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<p class="MsoNormal" style="margin-left:70.8pt"><span style="mso-fareast-language:EN-US">Hi Philip,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US">Here is some advice:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="margin-left:106.8pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="mso-fareast-language:EN-US"><span style="mso-list:Ignore">1.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="mso-fareast-language:EN-US">If you have a well-founded expectation for the direction of the effect (A>B, I>II, AI-BI>AII-BII) perform a one-tailed test. There is no sense in going back to a two-tailed
test.<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:106.8pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="mso-fareast-language:EN-US"><span style="mso-list:Ignore">2.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="mso-fareast-language:EN-US">Your clusteralpha=0.01 is more stringent than what most users would choose. I always go for 0.05 and never touch it (not playing around to find a value that gives me a “significant”
result). (These high thresholds 0.01 and smaller come from Gaussian Random Field theory, and are not required for permutation inference.)<o:p></o:p></span></p>
<p class="MsoListParagraph" style="margin-left:106.8pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2">
<![if !supportLists]><span lang="EN-US" style="mso-fareast-language:EN-US"><span style="mso-list:Ignore">3.<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span lang="EN-US" style="mso-fareast-language:EN-US">Did you analyze your data at the single participant level (using trials as your replications/degrees-of-freedom)? To be hopeful for a significant result
<b>over</b> participants, you need at least a few participants that show the effect at the single participant level and all over approximately the same area/frequency band/time interval. In addition, the other participants may not contradict this pattern by
showing an opposite effect over the same area/frequency band/time interval. <o:p>
</o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US">Good luck,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US">Eric Maris<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:70.8pt"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><b><span style="font-size:12.0pt;color:black">Van:
</span></b><span style="font-size:12.0pt;color:black">philip Joadavi <p.joadavi@gmail.com><br>
<b>Datum: </b>dinsdag 28 maart 2023 om 14:43<br>
<b>Aan: </b>"Maris, E.G.G. (Eric)" <e.maris@donders.ru.nl>, FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Onderwerp: </b>Fwd: 2x2 ANOVA at source level using cluster based permutation<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><br>
Dear Dr.Maris/ <span style="font-family:"Segoe UI",sans-serif;color:#212529">Schoffelen /Oostenveld</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">I posted a question on the mailing list about 2x2 ANOVA at the source level (please see below my email).<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">It's been 2 weeks and I have not found if there is anything wrong with my code. I would really really appreciate it if you could have a look at my code and let me know if I have done all the steps correctly.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Thanks a lot,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Philip<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">---------- Forwarded message ---------<br>
From: <strong><span style="font-family:"Calibri",sans-serif">philip Joadavi</span></strong> <<a href="mailto:p.joadavi@gmail.com">p.joadavi@gmail.com</a>><br>
Date: Wed, Mar 15, 2023 at 5:14 PM<br>
Subject: 2x2 ANOVA at source level using cluster based permutation<br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:106.2pt">
<o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Dear all,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">I would like to run ANOVA to test the main and interaction effects on my beamforming results. (I used DISC beamformer)<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">I've already looked at the FAQ on the FieldTrip website and also the questions in the mailing list.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">To check if I have done the steps correctly, I have also done the 2x2 ANOVA using SPM and I got significant results, but without FWE/FDR correction for multiple comparisons at the voxel level.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">When I apply the steps described in the FieldTrip and also the mailing list (for cluster-based permutation) I could not get any significant clusters. This is surprising for me because I get always nicer results
from permutation tests than I do not get from SPM.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">I think I'm doing something wrong and I would appreciate any help.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">So, as far as I understood, I can not use F statistics for 2x2 ANOVA, and therefore I used dependent sample T statistics for within-subject design as explained by Eric in the mailing list. <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">here is my code :<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">So, I have 2 conditions A and B, each with 2 levels (I & II).<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">For the averages, I used ft_ grandaverage for 2 conditions/levels, and I got a matrix of pow = [number of subjects x number of voxels] = [12x 411477]<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Here is the code:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">my data is arranged such that the columns are the conditions (A/B) and the rows are the levels (I/II).<o:p></o:p></p>
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<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% Main effect of levels (I/II)<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">I = ft_sourcegrandaverage([],GA{1,1:2});<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">II = ft_sourcegrandaverage([],GA{2,1:2});<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% Main effect of conditions (A/B)<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">A = ft_sourcegrandaverage([],GA{1:2,1});<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">B = ft_sourcegrandaverage([],GA{1:2,2});<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% Interaction effect<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg = [];<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.operation = <span style="color:#A020F0">
'subtract'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.parameter = <span style="color:#A020F0">
'pow'</span>; <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">INA = ft_math(cfg, GA{1,1}, GA{2,1});
<span style="color:forestgreen">% I - II (A)</span><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">INB = ft_math(cfg, GA{1,2}, GA{2,2});
<span style="color:forestgreen">% I - II (B)</span><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen"> <o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier;color:forestgreen">%% prepare the hypothesis testing<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg = [];<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.dim = GA{1}.dim;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.method = <span style="color:#A020F0">
'montecarlo'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.correctm = <span style="color:#A020F0">
'cluster'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.spmversion = <span style="color:#A020F0">
'spm12'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.parameter = <span style="color:#A020F0">
'pow'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier;color:black">cfg.numrandomization =
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'all'</span><span style="font-size:7.5pt;font-family:Courier;color:black">; </span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen"><o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal">
<span style="font-size:7.5pt;font-family:Courier">cfg.correcttail = <span style="color:#A020F0">
'alpha'</span>;<o:p></o:p></span></p>
<p style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:106.2pt;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;min-height:12px">
<span style="font-size:7.5pt;font-family:Courier"><o:p> </o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier;color:black">cfg.statistic =
</span><span style="font-size:7.5pt;font-family:Courier;color:#A020F0">'depsamplesT'</span><span style="font-size:7.5pt;font-family:Courier;color:black">;</span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen"><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.alpha = 0.05/2; <span style="color:forestgreen">
% two tails</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.clusteralpha = 0.01;<o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier;color:black">cfg.tail = 0; </span><span style="font-size:7.5pt;font-family:Courier;color:forestgreen">% I also tried 1 for one tail<o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.clustertail = <span style="color:black">cfg.tail</span>;<o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.uvar = 1; <span style="color:forestgreen">
% subject</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.ivar = 2; <span style="color:forestgreen">
% conditions</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">cfg.design = [repmat(1:numel(subjects),1,2); repelem([1 2],numel(subjects))];<o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier"> <o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier;color:#A020F0"><o:p> </o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">stat{1} = ft_sourcestatistics(cfg,I,II); <span style="color:forestgreen">% main effect (I/II)</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">stat{2} = ft_sourcestatistics(cfg,A,B); <span style="color:forestgreen">% main effect (A/B)</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier">stat{3} = ft_sourcestatistics(cfg,INA,INB); <span style="color:forestgreen">% Interaction</span><o:p></o:p></span></p>
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<span style="font-size:7.5pt;font-family:Courier"><o:p> </o:p></span></p>
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<span style="font-size:12.0pt;font-family:"Arial",sans-serif">Side note: I also tried the one-tail option, but the results were not significant eighter. </span><span style="font-size:9.0pt;font-family:Courier"><o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:Courier"><o:p> </o:p></span></p>
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<span style="font-size:9.0pt;font-family:Courier"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:106.2pt">I would appreciate any help!<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Best,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt">Philip<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:106.2pt"> <o:p></o:p></p>
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