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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Jan-Mathijs,
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Thanks for the fast reply. Data is indeed internally consistent. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">And I will read that paper in more detail... Thanks!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Best,<br>
Linda <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">dr. Linda Drijvers | postdoctoral researcher | https://cosilab.org
<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">www.ru.nl/english/people/drijvers-l/ | https://www.mpi.nl/people/drijvers-linda<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> fieldtrip <fieldtrip-bounces@science.ru.nl>
<b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs)<br>
<b>Sent:</b> woensdag 6 mei 2020 11:18<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] missing sample after using ft_componentanalysis with method bsscca<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Linda <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Is the data internally consistent after ft_componentanalysis? In other words, does the number of time points per trial (in data.time) match the number of columns in data.trial?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please note that the bsscca is a poorly maintained corner (and hardly ever used) of the code, so it might need improvement.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Feel free to send us a Pull Request through github for code improvements.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal">Jan-Mathijs<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">PS: bsscca returns ’shorter’ data than the input because of the way the algorithm works, as described in the reference paper.<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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<o:p></o:p></p>
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<p class="MsoNormal">On 6 May 2020, at 10:23, Drijvers, L. (Linda) <<a href="mailto:l.drijvers@donders.ru.nl">l.drijvers@donders.ru.nl</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 style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">P.S., sorry, mixed things up: data in comp_output.trial have 499 samples, while smps has 500 elements (presumably based on sampleinfo). So key question is: why
do the output trials after bsscca have 1 fewer sample than the input trials?<br>
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Best,<br>
Linda<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">dr. Linda Drijvers | postdoctoral researcher |<span class="apple-converted-space"> </span><a href="https://cosilab.org/"><span style="color:#954F72">https://cosilab.org</span></a></span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><a href="http://www.ru.nl/english/people/drijvers-l/"><span style="color:#954F72">www.ru.nl/english/people/drijvers-l/</span></a><span class="apple-converted-space"> </span>|<span class="apple-converted-space"> </span><a href="https://www.mpi.nl/people/drijvers-linda"><span style="color:#954F72">https://www.mpi.nl/people/drijvers-linda</span></a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">fieldtrip
<<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Drijvers, L. (Linda)<br>
<b>Sent:</b><span class="apple-converted-space"> </span>woensdag 6 mei 2020 09:59<br>
<b>To:</b><span class="apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
<b>Subject:</b><span class="apple-converted-space"> </span>[FieldTrip] missing sample after using ft_componentanalysis with method bsscca<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Dear all,<span class="apple-converted-space"> </span><br>
<br>
I’m analysing an EEG dataset using MATLAB 2016a + FieldTrip version 20200409.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I am trying to use ft_componentanalysis with cfg.method = ‘bsscca’ (see code):<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
cfg = [];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">cfg.channel = 1:length(data_Aclean.label)-2; <span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">cfg.method = 'bsscca';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">cfg.cellmode = 'yes';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">comp_output = ft_componentanalysis(cfg, data_Aclean);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">When I then try to use ft_databrowser with the following code:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cfg = [];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cfg.channel = [1:10];<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cfg.viewmode = 'component';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> cfg.layout = 'customlayout.mat';<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ft_databrowser(cfg, comp_output);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I get the following error:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><br>
Index exceeds matrix dimensions.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Error in ft_fetch_data (line 199)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> dat(:,ok) = data.trial{utrl}(chanindx,smps);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Error in ft_databrowser>redraw_cb (line 1630)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> dat = ft_fetch_data(opt.orgdata, 'header', opt.hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> 'allowoverlap', istrue(cfg.allowoverlap));<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Error in ft_databrowser (line 729)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">redraw_cb(h);<br>
<br>
A closer look at the data shows that while fsample for my data is 500, smps is 499 after running ft_componentanalysis with method bsscca. However, I can solve the error above by running ft_databrowser with comp_output = rmfield(comp_output, 'sampleinfo').<span class="apple-converted-space"> </span><br>
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My question is: what causes this discrepancy in smps (why does this one sample go missing)? Any help would be appreciated.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Best wishes,<br>
Linda Drijvers<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Calibri",sans-serif">dr. Linda Drijvers | postdoctoral researcher |
<a href="https://cosilab.org">https://cosilab.org</a></span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri",sans-serif"><a href="http://www.ru.nl/english/people/drijvers-l/">www.ru.nl/english/people/drijvers-l/</a> |
<a href="https://www.mpi.nl/people/drijvers-linda">https://www.mpi.nl/people/drijvers-linda</a></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a></span><o:p></o:p></p>
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