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<p class="MsoNormal">Hi Jan-Mathijs,<o:p></o:p></p>
<p class="MsoNormal">Thanks for this information, this makes sense. <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sara<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">"Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen@donders.ru.nl><br>
<b>Reply-To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Date: </b>Tuesday, June 2, 2020 at 4:28 AM<br>
<b>To: </b>FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject: </b>Re: [FieldTrip] ft_sourcestatistics output<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">Hi Sara, </span> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">Thanks for reaching out. I am sorry that you are confused by the textual output of the function.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">The statement ‘using connectivity of voxels in 3-D volume’ refers to the fact that you requested a cluster-based heuristic for multiple comparison correcion. Thus, the code needs to define how individual space-time-frequency
points are connected, hence the term connectivity in this context.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">The statement ‘using … for the single-sample statistics’: the single sample here refers to the fact that the test-statistic-of-interest, here an unpaired T-statistic, is computed for each individual (space-time-frequency)
sample of the data.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">If you have a good suggestion as to how to amend this text, please feel free to make a Pull Request on github with your suggestions included.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">Best wishes,</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:13.5pt">Jan-Mathijs</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 1 Jun 2020, at 21:04, Hussain, Sara (NIH/NINDS) [F] <<a href="mailto:sara.hussain@nih.gov">sara.hussain@nih.gov</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">Hi FieldTrippers-</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">I have a somewhat simple question. I am running some statistics on source-localized frequency domain data across two groups of subjects. I would like to use the independent
samples t-test statistic for cluster-based permutation testing. However, the output in the command window when I run my code seems to disagree with what I am specifying. I’ve followed the tutorials closely on this to ensure I am doing the analysis appropriately.</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">I am running the following:</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg=[];</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.parameter='pow';</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.method='montecarlo';</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.statistic='indepsamplesT';</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.correctm='cluster';</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.clusteralpha=0.05;</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.clusterstatistic='maxsum';</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.tail=0;</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.clustertail=0;</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.alpha=0.025;</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.numrandomization=1000;</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">cfg.design=[repmat(1,1,numel(cond_A)) repmat(2,1,numel(cond_B))]; %1=cond A, 2=cond B</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">stat=ft_sourcestatistics(cfg,cond_A{:},cond_B{:});</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">The command window prints the following. Bolded are the items that seem misleading. I have not specified any connectivity analysis. Also, the bit talking about single-sample
statistics leads me to believe that this is running a single sample t-test where a set of observations is being contrasted against some expected mean value:</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">using "ft_statistics_montecarlo" for the statistical testing</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><b><span style="font-size:8.5pt;font-family:Menlo">using connectivity of voxels in 3-D volume</span></b></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><b><span style="font-size:8.5pt;font-family:Menlo">using "ft_statfun_indepsamplesT" for the single-sample statistics</span></b></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">constructing randomized design</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">total number of measurements</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
33</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">total number of variables</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
1</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">number of independent variables</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
1</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">number of unit variables</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
0</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">number of within-cell variables</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
0</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">number of control variables</span></span><span class="apple-converted-space"><span style="font-size:8.5pt;font-family:Menlo"> </span></span><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">=
0</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">using a permutation resampling approach</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"><span class="s1"><span style="font-size:8.5pt;font-family:Menlo">computing a parametric threshold for clustering</span></span><span style="font-size:8.5pt;font-family:Menlo"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Any tips anyone has would be very much appreciated!<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Sara<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica">_______________________________________________<br>
fieldtrip mailing list<br>
</span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style="font-size:10.5pt;font-family:Helvetica;color:#954F72">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style="font-size:10.5pt;font-family:Helvetica"><br>
</span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style="font-size:10.5pt;font-family:Helvetica;color:#954F72">https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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