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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Dear All,</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">I have a mixed design (2 conditions x 2 groups), with 44 participants in group1, and 30 participants in group2, and I am planning to run cluster-based permutation tests on ERP
data to test:</span><o:p></o:p></p>
<ul style="margin-top:0cm;caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px" type="disc">
<li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;line-height:11.55pt;mso-list:l1 level1 lfo3">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">The main effect of condition (cond1 vs. cond2)</span><o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;line-height:11.55pt;mso-list:l1 level1 lfo3">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">The main effect of group (group1 vs. group2)</span><o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;line-height:11.55pt;mso-list:l1 level1 lfo3">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">The effect of condition in group1 (group1 cond1 vs. group1 cond2)</span><o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;line-height:11.55pt;mso-list:l1 level1 lfo3">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">The effect of condition in group2 (group2 cond1 vs. group2 cond2)</span><o:p></o:p></li><li class="MsoListParagraph" style="color:black;margin-top:0cm;margin-bottom:0cm;margin-bottom:.0001pt;line-height:11.55pt;mso-list:l1 level1 lfo3">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">The interaction effect between condition and group (group1 cond1 - group1 cond2) vs. (group2 cond1 - group2 cond2)</span><o:p></o:p></li></ul>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">I have used ft_timelockanalysis to create data structures for<span class="apple-converted-space"> </span></span><span style="font-size:9.0pt;font-family:"Courier New";color:black">COND1_ft,
COND2_ft, group1_ft, group2_ft;</span><span class="apple-converted-space"><span style="color:black"> </span></span><span style="font-size:9.0pt;font-family:"Courier New";color:black">COND1group1_ft, COND2group1_ft; COND1group2_ft, COND2group2_ft<span class="apple-converted-space"> </span></span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">but
I am having some doubts regarding design matrix and cfg.statistic. I have read the suggestions and comments in the discussion list, but I’m still not sure if I’m setting them up correctly. Below, I specify what I’m trying to do and how I have done it so far:<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">First, my understanding from a message dated some years ago<span class="apple-converted-space"> </span></span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckpoint.url-protection.com%2Fv1%2Furl%3Fo%3Dhttps%253A%2F%2Fmailman.science.ru.nl%2Fpipermail%2Ffieldtrip%2F2008-March%2F014371.html%26g%3DZTA5ZGFlZmVjOGUwZmI3NQ%3D%3D%26h%3DMTFjODNhYTQ3Y2Y3ZjExYzJlNDFhYWViMmNkOGY5ZjI4YTNkNGE2YmYyMWJhNTg4NDBmMzgzYWU1N2E2NGJjZQ%3D%3D%26p%3DY3AxZTp1Y2xhbmxpdmU6Y2hlY2twb2ludDpvZmZpY2UzNjVfZW1haWxzX2VtYWlsOmQ5MDRjMWVjMjg3ZWRiNjczMWYzZWE5MTZhNTllNjdhOnYx&data=02%7C01%7Cappc1%40leicester.ac.uk%7Ce899c343fb564cfb3c0808d869084e1f%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637374831680312333&sdata=J%2FIiZH2UHC2LxK5RquGqTBr7V1sNC1yk9diS8nIUUOc%3D&reserved=0" title="Protected by Check Point: https://mailman.science.ru.nl/pipermail/fieldtrip/2008-March/014371.html"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">https://mailman.science.ru.nl/pipermail/fieldtrip/2008-March/014371.html</span></a><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span></span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">is
that to perform permutation tests on a mixed design we should have a design matrix with Row 1 (condition), Row 2 (subject number), and Row 3 (group). In my case:</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">sbj = 74 %(i.e., 44 sbjs in group1, 30 subjs in group2);</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">design = zeros(3, 2*sbj);</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Set up Row 1</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">design(1, 1:sbj) = 1; %(Row 1 with cond1 from 1:74 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">design(1,sbj+1:2*sbj) = 2; %(Row 1 with cond2 from 75:148 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Set up Row 2</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">for i= 1:sbj</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> design(2,i) = i; %(Row 2 with sbj number from 1:74 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">end</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">for i=1:sbj</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> design(2,sbj+i)=i; %(Row 