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Hi JM</div>


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Thanks for your suggestion. </div>


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I checked the design matrix, and it seems fine. I am still confused what could be the problem...</div>


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Kind regards</div>


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Nan</div>


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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip@science.ru.nl><br>


<b>Sent:</b> Monday, 22 July 2024 12:13 PM<br>


<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>


<b>Cc:</b> Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen@donders.ru.nl><br>


<b>Subject:</b> Re: [FieldTrip] why the significant clusters being highlighted not in the correct position_topography_cluster based permutation test</font>


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⚠ Caution: External sender</p>


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<div>Hi NC,


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<div>Could it be that you mixed up the 1’s and 2’s in your design into ft_timelockstatistics, and that you are highlighting the sensors for which the opposite contrast yielded p-values < 0.025?</div>


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<div>BW,</div>


<div>JM</div>


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<div>On 18 Jul 2024, at 19:02, Chen, Nan via fieldtrip <fieldtrip@science.ru.nl> wrote:</div>


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Hi community</div>


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I have tried to follow the tutorial "cluster-based permutation test on event-related fields": </div>


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However, I am encountering an issue with the topography figure</div>


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As shown in the attached picture, the highlighted marker does not seem to be in the correct location. It appears misaligned with the area of the most intense color.</div>


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I am just wondering if anyone have any clues? Thanks</div>


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Here is my code:</div>


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figure;</div>


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% define parameters for plotting</div>


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timestep = 0.01; %(in seconds)</div>


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sampling_rate = 300; %% double check this: preprocessing file</div>


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sample_count = length(stat.time);</div>


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j = [0.05:timestep:0.25]; % Temporal endpoints (in seconds) of the ERP average computed in each subplot</div>


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m = [1:timestep*sampling_rate:sample_count]; % temporal endpoints in M/EEG samples</div>


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% get relevant values</div>


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pos_cluster_pvals = [stat.posclusters(:).prob];</div>


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pos_clust = find(pos_cluster_pvals < 0.025);</div>


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pos = ismember(stat.posclusterslabelmat, pos_clust);</div>


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% First ensure the channels to have the same order in the average and in the statistical output.</div>


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% This might not be the case, because ft_math might shuffle the order</div>


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[i1,i2] = match_str(GA_FacevsNoise.label, stat.label);</div>


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% plot</div>


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for k = 1:20;</div>


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cfg.figure = subplot(4,5,k);</div>


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cfg.xlim = [j(k) j(k+1)];</div>


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cfg.zlim = [-5e-14 5e-14];</div>


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pos_int = zeros(numel(GA_FacevsNoise.label),1);</div>


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pos_int(i1) = all(pos(i2, m(k):m(k+1)), 2); % change i2 i1, try11111111111111111</div>


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cfg.highlight = 'on';</div>


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cfg.highlightchannel = find(pos_int);</div>


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cfg.comment = 'xlim';</div>


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cfg.commentpos = 'title';</div>


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cfg.layout = 'CTF275_helmet.mat';</div>


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cfg.figure = 'gca';</div>


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ft_topoplotER(cfg, GA_FacevsNoise);</div>


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end</div>


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<span><span id="x_cid:f4d067c8-558f-441b-aba2-8afae83e9356"><image.png></span></span></div>


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Kind regards</div>


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NC</div>


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<span style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">


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<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="VoSPdFjzEJc+AvUl3BrvnkgyoqcRFQv5QekR0npF/LHqsRDz1RFxIraVqWxSs0r9p5mhgxbjfqRZRls2P7XHjWDcjZ9Gh2h3QuV5jI2eofuojJkqvRelfUS8Fn0+WskpYq2RP4QhiJXBvRBSZ1+t1XHGxEIFBF/XZW4lFyjGWvw=" originalsrc="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" shash="kOEu0tAubL9Lr4weNi9jiH+3Js0rMP+9CSoxNMhCOhk+BxWUYhFIDOyatY8nwN/idc4efxN0NAfcNT6L767tasNuZpfaHU5y9mmbdAnHl8b+tBGnGQup7CyFl6ikdG/JVUqE9X5BPboes7ONNMkxqhChAWfuoCvPcXsAIkY/URw=" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">


<a href="https://doi.org/10.1371/journal.pcbi.1002202" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="gO8VCJHZpq+qu4p0by9qsFlvu3xUvvlnxQYOsOJsgoinZio0d6OGgrZKlgZKniSvuN4qpIxWl89gFBehSx/wrmE7KXZX7o3BmPPlr5LYMX0kig7LEC1sEXNfUBj1XfaGspuA7d5wTcKqlfxhio7ICmyyDw/mOOlng2oSE5oXrPc=" originalsrc="https://doi.org/10.1371/journal.pcbi.1002202" shash="U1EvpLMIfG0pECX05DMAk42LthnQNvF0PpNAcvL9sDkxljxU1eiyQzzWYPg6z2+MZVpCPI0020lUp/WYKmBsm/2V883C9uGklGjI8/Y0vF45AcYk4nT3Q2Fcg4gn/z5VFN6aBseEN2FYozo4aVV1CLKDWlWrxkV/O3uyOhQqWJM=" style="font-family:Helvetica; font-size:14px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://doi.org/10.1371/journal.pcbi.1002202</a></div>


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