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<font face="Dialog" size="2">Dear Martin,</font> </p>
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<font face="Dialog" size="2">thanks a lot for your help! I will try it within the next days.</font> </p>
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<font face="Dialog" size="2">Best regards,</font> </p>
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<font face="Dialog" size="2">Gregor</font><br><br><font face="Dialog" STYLE="font-size: 10pt"><br>--
<BR>Dr. rer. nat. Gregor Volberg <gregor.volberg@psychologie.uni-regensburg.de> ( mailto:gregor.volberg@psychologie.uni-regensburg.de )
<BR>University of Regensburg
<BR>Institute for Experimental Psychology
<BR>93040 Regensburg, Germany
<BR>Tel: +49 941 943 3862
<BR>Fax: +49 941 943 3233
<BR><a href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
</a><BR><br><br></font>>>> Martin Vinck <martinvinck@gmail.com> 2/17/2011 9:43 AM >>><br>Dear Gregor,<br><br>Thank you for your interest.<br><br>Please find, in the latest release, the WPLI functionality in <br>ft_connectivityanalysis.<br><br>Best regards,<br><br>Martin Vinck.<br><br><br>On Feb 11, 2011, at 10:46 AM, fieldtrip-request@donders.ru.nl wrote:<br><br>> Send fieldtrip mailing list submissions to<br>> fieldtrip@donders.ru.nl<br>><br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> <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>> fieldtrip-request@donders.ru.nl<br>><br>> You can reach the person managing the list at<br>> fieldtrip-owner@donders.ru.nl<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. Re: Fwd: Modification of ft_timelockgrandaverage<br>> cfg.keepindividual (Lucie Charles)<br>> 2. WPLI weighted phase-locking index: available infieldtrip?<br>> (Gregor Volberg)<br>> 3. bug in ft_componentanalysis (Baptiste Gauthier)<br>><br>><br>> ----------------------------------------------------------------------<br>><br>> Message: 1<br>> Date: Thu, 10 Feb 2011 14:03:30 +0100<br>> From: Lucie Charles <lucie.charles.ens@googlemail.com><br>> To: Email discussion list for the FieldTrip project<br>> <fieldtrip@donders.ru.nl><br>> Subject: Re: [FieldTrip] Fwd: Modification of ft_timelockgrandaverage<br>> cfg.keepindividual<br>> Message-ID:<br>> <AANLkTi=m90GkTFMb_=44HMGLuriGGz-mw4eBBawWTZGJ@mail.gmail.com><br>> Content-Type: text/plain; charset="iso-8859-1"<br>><br>> Thank you very much for this very detailed response.<br>><br>> I didn't know (or forgot) that ft_timelockstatistics could take <br>> several data<br>> sets as an input (I thought we always needed the big data matrix <br>> with all<br>> the subjects). That makes much more sense to remove the option in this<br>> context.<br>><br>> Thanks again,<br>><br>> Lucie<br>><br>> 2011/2/10 jan-mathijs schoffelen <jan.schoffelen@donders.ru.nl><br>><br>>> Dear Lucie,<br>>><br>>> Thank you very much for your feedback. I take the liberty to anyhow <br>>> post<br>>> this to the discussion list, so that other people may take notice / <br>>> join in<br>>> the discussion / etc.<br>>><br>>> Thanks a lot for this quick response : I understand the logic <br>>> behind this.<br>>> It's true that I noticed some inconsistencies due to the <br>>> interpretation of<br>>> the field dimord which can't be well defined if you have both <br>>> individual and<br>>> average data in your structure.