2 with sbj number from 75:148 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">end</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Set up Row 3</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">design(3, [1:44 75:118]) = 1; %(Row 3 with group1 from 1:44 and 75:118 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">design(3, [45:74 119:sbj*2]) = 2; %(Row 3 with group2 from 45:74 and 119:148 column)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.design = design;</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">With the following configuration:</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.method = 'montecarlo';</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.ivar = 1 %(row with independent variable, i.e., condition number)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.uvar = 2 %(row with unit variables, i.e., subject number)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.wvar = 3 %(row with within-cell variable, i.e., group number)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">And, with the rest of the configuration set up as follows:<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.minnbchan = 2;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.neighbours = neighbours; <span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.alpha = 0.05;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.tail = 0; %two-sided test</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.correcttail = 'alpha'; %conceptually equivalent to performing a Bonferroni correction for the two tails</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.numrandomization = 10000;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.correctm = 'cluster';</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.clusterstatistic = 'maxsum';<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.clusteralpha = 0.05;<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.clustertail = 0;</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">However, I am not sure about the design matrix because when I try to run the previous code, I get the following error messages:</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">Error using resampledesign (line 153)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">the design matrix variables should be constant within a block</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">Error in ft_statistics_montecarlo (line 215)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">resample = resampledesign(cfg, design);</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">Error in ft_timelockstatistics (line 182)</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> [stat, cfg] = statmethod(cfg, dat, design);</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Second, I am not sure which<span class="apple-converted-space"> </span><i>cfg.statistic</i><span class="apple-converted-space"> </span>I should be using<span class="apple-converted-space"> </span>in
the mixed design. If I use subject number as my unit of observation (UO), then, in one case, UO is assigned to only one of two groups (between UO-design; independent samples), but at the same time, every UO is assigned to two experimental conditions (within
UO-design; dependent samples) (</span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckpoint.url-protection.com%2Fv1%2Furl%3Fo%3Dhttp%253A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Fcluster_permutation_timelock%2F%253Fs%26g%3DODA3YTA1ZjRiNWVhMDZmNA%3D%3D%26h%3DN2U4N2NkMjVjZWI4ODE4ZjM2OWI2NTllYjk5ZjRmNTM3MDM0YTE2ZWVjOTA2M2Q4NGY5NjYzODI4MTMxMTFmYg%3D%3D%26p%3DY3AxZTp1Y2xhbmxpdmU6Y2hlY2twb2ludDpvZmZpY2UzNjVfZW1haWxzX2VtYWlsOmQ5MDRjMWVjMjg3ZWRiNjczMWYzZWE5MTZhNTllNjdhOnYx&data=02%7C01%7Cappc1%40leicester.ac.uk%7Ce899c343fb564cfb3c0808d869084e1f%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637374831680322333&sdata=2Lfp1tH7U8voUiSwSZ1mcsV%2Fcr99xLUnZ9g3hDyBRnA%3D&reserved=0" title="Protected by Check Point: http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/?s"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif">http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock/?s</span></a><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">).<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">So, my question is: Is there any way<span class="apple-converted-space"> </span>to use a single cfg.statistic with a mixed design or should I run two separate tests: one with<span class="apple-converted-space"> </span></span><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.statistic
= 'depsamplesT';<span class="apple-converted-space"> </span></span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">to test the main effect of condition (cond1 vs. cond2), the effect of condition in group1 (group1 cond1 vs.
