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<p class="MsoNormal"><span style="color:#1F497D">Hi Sophie,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">many thanks!! <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Kirsten<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Arana, S.L. (Sophie) [mailto:S.Arana@donders.ru.nl]
<br>
<b>Gesendet:</b> Montag, 13. Mai 2019 12:17<br>
<b>An:</b> Herfurth, Kirsten; fieldtrip@science.ru.nl<br>
<b>Betreff:</b> Re: Error occurs when applying searchgrid for lambda in MVPA light toolbox<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Hi Kirsten,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">thank you for the code, I can now replicate the error. The reason I could not replicate it earlier was because I had not pulled the latest changes in the MVPA toolbox. Now I get the same error
and to me this looks like a bug in the code caused by the latest change. The weights are not properly split into train and test set when doing the nested cross-validation for selecting lambda.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">I am not sure where in the code to best fix this, so I created an issue over on Matthias's github. He's usually very fast in fixing things :)<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">If you have a github account you could watch his repo to be notified about conversations on this issue <a href="https://github.com/treder/MVPA-Light">https://github.com/treder/MVPA-Light</a>.<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black"><o:p> </o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Best,<o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Sophie<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> Herfurth, Kirsten <Kirsten.Herfurth@uk-erlangen.de><br>
<b>Sent:</b> Friday, May 10, 2019 2:27 PM<br>
<b>To:</b> Arana, S.L. (Sophie); fieldtrip@science.ru.nl<br>
<b>Subject:</b> AW: Error occurs when applying searchgrid for lambda in MVPA light toolbox</span><span style="font-size:12.0pt;color:#212121">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:#212121"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D">Dear Sophie,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">thanks a lot for your quick answer.
</span><span lang="EN-US" style="color:#1F497D">The configuration I used is the following:</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg = [] ;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'mvpa'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.classifier =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'logreg'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;
</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.metric =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'accuracy'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.k = 3;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.param.reg =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'l2'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.param.lambda =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'auto'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.mvpa.param.plot = 1;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.latency = [0.5, 0.7];</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.avgovertime =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#A020F0">'yes'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.design = [ones(nFIC,1); 2*ones(nFC,1);];</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">stat = ft_timelockstatistics(cfg, dataFIC_LP, dataFC_LP)</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D">It seems to be important to write cfg.mvpa.param instead of cfg.param, otherwise it just ignores the L2 regularization and runs ‘logf’ instead.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D">I hope you can replicate the error this way.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D">Thanks in advance, best,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#1F497D">Kirsten</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#212121">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:#212121"> Arana, S.L. (Sophie) [mailto:S.Arana@donders.ru.nl]
<br>
<b>Gesendet:</b> Donnerstag, 9. Mai 2019 11:18<br>
<b>An:</b> fieldtrip@science.ru.nl<br>
<b>Cc:</b> Herfurth, Kirsten<br>
<b>Betreff:</b> Re: Error occurs when applying searchgrid for lambda in MVPA light toolbox</span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Dear Kirsten,</span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black"> </span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">I could not replicate your error with the MVPAlight toolbox. Could you post the code you used on the tutorial data that gave you the error?</span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black"> </span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Best,</span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
<p><span style="font-family:"Calibri","sans-serif";color:black">Sophie</span><span style="font-family:"Calibri","sans-serif";color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> fieldtrip <fieldtrip-bounces@science.ru.nl> on behalf of Herfurth, Kirsten <Kirsten.Herfurth@uk-erlangen.de><br>
<b>Sent:</b> Tuesday, May 7, 2019 1:08 PM<br>
<b>To:</b> fieldtrip@science.ru.nl<br>
<b>Subject:</b> [FieldTrip] Error occurs when applying searchgrid for lambda in MVPA light toolbox</span><span style="font-size:12.0pt;color:#212121">
</span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#212121">Dear fieldtrip developers,</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#212121">I’m extremely enthusiastic about the newly implemented MVPA light toolbox on fieldtrip, thanks a lot! I’m trying out logistic regression on my data and would like to do
a search grid for lambda with cfg.mvpa.param.lambda = ‘auto’. However, I get the following error message in line 433 of train_logreg.m when calculating the gradient g = ((cfg.weights .* sigma)' * YX)'/N - sumyxN + lambda * w: matrix dimensions must agree.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#212121">If I just pass one value for lambda, it works fine.
</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#212121">The same error occurs with the tutorial data. Here, cfg.weights has a 100x1 dimension, and sigma is 80x1 in size. I’m using Matlab 2017b and the most recent fieldtrip
2019-04-19 version.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#212121">I don’t know where to fix this and would be very grateful for your help.</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span lang="EN-US" style="color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:#212121">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="color:#212121">Kirsten Herfurth<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121">Post-Doc at the MEG-lab in Erlangen, Germany</span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="color:#212121"> </span><span style="color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#212121"> <o:p></o:p></span></p>
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