<br>>><br>>><br>>> OK<br>>><br>>> However, I think many people were happy with this option as it was. <br>>> It's<br>>> quite handy to keep both the average and individual data because <br>>> you can<br>>> compute statistics and at the same time you don't have to redo the <br>>> average<br>>> every time. I think a lot of scripts rely on that at least in our <br>>> lab.<br>>><br>>><br>>> The historical purpose for supporting cfg.keepindividual = 'yes', <br>>> was in<br>>> order to get a representation of all single subjects' data in a <br>>> single data<br>>> matrix: data.individual. Nowadays, ft_timelockstatistics supports <br>>> multiple<br>>> data structures in the input, i.e. ft_timelockstatistics(cfg, <br>>> subj1, subj2<br>>> subj3, etc) so I think the call to ft_timelockgrandaverage could <br>>> even be<br>>> bypassed.<br>>> The FieldTrip development team is very keen on providing backward<br>>> compatibility support. While in general this is feasible for the <br>>> functions<br>>> which are in FieldTrip, it is very difficult to realize for lab-<br>>> specific<br>>> scripts. In this particular example I think that clarity of the data<br>>> representation should prevail over backward compatibility issues,<br>>> particularly because in this case there's an easy workaround: just <br>>> call<br>>> ft_timelockgrandaverage twice. Moreover, a clean and unambiguous data<br>>> representation is a prerequisite for further developing the <br>>> software, and<br>>> keeping the historical 'oddity' will only hamper code development.<br>>><br>>> Furthermore, it's a bit strange to have a function called<br>>> ft_timelockgrandaverage which doesn't compute any grandaverage in <br>>> some cases<br>>> !<br>>><br>>><br>>> I agree, yet see my point above. Some people may just like to have <br>>> the data<br>>> represented in a single matrix.<br>>><br>>><br>>> I would suggest to keep the function as it is but add more options <br>>> (such as<br>>> cfg.dimord = 'avg' or 'individual') to make the experimenter aware <br>>> of this<br>>> issue and to solve further computation problem.<br>>><br>>><br>>> I hope I could convince you that our philosophy makes sense and <br>>> that you<br>>> and your lab-mates are willing to make the effort of adjusting the <br>>> scripts a<br>>> bit for future analyses. If very problematic, I would advice for <br>>> the current<br>>> analyses to rely on an old version of ft_timelockgrandaverage.<br>>><br>>> Best wishes,<br>>><br>>> Jan-Mathijs<br>>><br>>><br>>><br>>> Thank you again,<br>>><br>>> Lucie<br>>><br>>> PS : I've sent this email only to you as this is just a suggestion <br>>> which<br>>> might not be relevant for all users.<br>>><br>>><br>>> 2011/2/10 jan-mathijs schoffelen <jan.schoffelen@donders.ru.nl><br>>><br>>>> Dear Lucie,<br>>>><br>>>> Yes, indeed this has recently been changed. The logic behind it is <br>>>> the<br>>>> following:<br>>>><br>>>> One either typically wants to keep the individuals, OR the average.<br>>>><br>>>> If in your case you need the average, you have to specify<br>>>> cfg.keepindividual = 'no';<br>>>><br>>>> Keeping both the average and the individual leads to an inconsistent<br>>>> definition of the data structure.<br>>>> The field 'dimord' does not allow for an unequivocal <br>>>> interpretation of<br>>>> both indidual and avg are present.<br>>>><br>>>> If you need both the individual, and the avg, you now need to run<br>>>> ft_timelockgrandaverage twice, once with cfg.keepinididual = <br>>>> 'yes', and once<br>>>> with cfg.keepindividual = 'no';<br>>>><br>>>> Best wishes,<br>>>><br>>>> Jan-Mathijs<br>>>><br>>>><br>>>> On Feb 10, 2011, at 11:58 AM, Lucie Charles wrote:<br>>>><br>>>> Hello everyone,<br>>>><br>>>> It seems that there has been a modification of <br>>>> ft_timelockgrandaverage :<br>>>> now if you specify cfg.keepindividual = 'yes', the grandaverage is <br>>>> computed<br>>>> but is not included in the output of the function (see above).