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Hi Linda,
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<div class="">I have adjusted ft_componentanalysis, to remove the sampleinfo field from the output in case bsscca is used as method.</div>
<div class="">This change will be available at the DCCN cluster soon, is alreadly available on the master development branch on github, and will in the release version on github soon.</div>
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<div class="">Best wishes,</div>
<div class="">Jan-Mathijs</div>
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<div class="">On 6 May 2020, at 11:34, Drijvers, L. (Linda) <<a href="mailto:l.drijvers@donders.ru.nl" class="">l.drijvers@donders.ru.nl</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Jan-Mathijs,<span class="Apple-converted-space"> </span><br class="">
<br class="">
Thanks for the fast reply. Data is indeed internally consistent.<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">And I will read that paper in more detail... Thanks!<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best,<br class="">
Linda<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">dr. Linda Drijvers | postdoctoral researcher |<span class="Apple-converted-space"> </span><a href="https://cosilab.org/" style="color: purple; text-decoration: underline;" class="">https://cosilab.org</a><o:p class=""></o:p></span></b></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL<o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://www.ru.nl/english/people/drijvers-l/" style="color: purple; text-decoration: underline;" class="">www.ru.nl/english/people/drijvers-l/</a><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span><a href="https://www.mpi.nl/people/drijvers-linda" style="color: purple; text-decoration: underline;" class="">https://www.mpi.nl/people/drijvers-linda</a><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl" class="">fieldtrip-bounces@science.ru.nl</a>><span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Schoffelen, J.M. (Jan Mathijs)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>woensdag 6 mei 2020 11:18<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" class="">fieldtrip@science.ru.nl</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [FieldTrip] missing sample after using ft_componentanalysis with method bsscca<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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Hi Linda<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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 class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Please note that the bsscca is a poorly maintained corner (and hardly ever used) of the code, so it might need improvement.<o:p class=""></o:p></div>
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Feel free to send us a Pull Request through github for code improvements.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Best,<o:p class=""></o:p></div>
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Jan-Mathijs<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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PS: bsscca returns ’shorter’ data than the input because of the way the algorithm works, as described in the reference paper.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""></o:p></div>
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On 6 May 2020, at 10:23, Drijvers, L. (Linda) <<a href="mailto:l.drijvers@donders.ru.nl" style="color: purple; text-decoration: underline;" class="">l.drijvers@donders.ru.nl</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class="">
<br class="">
Best,<br class="">
Linda<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">dr. Linda Drijvers | postdoctoral researcher |<span class="apple-converted-space"> </span><a href="https://cosilab.org/" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">https://cosilab.org</span></a></span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL</span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://www.ru.nl/english/people/drijvers-l/" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">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" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(149, 79, 114);" class="">https://www.mpi.nl/people/drijvers-linda</span></a></span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span class="apple-converted-space"><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">fieldtrip
<<a href="mailto:fieldtrip-bounces@science.ru.nl" style="color: purple; text-decoration: underline;" class="">fieldtrip-bounces@science.ru.nl</a>><span class="apple-converted-space"> </span><b class="">On Behalf Of<span class="apple-converted-space"> </span></b>Drijvers,
L. (Linda)<br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>woensdag 6 mei 2020 09:59<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl" style="color: purple; text-decoration: underline;" class="">fieldtrip@science.ru.nl</a><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>[FieldTrip] missing sample after using ft_componentanalysis with method bsscca<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear all,<span class="apple-converted-space"> </span><br class="">
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I’m analysing an EEG dataset using MATLAB 2016a + FieldTrip version 20200409.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am trying to use ft_componentanalysis with cfg.method = ‘bsscca’ (see code):<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class="">
cfg = [];<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">cfg.channel = 1:length(data_Aclean.label)-2; <span class="apple-converted-space"> </span><o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">cfg.method = 'bsscca';<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">cfg.cellmode = 'yes';<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">comp_output = ft_componentanalysis(cfg, data_Aclean);<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">When I then try to use ft_databrowser with the following code:<o:p class=""></o:p></span></p>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> cfg = [];<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> cfg.channel = [1:10];<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> cfg.viewmode = 'component';<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> cfg.layout = 'customlayout.mat';<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> ft_databrowser(cfg, comp_output);<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">I get the following error:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><br class="">
Index exceeds matrix dimensions.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Error in ft_fetch_data (line 199)<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> dat(:,ok) = data.trial{utrl}(chanindx,smps);<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Error in ft_databrowser>redraw_cb (line 1630)<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> dat = ft_fetch_data(opt.orgdata, 'header', opt.hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', chanindx,<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> 'allowoverlap', istrue(cfg.allowoverlap));<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Error in ft_databrowser (line 729)<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">redraw_cb(h);<br class="">
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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 class="">
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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 class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best wishes,<br class="">
Linda Drijvers<o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">dr. Linda Drijvers | postdoctoral researcher |<span class="Apple-converted-space"> </span><a href="https://cosilab.org/" style="color: purple; text-decoration: underline;" class="">https://cosilab.org</a></span></b><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif;" class="">Donders Institute for Brain, Cognition and Behaviour, Radboud University, NL</span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10pt; font-family: Calibri, sans-serif;" class=""><a href="http://www.ru.nl/english/people/drijvers-l/" style="color: purple; text-decoration: underline;" class="">www.ru.nl/english/people/drijvers-l/</a><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span><a href="https://www.mpi.nl/people/drijvers-linda" style="color: purple; text-decoration: underline;" class="">https://www.mpi.nl/people/drijvers-linda</a></span><span style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 10.5pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">
fieldtrip mailing list<br class="">
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" style="color: purple; text-decoration: underline;" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br class="">
<a href="https://doi.org/10.1371/journal.pcbi.1002202" style="color: purple; text-decoration: underline;" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></span><o:p class=""></o:p></div>
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<o:p class=""> </o:p></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
mailing list</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=""><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" class="">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></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=""><a href="https://doi.org/10.1371/journal.pcbi.1002202" class="">https://doi.org/10.1371/journal.pcbi.1002202</a></span></div>
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