'tfce'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.correcttail =
<span style="color:#A709F5">'prob'</span>;<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.minnbchan = 2;
<span style="color:#008013">% minimal number of neighbouring channels</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;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:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.ivar = 1;
<span style="color:#008013">% the 1st row in cfg.design contains the independent variable</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">cfg.uvar = 2;
<span style="color:#008013">% the 2nd row in cfg.design contains the subject number</span><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">%Effect of perception</span><span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">R_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_vis{:}, R_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">L_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, L_alpha_vis{:}, L_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">H_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, H_alpha_vis{:}, H_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;color:#008013;mso-fareast-language:EN-GB">% Effect of cycling</span><span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">RLvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_vis{:}, L_alpha_vis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">RHvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_vis{:}, H_alpha_vis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">LHvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, L_alpha_vis{:}, H_alpha_vis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">RLinvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_invis{:}, L_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">RHinvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, R_alpha_invis{:}, H_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB">LHinvis_stat_cluster_preRDM_noavg = ft_timelockstatistics(cfg, L_alpha_invis{:}, H_alpha_invis{:});<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-bottom:0cm;margin-bottom:.0001pt;line-height:normal">
<span style="font-size:10.0pt;font-family:Consolas;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;line-height:106%">I am not sure of the following:
<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpFirst" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;line-height:106%"><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:10.0pt;line-height:106%">The design of test – am I doing this right? I am comparing two conditions at a time, choosing the comparisons that would allow me to check the main effects of cycling and of perception
if this were a Repeated Measures ANOVA. But I am not sure if this is the appropriate way to go about this, as I feel this might not be adequately capturing the repeated measures design of the experiment? How would I go about this? How would I have to change
the cfg.design? Also, is </span><span style="font-size:10.0pt;line-height:106%;font-family:Consolas;color:#A709F5;mso-fareast-language:EN-GB">'ft_statfun_depsamplesT'
</span><span style="font-size:10.0pt;line-height:106%">the appropriate statistic?<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"><span style="font-size:10.0pt;line-height:106%">On the other hand, I am not sure there is a way to capture the repeated measures design while doing a permutation test? For instance, I have seen some threads on the mailing
about the possibility of testing for interaction effects using a permutation test and about how this is not possible since that is testing for a linear (parametric) model to explain the variance in the dependent variable.<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"><span style="font-size:10.0pt;line-height:106%">I have read this thread (<a href="https://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/017428.html">https://mailman.science.ru.nl/pipermail/fieldtrip/2011-December/017428.html</a>)
and though they seem relevant to my analysis, I am not sure how to implement Jan-Mathijs’s suggestions.
<o:p></o:p></span></p>
<p class="MsoListParagraphCxSpMiddle"><span style="font-size:10.0pt;line-height:106%"><o:p> </o:p></span></p>
<p class="MsoListParagraphCxSpLast" style="text-indent:-18.0pt;mso-list:l0 level1 lfo1">
<![if !supportLists]><span style="font-size:10.0pt;line-height:106%"><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:10.0pt;line-height:106%">When I run the analysis described above, I don’t find any significant clusters (or any clusters at all, although when I run a cluster based analysis without tfce, some clusters are
identified, however, they are also not significant). Looking at the visualisation of my data, it doesn’t seem like that should be the case (although, I do understand that visual inspection is not the best estimate of statistical significance of a cluster).
Furthermore, when I compare the mean alpha amplitudes of my various conditions for my time window of interest and limited to parieto-occipital channels (chosen based on
<i>a priori</i> assumptions from previous studies and papers on this experimental paradigm), I do find significant effects. Again, I suppose this doesn’t have to translate to finding significant clusters? But I am a little confused thinking about the fact that
if I had no <i>a priori </i>knowledge to base my analysis on, and I ran a cluster based analysis to find time windows/channels of interest and found no significant clusters, I would probably not have dug any deeper and missed the significant effects we do
find when considering alpha amplitude at the parieto-occipital channels? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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