<br>>>><br>>>> Why is that ? Many of my scripts rely on this option and I wanted <br>>>> to know<br>>>> if there was a good reason for it.<br>>>><br>>>> Thanks,<br>>>><br>>>> Lucie<br>>>><br>>>> New version of ft_timelockgrandaverage (downloaded yesterday), line<br>>>> 159-176<br>>>><br>>>> %--------------------------------------------<br>>>> % % collect the results<br>>>> %--------------------------------------------<br>>>><br>>>> grandavg = [];<br>>>> grandavg.label = cfg.channel; % cell-array<br>>>> %grandavg.fsample = varargin{1}.fsample; % fsample is obsolete<br>>>> grandavg.time = ResultsTime; % 1 x Nsamples<br>>>><br>>>> %KEEP INDIVIDUAL MEANS?<br>>>> if strcmp(cfg.keepindividual, 'yes')<br>>>> * grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples<br>>>> grandavg.dimord = 'subj_chan_time';*<br>>>> else<br>>>> * grandavg.avg = ResultGrandavg; % Nchan x Nsamples*<br>>>> grandavg.var = ResultVar; % Nchan x Nsamples<br>>>> grandavg.dimord = 'chan_time';<br>>>> end<br>>>><br>>>> Older version of ft_timelockgrandaverage (april 2010)<br>>>><br>>>> %--------------------------------------------<br>>>> % % collect the results<br>>>> %--------------------------------------------<br>>>><br>>>> %SWITCH CHANNEL TO LABEL?<br>>>> grandavg.label = cfg.channel; % cell-array<br>>>> grandavg.fsample = varargin{1}.fsample;<br>>>> grandavg.avg = ResultGrandavg; % Nchan x Nsamples<br>>>> grandavg.var = ResultVar; % Nchan x Nsamples<br>>>> grandavg.time = ResultsTime; % 1 x Nsamples<br>>>><br>>>> %KEEP INDIVIDUAL MEANS?<br>>>> if strcmp(cfg.keepindividual, 'yes')<br>>>> grandavg.individual = avgmat; % Nsubj x Nchan x Nsamples<br>>>> grandavg.dimord = 'subj_chan_time';<br>>>> else<br>>>> grandavg.dimord = 'chan_time';<br>>>> end<br>>>><br>>>><br>>>> --<br>>>> Lucie CHARLES<br>>>><br>>>> INSERM-CEA Cognitive Neuroimaging unit<br>>>><br>>>> CEA/SAC/DSV/DRM/NeuroSpin<br>>>> B?t 145, Point Courrier 156<br>>>> F-91191 Gif/Yvette, FRANCE<br>>>> Tel : +33 1 69 08 99 74<br>>>> Fax : +33 1 69 08 79 73<br>>>> _______________________________________________<br>>>> fieldtrip mailing list<br>>>> fieldtrip@donders.ru.nl<br>>>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>>>><br>>>><br>>>> Dr. J.M. (Jan-Mathijs) Schoffelen<br>>>> Donders Institute for Brain, Cognition and Behaviour,<br>>>> Centre for Cognitive Neuroimaging,<br>>>> Radboud University Nijmegen, The Netherlands<br>>>> J.Schoffelen@donders.ru.nl<br>>>> Telephone: 0031-24-3614793<br>>>><br>>>><br>>>> _______________________________________________<br>>>> fieldtrip mailing list<br>>>> fieldtrip@donders.ru.nl<br>>>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>>>><br>>><br>>><br>>><br>>> --<br>>> Lucie CHARLES<br>>><br>>> INSERM-CEA Cognitive Neuroimaging unit<br>>><br>>> CEA/SAC/DSV/DRM/NeuroSpin<br>>> B?t 145, Point Courrier 156<br>>> F-91191 Gif/Yvette, FRANCE<br>>> Tel : +33 1 69 08 99 74<br>>> Fax : +33 1 69 08 79 73<br>>><br>>><br>>> Dr. J.M. (Jan-Mathijs) Schoffelen<br>>> Donders Institute for Brain, Cognition and Behaviour,<br>>> Centre for Cognitive Neuroimaging,<br>>> Radboud University Nijmegen, The Netherlands<br>>> J.Schoffelen@donders.ru.nl<br>>> Telephone: 0031-24-3614793<br>>><br>>><br>>> _______________________________________________<br>>> fieldtrip