<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=NL style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Grazia,<o:p></o:p></span></p><p class=MsoNormal><span lang=NL 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'>uh, jah, my bad, try cfg.elec instead ;) <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,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Jörn<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><div><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'>--<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'><o:p> </o:p></span></b></p><p class=MsoNormal><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'>Jörn M. Horschig, PhD</span></b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'>, Software Engineer</span><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:black;mso-fareast-language:NL'><o:p></o:p></span></b></p><p class=MsoNormal><span lang=NL style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'><a href="http://www.artinis.com/"><span lang=EN-US style='color:#626264'>Artinis Medical Systems</span></a></span><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#626264;mso-fareast-language:NL'> | +31 481 350 980 </span><b><span style='font-size:9.0pt;font-family:"Verdana",sans-serif;color:#255A9E;mso-fareast-language:NL'><o:p></o:p></span></b></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'><o:p> </o:p></span></p><div style='border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt'><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><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-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>Grazia Di Pisa<br><b>Sent:</b> Wednesday, October 21, 2015 12:28 PM<br><b>To:</b> fieldtrip@science.ru.nl<br><b>Subject:</b> Re: [FieldTrip] Interpolation and ft_channelrepair<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi <span style='color:#222222;background:white'>Jörn</span>,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Thanks for the advice - I've just tried to add cfg.sens = sens but still the same error.<o:p></o:p></p></div><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Any other suggestions?<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>thanks,<o:p></o:p></p><div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"JaneAusten",serif'>~ grazia</span><o:p></o:p></p></div></div></div></div><div><div><div><p class=MsoNormal><span style='color:black'><o:p> </o:p></span></p></div></div></div><p class=MsoNormal><o:p> </o:p></p><div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 21Oct, 2015, at 12:00, <a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Send fieldtrip mailing list submissions to<br><span class=apple-tab-span> </span><a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class=apple-tab-span> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>or, via email, send a message with subject or body 'help' to<br><span class=apple-tab-span> </span><a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a><br><br>You can reach the person managing the list at<br><span class=apple-tab-span> </span><a href="mailto:fieldtrip-owner@science.ru.nl">fieldtrip-owner@science.ru.nl</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of fieldtrip digest..."<br><br><br>Today's Topics:<br><br> 1. Call for new post docs in the Obleser lab | Auditory<br> Cognition (Jonas Obleser)<br> 2. Spectrum normalization (Wunderle, Thomas)<br> 3. Interpolation and ft_channelrepair (Grazia Di Pisa)<br> 4. Re: Interpolation and ft_channelrepair<br> (=?UTF-8?Q?J=C3=B6rn_M._Horschig?