<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr">Hi
Jan-Mathijs,<br><br>Thank you so much for your swift and thorough answer! <br><br>Sadly, removing the .trl, .channels and .dimord fields did not solve my problem. It did halve the number of warnings I get (from 8 to 4). A few quick tests showed me this came down to removing the .trl field and not the other ones. <br>I also get a warning about inconsistent sampleinfo, which I forgot to mention in my original email.<br><br>Could it be a problem with my FT path? I had path-related errors with SPM earlier, and I ended up solving them by adding ft_defaults in my startup.m file. <br><br>Another thing I found out is that the error I get (<font face="courier new, monospace">Array dimensions must match for binary array op.</font><font face="arial, sans-serif">) doesn't always happen at the same time. The processing counter goes up to trial 3, and then frequency somewhere between 1 and 24. I'm not sure what this means, though.<br><br>Do you have any suggestions? <br><br>Thank you! <br><br>Thomas<br><br></font></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le lun. 3 juin 2019 à 11:35, Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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Hi Thomas,
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<div>Thanks for your informative e-mail :). </div>
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<div>Here's what I did:<br>
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<b>1- Get the data for a subset of my choosing (I tried everything with a small 4-channel, 55-trials subset)<br>
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<div><b>2- Put that data into a structure built as follows, adding fields that FieldTrip required:</b><br>
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<div><font face="courier new, monospace"> fsample: 1017 </font>(I know this is weird but we're stuck with it)</div>
<div><font face="courier new, monospace"> channels: [1 17 25 29] </font>Added to keep track of in-house bookkeeping</div>
<div><font face="courier new, monospace"> label: {'Ch:1 idElectrodeSite:181' 'Ch:17 idElectrodeSite:183' 'Ch:25 idElectrodeSite:184'
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'Ch:29 idElectrodeSite:185'} </font>Not the right structure, but I don't have header files to get them from</div>
<div><font face="courier new, monospace"> trial: {55×1 cell} </font>One cell per trial, with each being<font face="courier new, monospace"> [chan x time]</font></div>
<div><font face="courier new, monospace"> time: {55×1 cell} </font>One cell per trial, each going from -750ms to 750ms (around target onset) This includes a 250ms pad on each side.</div>
<div><font face="courier new, monospace"> trl: [55×3 double] </font>Built from scratch as if the trials were continuous. (Inspired by the FT function that does this) </div>
<div><font face="courier new, monospace"> dimord: 'chan_time' </font>Added by hand, can't get Fieldtrip to recognize it</div>
<div><font face="courier new, monospace"> sampleinfo: [55×2 double] </font>The first two columns of
<font face="courier new, monospace">trl</font></div>
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<div>You may need to get rid of the following fields: ’trl’ ‘dimord’ and ‘channels’. Once this is done, I think you are ready to go, without warnings and errors.</div>
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<div><font face="arial, sans-serif"><b>3- Try to use ft_freqanalysis using the following cfg (also attached)<br>
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<div><font face="courier new, monospace">cfg = [];<br>
cfg.method= 'tfr';<br>
cfg.pad = 'nextpow2';<br>
cfg.width = 7;<br>
cfg.gwidth = 3;<br>
cfg.foi = [15:1:60];<br>
cfg.toi = 'all';</font><br>
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I first get the message: <br>
</font><font face="courier new, monospace">the input is raw data with 4 channels and 55 trial<br>
</font><font face="arial, sans-serif">This would be encouraging, but then,
</font><span style="font-family:arial,sans-serif">I get the following warnings:</span></div>
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Warning: could not determine dimord of "trial" in: </font><font face="arial, sans-serif">(structure shown above)</font><br>
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<div><font face="courier new, monospace">Warning: could not determine dimord of "trl" in: </font><span style="font-family:arial,sans-serif">(structure shown above)<br>
...but four pairs of them.<br>
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Looking through the debugger, I found out they're given when </span><span style="font-family:arial,sans-serif">ft_freqanalysis, calls ft_checkdata and ft_selectdata. <br>
</span><span style="font-family:arial,sans-serif"><b>Are these warnings something I should be worried about, or can everything work well the way it is?</b> <br>
Also, how is it that FT 'could not determine dimord' when I give it one in the data structure, and it seems to understand the way it works given the message it sends at the beginning?<br>
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<div><span style="font-family:arial,sans-serif">After the warnings, I get this:<br>
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the call to "ft_selectdata" took 16 seconds<br>
processing trials<br>
trial 2, frequency 32 (46.18 Hz)<br>
<font color="#ff0000">Array dimensions must match for binary array op.<br>
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Error in ft_freqanalysis (line 679)<br>
trlcnt(1, ifoi, :) = trlcnt(1, ifoi, :) + shiftdim(double(acttboi(:)'),-1);<br>
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<div><font face="arial, sans-serif">...which I simply don't know how to solve.<br>
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<b>So in summary:</b> <br>
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1- Is it possible to make FT work without using original files to get the data?<br>
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Yes!</div>
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<div><font face="arial, sans-serif">2- If it is, what have I done wrong, and how could I make it work?<br>
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See above.</div>
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<div><font face="arial, sans-serif">3- Are the warnings worrisome or is it just a natural consequence of trying to jerry-rig data in FT?<br>
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Not worrisome, they should go away if you do exactly as I told :).</div>
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<div><font face="arial, sans-serif">4- Any idea on how to solve the error message I get is appreciated, but a secondary objective. <br>
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<div>Probably it goes away.</div>
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<div>Keep up the good work and with best wishes,</div>
<div>Jan-Mathijs</div>
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<div><font face="arial, sans-serif"><br>
I attached the function I made to build the data structure in case it could help.<br>
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Thank you very much for reading this long-winded message!<br>
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Regards<br>
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Thomas Lusignan, B. Sc. <br>
Paul Cisek's Lab<br>
Université de Montréal</font></div>
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