group1 cond2), and the effect of condition in group2 (group2 cond1 vs. group2 cond2), and another test<span class="apple-converted-space"> </span></span><span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.statistic = 'indepsamplesT';<span class="apple-converted-space"> </span></span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">to
test the main effect of group (group1 vs. group2)?</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">After this, I would then test:</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Main effect of Condition</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">[statCOND] = ft_timelockstatistics(cfg, COND1_ft{:}, COND2_ft{:}); <span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Main effect of Group</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">[statGROUP] = ft_timelockstatistics(cfg, group1_ft{:}, group2_ft{:});</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Main Effect of Condition in Group1</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">[statCONDgroup1] = ft_timelockstatistics(cfg, COND1group1_ft{:},COND2group1_ft{:});<span class="apple-converted-space"> </span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Main Effect of Condition in Group2</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">[statCONDgroup2] = ft_timelockstatistics(cfg, COND1group2_ft{:},COND2group2_ft{:});</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Finally, to test the interaction effect ((group1 cond1 - group1 cond2) vs. (group2 cond1 - group2 cond2)), I was planning to use</span> <span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">cfg.statistic
=</span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif"> <span style="color:black">'indepsamplesT’</span></span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">(as in (</span><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckpoint.url-protection.com%2Fv1%2Furl%3Fo%3Dhttp%253A%2F%2Fwww.fieldtriptoolbox.org%2Ffaq%2Fhow_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests%2F%26g%3DOGUwN2JmNGFiYjU2NzY5YQ%3D%3D%26h%3DOWRlYTI1NTQzZGQyMDdiYWRiNDk0YzYzMzMzNWFhYzFkNmU3ZDkxOTU3OTJmZGYwOTY0YWE1Yjk0ZDVkZjdhNg%3D%3D%26p%3DY3AxZTp1Y2xhbmxpdmU6Y2hlY2twb2ludDpvZmZpY2UzNjVfZW1haWxzX2VtYWlsOmQ5MDRjMWVjMjg3ZWRiNjczMWYzZWE5MTZhNTllNjdhOnYx&data=02%7C01%7Cappc1%40leicester.ac.uk%7Ce899c343fb564cfb3c0808d869084e1f%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637374831680322333&sdata=Pn7%2F7OTE%2FkWUGhqp%2Bnmx4Y7JlYYA6hGwOBOKXvMsIOU%3D&reserved=0" title="Protected by Check Point: http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/"><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black;text-decoration:none">http://www.fieldtriptoolbox.org/faq/how_can_i_test_an_interaction_effect_using_cluster-based_permutation_tests/</span></a><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">)</span><span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif"> <span style="color:black"> and</span></span> <span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">then,
first, calculate the differences as follows:</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg = [];</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.operation = 'subtract';</span><o:p></o:p></p>
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<span style="font-size:9.0pt;font-family:"Courier New";color:black">cfg.parameter = 'avg';</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">for i =1:length(COND1group1_ft)</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt;caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">CONDgroup1DIFF_ft{i} = ft_math(cfg, COND1group1_ft{i}, COND2group1_ft{i});</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">end</span><o:p></o:p></p>
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<span style="font-size:9.0pt;font-family:"Courier New";color:black">for i = 1:length(COND1group2_ft)</span><o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt;caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">CONDgroup2DIFF_ft{i} = ft_math(cfg, COND1group2_ft{i}, COND2group2_ft{i});</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">end</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Second, set up the configuration as above and run the following:</span><o:p></o:p></p>
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<span style="font-size:9.0pt;font-family:"Courier New";color:black">%Test Interaction Effect between Condition and Group</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:9.0pt;font-family:"Courier New";color:black">[statCONDbyGROUP] = ft_timelockstatistics(cfg,CONDgroup1DIFF_ft{:},CONDgroup2DIFF_ft{:});</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Apologise for the long email, but I hope it makes sense. I’d be grateful to any advice or suggestion about the design matrix and cfg.statistic.</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black"> </span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Best wishes,</span><o:p></o:p></p>
<p class="MsoNormal" style="caret-color: rgb(0, 0, 0);font-variant-caps: normal;orphans: auto;text-align:start;widows: auto;-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0px;word-spacing:0px">
<span style="font-size:10.0pt;font-family:"Calibri Light",sans-serif;color:black">Ascen</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">--------------------------------</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Dr Ascensión Pagán</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Lecturer, Department of Psychology</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Faculty of Health and Life Sciences</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Northumbria University</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">Newcastle upon Tyne</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">NE1 8ST</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman",serif;color:black">UK</span><o:p></o:p></p>
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<p class="MsoNormal"><a href="mailto:ascension.pagan@northumbria.ac.uk">ascension.pagan@northumbria.ac.uk</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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