=)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Tue, 20 Oct 2015 06:07:51 -0500<br>From: Jonas Obleser <<a href="mailto:jonas@obleser.de">jonas@obleser.de</a>><br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>, <a href="mailto:AUDITORY@LISTS.MCGILL.CA">AUDITORY@LISTS.MCGILL.CA</a><br>Subject: [FieldTrip] Call for new post docs in the Obleser lab |<br><span class=apple-tab-span> </span>Auditory<span class=apple-tab-span> </span>Cognition<br>Message-ID: <<a href="mailto:71625964-4C4D-41CA-BEDB-171CEFBC87F8@obleser.de">71625964-4C4D-41CA-BEDB-171CEFBC87F8@obleser.de</a>><br>Content-Type: text/plain; charset=utf-8<br><br>The research group ?Auditory Cognition? (headed by Jonas Obleser; auditorycognition.com), now at the University of L?beck, is seeking to hire two Postdoctoral researchers, initially for 3 years, with the option of extension.<br><br>These positions fall into the larger framework of an ERC Consolidator grant ?The listening challenge: How ageing brains adapt? (AUDADAPT) recently awarded to Jonas Obleser, and will allow the joint development of cognitive-neuroscience and psychological research projects targeting adaptive control in the auditory modality of middle-aged adults.<br><br>Please download the full job advert here: <a href="https://www.dropbox.com/s/sqc9c94ewl6bjjh/Ausschreibung_1031_15_Wiss%20MitarbeiterIn_Psychologie_EN.pdf?dl=1">https://www.dropbox.com/s/sqc9c94ewl6bjjh/Ausschreibung_1031_15_Wiss%20MitarbeiterIn_Psychologie_EN.pdf?dl=1</a> <br><br>Note the application deadline of November 12 (postal receipt).<br><br><a href="http://auditorycognition.com">http://auditorycognition.com</a><br><a href="http://uni-luebeck.de">http://uni-luebeck.de</a><br><br><br><br><br>------------------------------<br><br>Message: 2<br>Date: Tue, 20 Oct 2015 14:58:25 +0000<br>From: "Wunderle, Thomas" <<a href="mailto:thomas.wunderle@esi-frankfurt.de">thomas.wunderle@esi-frankfurt.de</a>><br>To: "<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>" <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>Subject: [FieldTrip] Spectrum normalization<br>Message-ID:<br><span class=apple-tab-span> </span><<a href="mailto:27E5CAD9145EEC41BB9B34C01716A198880C3CD4@UM-excdag-a02.um.gwdg.de">27E5CAD9145EEC41BB9B34C01716A198880C3CD4@UM-excdag-a02.um.gwdg.de</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi all,<br><br>I have a question about how FieldTrip normalizes the output of a spectral analyses using ft_freqanalysis.<br>This is important for me, because I need the absolute value of the spectrum for a publication.<br><br>I was scanning through the code trying to find the normalization steps.<br>In particular, I don't understand the following steps:<br><br><br>1.) The tapers (e.g. hanning) are normalized prior to the multiplication with the data by the following code:<br>tap = tap./norm(tap, 'fro'); (line 195 in the function fr_specest_mtmfft)<br>What is the rationale of dividing through this special norm of the taper itself?<br><br><br>2.) After calculating the fft, the specrum is scaled (i.e. in the function fr_specest_mtmfft) by:<br><br>dum = dum .* sqrt(2 ./ endnsample); (line 251)<br><br>Later on, to get to the power spectrum, the abs of the spectrum is taken and squared<br><br>powdum = abs(spectrum(acttap,:,foiind(ifoi),acttboi)) .^2; (line 629 in ft_frequanalysis)<br><br><br><br>This puzzles me, because scanning through the literature, the power spectrum should be given by<br><br>(2*abs(X)^2) ./ (nfft^2) -> unit: V^2 (X=signal, nfft = number of data points)<br><br>and the PSD by<br><br>(2*abs(X)^2) ./ (nfft*Fs) -> unit: V^2/Hz (X=signal, nfft = number of data points, Fs=sampling rate)<br><br><br><br>Alternatively, one can get the amplitude spectrum from the power spectrum by taking the square root of the PSD:<br><br>sqrt(PSD) -> unit: V/sqrt(Hz)<br><br>which is still different from<br><br>(2*abs(X)) ./ (nfft*Fres) -> unit: V/Hz ? (Fres = frequency resolution = Fs/nfft)<br><br><br><br>The result of these equations are different from what comes out of the FieldTrip code.<br><br>So what is the unit of the spectrum in FieldTrip?<br><br>What is the rationale of scaling the complex spectrum by sqrt(2/nfft) ?<br><br>Furthermore, is the unit for the different spectral estimation methods the same? That is, using mtmfft, mtmconvol, wavelet,...?<br><br>It would help me a lot if someone could clarify these points.