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<font size="4" class="">Hi Sara, </font>
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<div class=""><font size="4" class="">Thanks for reaching out. I am sorry that you are confused by the textual output of the function.</font></div>
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<div class=""><font size="4" class="">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.</font></div>
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</font></div>
<div class=""><font size="4" class="">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.</font></div>
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</font></div>
<div class=""><font size="4" class="">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.</font></div>
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<div class=""><font size="4" class="">Best wishes,</font></div>
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<div class=""><font size="4" class="">Jan-Mathijs</font></div>
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<blockquote type="cite" class="">
<div class="">On 1 Jun 2020, at 21:04, Hussain, Sara (NIH/NINDS) [F] <<a href="mailto:sara.hussain@nih.gov" class="">sara.hussain@nih.gov</a>> wrote:</div>
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<div class="WordSection1" style="page: WordSection1; 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;">
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<span class="s1">Hi FieldTrippers-<o:p class=""></o:p></span></div>
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<span class="s1"><o:p class=""> </o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">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.<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1"><o:p class=""> </o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">I am running the following:<o:p class=""></o:p></span></div>
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<span class="s1"><o:p class=""> </o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg=[];<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.parameter='pow';<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.method='montecarlo';<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.statistic='indepsamplesT';<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.correctm='cluster';<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.clusteralpha=0.05;<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.clusterstatistic='maxsum';<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.tail=0;<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.clustertail=0;<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.alpha=0.025;<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.numrandomization=1000;<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">cfg.design=[repmat(1,1,numel(cond_A)) repmat(2,1,numel(cond_B))]; %1=cond A, 2=cond B<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">stat=ft_sourcestatistics(cfg,cond_A{:},cond_B{:});<o:p class=""></o:p></span></div>
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<span class="s1"><o:p class=""> </o:p></span></div>
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<span class="s1">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:<o:p class=""></o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1"><o:p class=""> </o:p></span></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">using "ft_statistics_montecarlo" for the statistical testing</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1"><b class="">using connectivity of voxels in 3-D volume</b></span><b class=""><o:p class=""></o:p></b></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1"><b class="">using "ft_statfun_indepsamplesT" for the single-sample statistics</b></span><b class=""><o:p class=""></o:p></b></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">constructing randomized design</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">total number of measurements<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 33</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">total number of variables</span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 1</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">number of independent variables</span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 1</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">number of unit variables<span class="Apple-converted-space"> </span></span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 0</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">number of within-cell variables</span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 0</span><o:p class=""></o:p></div>
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<span class="s1">number of control variables</span><span class="apple-converted-space"> <span class="Apple-converted-space"> </span></span><span class="s1">= 0</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">using a permutation resampling approach</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 8.5pt; font-family: Menlo;" class="">
<span class="s1">computing a parametric threshold for clustering</span><o:p class=""></o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class="">
<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">Any tips anyone has would be very much appreciated!<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt;" class="">Sara<o:p class=""></o:p></span></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://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: rgb(149, 79, 114); text-decoration: underline; 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://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><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="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="color: rgb(149, 79, 114); text-decoration: underline; 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://doi.org/10.1371/journal.pcbi.1002202</a></div>
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