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Dear Lucija,
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<div class="">The fact that you get a p-value of 1 throughout (in combination with the cfg that you have used for ft_timelockstatistics) indicates that either:</div>
<div class="">-there are no data points that survive the a priori threshold for clustering, or</div>
<div class="">-the observed clusters in the data (after thresholding the T-statistic at the nominal level) yield a cluster-based test statistic that is smaller than any of the test statistics obtained for the null distribution.</div>
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<div class="">With respect to the error you get when computing the difference of the average across subjects: you don’t specify it, but I suspect that the number of subjects with and without ulcer is different. But on the off change that this is not the case,
I recommend to compute the average across subjects first (per condition), and then use ft_math to do the subtraction. Of course, you’d need to check (and ensure) that the data matrices are compatible, i.e. with respect to the channels and (number of) time
points.</div>
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<div class="">Good luck and keep up the good work,</div>
<div class="">Jan-Mathijs</div>
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<blockquote type="cite" class="">
<div class="">On 15 Jul 2023, at 15:18, Lucija via fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>> wrote:</div>
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Dear community,<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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I'm Lucija and currently I'm analysing the plantar pressure data collected with Pedar-X system. I'm using SPM-method to analyse the data. The data files are ascii. and fgt. files. The data size is 90x40x number of subjects. For my research, I'm comparing two
groups of different sizes with independent sample t-test. I tried using function ft_timelockstatistics to perform statistical analysis.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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This is the code I used:<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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cfg = []; <span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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cfg.channel = 'all';<o:p class=""></o:p></div>
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cfg.neighbours = neighbours;<o:p class=""></o:p></div>
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cfg.latency = [1 norm_frames];<o:p class=""></o:p></div>
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cfg.avgovertime = 'no';<o:p class=""></o:p></div>
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cfg.parameter = 'avg';<o:p class=""></o:p></div>
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cfg.method = 'montecarlo';<o:p class=""></o:p></div>
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cfg.statistic = 'ft_statfun_indepsamplesT';<o:p class=""></o:p></div>
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cfg.alpha = 0.05;<o:p class=""></o:p></div>
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cfg.correctm = 'cluster';<o:p class=""></o:p></div>
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cfg.correcttail = 'prob';<o:p class=""></o:p></div>
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cfg.numrandomization = 500; <span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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cfg.labels = neighbours;<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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cfg.design(1,1:(Nsub_ulcer+Nsub_noulcer)) = [ones(1,Nsub_ulcer) 2*ones(1,Nsub_noulcer)];<o:p class=""></o:p></div>
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cfg.ivar = 1;<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<span style="font-size: 10pt; font-family: Consolas;" class="">stat = ft_timelockstatistics(cfg, DataC1{:}, DataC2{:});</span><o:p class=""></o:p></div>
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After running the statistics, I am getting p-values equal to 1 for many sensors. I understand there might be no significant differences because of the variation between the groups, but the fact that the probabilities are almost all 1 seems incorrect to me.
Does anyone see the error in the code that might have caused this problem?<o:p class=""></o:p></div>
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I have also tried plotting the data by calculating the average difference between the groups. I have used this code for plotting:<o:p class=""></o:p></div>
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cfg = []<o:p class=""></o:p></div>
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cfg.parameter = 'avg'<o:p class=""></o:p></div>
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cfg.operation = 'subtract'<o:p class=""></o:p></div>
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for i = 1:Nsub_ulcer<o:p class=""></o:p></div>
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data{i} = ft_math(cfg, DataC1{i})<o:p class=""></o:p></div>
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end<o:p class=""></o:p></div>
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for k = 1: Nsub_noulcer<o:p class=""></o:p></div>
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data{k} = ft_math(cfg, DataC2{k})<o:p class=""></o:p></div>
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end<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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cfg.gridscale = 90<o:p class=""></o:p></div>
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cfg.projection = 'orthographic'<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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cfg.viewpoint = 'left'<o:p class=""></o:p></div>
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cfg.style = 'both';<o:p class=""></o:p></div>
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cfg.layout = 'ast_insole_xw';<o:p class=""></o:p></div>
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cfg.highlight = 'on';<o:p class=""></o:p></div>
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cfg.highlightchannel = find(stat.mask);<o:p class=""></o:p></div>
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cfg.comment = 'no';<o:p class=""></o:p></div>
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cfg.colorbar = 'yes'<o:p class=""></o:p></div>
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figure; ft_topoplotER(cfg,<span class="Apple-converted-space"> </span><span style="font-size: 10pt; font-family: Consolas;" class="">data{:}</span>)<o:p class=""></o:p></div>
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I am getting an error with the cfg.operation where arrays have incompatible sizes for this operation. Does anyone know the solution to this error?<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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Any help would be appreciated!<o:p class=""></o:p></div>
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<o:p class=""></o:p></div>
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Kind regards,<o:p class=""></o:p></div>
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<span lang="HR" class="">Lucija Ninčević<o:p class=""></o:p></span></div>
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<span lang="HR" class="">Master student at Vrije Universiteit Amsterdam</span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">fieldtrip
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<a href="https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!6hZzyflII3grBizkj-kgyIhpW3NK5XjEfx7qLa_Mo9NuWdOIpJVMYLZy7Ap_DTvMlbLrm6ys5IGX7l8zvGKvLNYp504eZhfweOowLQ$" style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.com/v3/__https://doi.org/10.1371/journal.pcbi.1002202__;!!HJOPV4FYYWzcc1jazlU!6hZzyflII3grBizkj-kgyIhpW3NK5XjEfx7qLa_Mo9NuWdOIpJVMYLZy7Ap_DTvMlbLrm6ys5IGX7l8zvGKvLNYp504eZhfweOowLQ$</a><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span></div>
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