<br><br>Thanks in advance,<br>Thomas<br><br><br>-----<br>Dr. Thomas Wunderle<br>Ernst Str?ngmann Institute (ESI) for Neuroscience<<a href="http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews">http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews</a>><br>in Cooperation with Max Planck Society <<a href="http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews">http://www.ncbi.nlm.nih.gov/feed/rss.cgi?ChanKey=PubMedNews</a>><br>Deutschordenstrasse 46<br>60528 Frankfurt am Main, Germany<br><a href="http://www.esi-frankfurt.de%3chttp:/www.esi-frankfurt.de/">www.esi-frankfurt.de<http://www.esi-frankfurt.de/</a>><br><a href="mailto:thomas.wunderle@esi-frankfurt.de%3cmailto:thomas.wunderle@esi-frankfurt.de">thomas.wunderle@esi-frankfurt.de<mailto:thomas.wunderle@esi-frankfurt.de</a>><br>Tel: +49 69 96769 516<br>Fax: +49 69 96769 555<br><br>Sitz der Gesellschaft: Frankfurt am Main<br>Registergericht: Amtsgericht Frankfurt - HRB 84266<br>Gesch?ftsf?hrer: Prof. Dr. Pascal Fries<br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151020/eebaf460/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20151020/eebaf460/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Wed, 21 Oct 2015 10:30:07 +0200<br>From: Grazia Di Pisa <<a href="mailto:g.dipisa@gmail.com">g.dipisa@gmail.com</a>><br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>Subject: [FieldTrip] Interpolation and ft_channelrepair<br>Message-ID: <<a href="mailto:A46541FB-BC67-44E7-A9CD-541FB39B7C54@gmail.com">A46541FB-BC67-44E7-A9CD-541FB39B7C54@gmail.com</a>><br>Content-Type: text/plain; charset=utf-8<br><br>Dear all,<br><br>I?m trying to do interpolation to repair some bad channels, but I?m getting the error below.<br>I've read the ft_fetch_sens help but I don?t understand how I should specify the electrodes.<br><br>Is there a file I should upload or am I missing something in my code? <br>Any help or hint is very much appreciated!<br><br>thanks in advance,<br>~ grazia<br><br><br>//<br>Error using ft_fetch_sens (line 183)<br>no electrodes or gradiometers specified.<br><br>Error in ft_channelrepair (line 115)<br>sens = ft_fetch_sens(cfg, data);<br><br>Error in new_analyse_GDP (line 42)<br>ft_channelrepair(cfg, data)<br>//<br><br>This is my code:<br><br>15 <span class=apple-tab-span> </span>cfg = [];<br>16 <span class=apple-tab-span> </span>cfg_neighb <span class=apple-tab-span> </span>= [];<br>17<span class=apple-tab-span> </span>cfg_neighb.method<span class=apple-tab-span> </span>= 'triangulation'; <br>18 cfg.senstype <span class=apple-tab-span> </span>= 'EEG';<br>19 cfg_neighb.layout <span class=apple-tab-span> </span>= 'biosemi64.lay';<br>20 neighbours <span class=apple-tab-span> </span>= ft_prepare_neighbours(cfg_neighb);<br>21 <br>22 cfg.neighbours <span class=apple-tab-span> </span>= neighbours;<br>23 cfg.channel <span class=apple-tab-span> </span>= {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9',}; <br>24 cfg.feedback <span class=apple-tab-span> </span> = 'yes';<br>25 cfg.layout <span class=apple-tab-span> </span>= 'biosemi64.lay';<br>26 lay <span class=apple-tab-span> </span>= ft_prepare_layout(cfg);<br>27 <br>28 sens <span class=apple-tab-span> </span>= data;<br>29 sens.type <span class=apple-tab-span> </span>= 'eeg';<br>30 sens.label<span class=apple-tab-span> </span>= lay.label;<br>31 sens.chanpos <span class=apple-tab-span> </span>= lay.pos;<br>32 sens.chanpos(:,3) <span class=apple-tab-span> </span>= 0;<br>33 <br>34 ft_neighbourplot(cfg, data)<br>35 <br>36 cfg <span class=apple-tab-span> </span>= [];<br>37 cfg.method <span class=apple-tab-span> </span>= 'nearest';<br>38 cfg.badchannel <span class=apple-tab-span> </span>= {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9'};<br>39 cfg.neighbours <span class=apple-tab-span> </span> = neighbours;<br>40 cfg.trials <span class=apple-tab-span> </span> = 'all';<br>41 <br>42 ft_channelrepair(cfg, data)<br><br><br><br><br><br><br><br>------------------------------<br><br>Message: 4<br>Date: Wed, 21 Oct 2015 10:42:03 +0200<br>From: "=?UTF-8?Q?J=C3=B6rn_M._Horschig?