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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Hi,<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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">thanks for your answer. It seems that I was a little imprecise. Of course the original data set doesn't change but if I export the a data set
after setting a new reference in Brainvision Analyzer the header looks like that:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Original header real.vhdr<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">===============================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Brain Vision Data Exchange Header File Version 1.0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">; Data created by the Vision Recorder<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">[...]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Ch4=Fz,,0.1,µV<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"> realnewRef.vhdr<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">===============================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Brain Vision Data Exchange Header File Version 1.0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">; Data created from history path: real/Raw Data/New Reference<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">[...]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Ch4=Fz,Avg,,µV<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">This was just a test I did with some random data. I don't have acess to the orginal recording for the data sets I want to read in. The header
from them look like<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Brain Vision Data Exchange Header File Version 1.0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">; Data created from history path: passive3101/Raw Data/Filters/New Reference/Attentive<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">[...]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Ch12=Fz,ref new,,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Like I said what's really strange that I think I was able to preprocess the exact same data set a couple of month ago.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Thanks for your help!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Julian<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" 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:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip-bounces@donders.ru.nl [mailto:fieldtrip-bounces@donders.ru.nl]
<b>Im Auftrag von </b>Casper van Heck<br>
<b>Gesendet:</b> Wednesday, January 25, 2012 10:10 AM<br>
<b>An:</b> Email discussion list for the FieldTrip project<br>
<b>Betreff:</b> Re: [FieldTrip] Missing resolution Information in *vhdr causes ft_preprocessing to return only NaNs<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Julian,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">It is my understanding that the header file doesn't change at all, since Brainvision Analyzer stores all changes either in the 'history' files or temporary files in the history folder. The *.vhdr and *.eeg (and marker files, if any) should
be unchanged after preprocessing. Therefore, resolution information should still be there.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Could you check the contents of the header file with notepad?<o:p></o:p></p>
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<p class="MsoNormal">It should say something like this for every channel under "[Channel Infos]":<o:p></o:p></p>
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<div>
<p class="MsoNormal">Ch27=Fz,,0.0715,µV<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Also, you could try to open it with Brainvision Analyzer, and see if that gives an error of sorts.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Sincerely,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Casper van Heck<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Jan 24, 2012 at 11:54 PM, Karch, Julian <<a href="mailto:karch@mpib-berlin.mpg.de">karch@mpib-berlin.mpg.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I'm working on a brainvision EEG dataset which was preprocessed by someone else using Brainvision Analyzer. One part of his preprocessing was to set a new reference.
This processing step makes the resolution information in the *vhdr file disappear. Because of that hdr.orig.resolution=NaN for all channels. As result of that the lines</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New"">calib = diag(hdr.resolution(chanindx));</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New""> <span style="color:forestgreen">
% using a sparse multiplication speeds it up</span></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;
text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New""> dat = full(sparse(calib) * dat);</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">in read_brainvision_eeg produce only NaN. This again results in trials which only contain NaNs.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I do weekly updates of fieldtrip using svn. Because I'm quite sure if was able to read in, using ft_preprocssing, the excact same dataset, even with the same
cfg file, earlier this year I checked the modifications for the last half year or so but I couldn't find any change which could have broken it.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">My two questions are. How would you handle this problem? Just plug in some random numbers like 0.1 ? Is this an issue with fieldtrip or am I doing something wrong?
Were there any changes to the involved functions which could have changed the behavior in that way?</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Thanks in advance!</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Best,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Julian</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Julian Karch
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Research Assistant</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Center for Lifespan Psychology</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">MPI for Human Development</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Lentzeallee 94, 14195 Berlin, Germany</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">phone:
<a href="tel:%2B49-30-82406-296" target="_blank">+49-30-82406-296</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">fax:
<a href="tel:%2B49-30-8249939" target="_blank">+49-30-8249939</a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">web:
</span><a href="http://www.mpib-berlin.mpg.de" target="_blank"><span lang="EN-US">http://www.mpib-berlin.mpg.de</span></a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><br>
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