=" <<a href="mailto:jorn@artinis.com">jorn@artinis.com</a>><br>To: "'FieldTrip discussion list'" <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>Subject: Re: [FieldTrip] Interpolation and ft_channelrepair<br>Message-ID: <<a href="mailto:002b01d10bdc$5d377040$17a650c0$@artinis.com">002b01d10bdc$5d377040$17a650c0$@artinis.com</a>><br>Content-Type: text/plain;<span class=apple-tab-span> </span>charset="UTF-8"<br><br>Dear Grazia,<br><br>try adding cfg.sens = sens; before line 42. That will set the sensor definition so that ft_channelrepair knows the location of your channels, which is otherwise not obvious.<br><br>Best,<br>J?rn<br><br>--<br><br>J?rn M. Horschig, PhD, Software Engineer<br>Artinis Medical Systems | +31 481 350 980 <br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>-----Original Message-----<br>From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> [mailto:fieldtrip-<br><a href="mailto:bounces@science.ru.nl">bounces@science.ru.nl</a>] On Behalf Of Grazia Di Pisa<br>Sent: Wednesday, October 21, 2015 10:30 AM<br>To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>Subject: [FieldTrip] Interpolation and ft_channelrepair<br><br>Dear all,<br><br>I?m trying to do interpolation to repair some bad channels, but I?m getting<br>the error below.<br>I've read the ft_fetch_sens help but I don?t understand how I should specify<br>the electrodes.<br><br>Is there a file I should upload or am I missing something in my code?<br>Any help or hint is very much appreciated!<br><br>thanks in advance,<br>~ grazia<br><br><br>//<br>Error using ft_fetch_sens (line 183)<br>no electrodes or gradiometers specified.<br><br>Error in ft_channelrepair (line 115)<br>sens = ft_fetch_sens(cfg, data);<br><br>Error in new_analyse_GDP (line 42)<br>ft_channelrepair(cfg, data)<br>//<br><br>This is my code:<br><br>15 <span class=apple-tab-span> </span>cfg = [];<br>16 <span class=apple-tab-span> </span>cfg_neighb <span class=apple-tab-span> </span>= [];<br>17<span class=apple-tab-span> </span>cfg_neighb.method<span class=apple-tab-span> </span>= 'triangulation';<br>18 cfg.senstype <span class=apple-tab-span> </span>= 'EEG';<br>19 cfg_neighb.layout <span class=apple-tab-span> </span>= 'biosemi64.lay';<br>20 neighbours <span class=apple-tab-span> </span>= ft_prepare_neighbours(cfg_neighb);<br>21<br>22 cfg.neighbours <span class=apple-tab-span> </span>= neighbours;<br>23 cfg.channel <span class=apple-tab-span> </span>= {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9',};<br>24 cfg.feedback <span class=apple-tab-span> </span> = 'yes';<br>25 cfg.layout <span class=apple-tab-span> </span>= 'biosemi64.lay';<br>26 lay <span class=apple-tab-span> </span>= ft_prepare_layout(cfg);<br>27<br>28 sens <span class=apple-tab-span> </span>= data;<br>29 sens.type <span class=apple-tab-span> </span>= 'eeg';<br>30 sens.label<span class=apple-tab-span> </span>= lay.label;<br>31 sens.chanpos <span class=apple-tab-span> </span>= lay.pos;<br>32 sens.chanpos(:,3) <span class=apple-tab-span> </span>= 0;<br>33<br>34 ft_neighbourplot(cfg, data)<br>35<br>36 cfg <span class=apple-tab-span> </span>= [];<br>37 cfg.method <span class=apple-tab-span> </span>= 'nearest';<br>38 cfg.badchannel <span class=apple-tab-span> </span>= {'Fp1', 'Fp2', 'AF7', 'AF3','AF8','F7','F5','FT9'};<br>39 cfg.neighbours <span class=apple-tab-span> </span> = neighbours;<br>40 cfg.trials <span class=apple-tab-span> </span> = 'all';<br>41<br>42 ft_channelrepair(cfg, data)<br><br><br><br><br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p></blockquote><p class=MsoNormal><br><br><br><br>------------------------------<br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br><br>End of fieldtrip Digest, Vol 59, Issue 17<br>*****************************************<o:p></o:p></p></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>