mailing list<br>>> fieldtrip@donders.ru.nl<br>>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>>><br>><br>><br>><br>> --<br>> Lucie CHARLES<br>><br>> INSERM-CEA Cognitive Neuroimaging unit<br>><br>> CEA/SAC/DSV/DRM/NeuroSpin<br>> B?t 145, Point Courrier 156<br>> F-91191 Gif/Yvette, FRANCE<br>> Tel : +33 1 69 08 99 74<br>> Fax : +33 1 69 08 79 73<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110210/cd847c20/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110210/cd847c20/attachment-0001.html</a><br>> ><br>><br>> ------------------------------<br>><br>> Message: 2<br>> Date: Fri, 11 Feb 2011 09:46:51 +0100<br>> From: "Gregor Volberg" <Gregor.Volberg@psychologie.uni-regensburg.de><br>> To: "FieldTrip List" <fieldtrip@donders.ru.nl><br>> Subject: [FieldTrip] WPLI weighted phase-locking index: available in<br>> fieldtrip?<br>> Message-ID: <4D55058B020000570000882D@gwsmtp1.uni-regensburg.de><br>> Content-Type: text/plain; charset="us-ascii"<br>><br>><br>> Dear fieldtrip developers,<br>><br>> I was just reading the pre-print of an upcoming article in <br>> Neuroimage by Martin Vinck, Robert Oostenveld et al., "An improved <br>> index of phase-synchronization...". As I understand, the proposed <br>> phase-locking index WPLI is not complicated by volume conduction, <br>> and an unbiased version of the WPLI can be computed that is not <br>> affected by trial number. This would be exactely what I need for the <br>> analysis of data from a spatial cueing paradigm.<br>><br>> In the last paragraph, it is announced that the WPLI is made <br>> available in the fieldtrip toolbox. However, I did not yet find it <br>> (i was searching for it as an option in ft_connectivityanalysis, <br>> last Friday's fieldtrip version). May I ask whether it is planned to <br>> include WPLI / debiased WPLI into that function? Or was it perhaps <br>> intended to be computed by hand from the cross-spectrum.<br>><br>> Thanks a lot,<br>> Gregor<br>> --<br>> Dr. rer. nat. Gregor Volberg <gregor.volberg@psychologie.uni-regensburg.de<br>> > ( mailto:gregor.volberg@psychologie.uni-regensburg.de )<br>> University of Regensburg<br>> Institute for Experimental Psychology<br>> 93040 Regensburg, Germany<br>> Tel: +49 941 943 3862<br>> Fax: +49 941 943 3233<br>> <a href="http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html">http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html</a><br>><br>><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110211/fb7d5418/attachment-0001.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110211/fb7d5418/attachment-0001.html</a><br>> ><br>><br>> ------------------------------<br>><br>> Message: 3<br>> Date: Fri, 11 Feb 2011 10:46:13 +0100<br>> From: Baptiste Gauthier <gauthierb.ens@gmail.com><br>> To: fieldtrip@donders.ru.nl<br>> Subject: [FieldTrip] bug in ft_componentanalysis<br>> Message-ID:<br>> <AANLkTinBvzzMTF3g7zd=3Jaihg1mSjq1cAOZ2NAGCAh0@mail.gmail.com><br>> Content-Type: text/plain; charset="iso-8859-1"<br>><br>> Dear Fieldtrip users,<br>><br>> I noticed a little error in ft_componentanalysis since your latest <br>> update<br>> (2011/02/09) :<br>> While using the function, I got this error message :<br>><br>> "??? Error using ==> toc<br>> You must call TIC without an output argument before calling TOC <br>> without an<br>> input argument.<br>><br>> Error in ==> ft_componentanalysis at 465<br>> fprintf('total time in componentanalysis %.1f seconds\n', stopwatch<br>> (toc));<br>><br>> Error in ==> temprod_NEW_runicaonspectra at 37<br>> comp = ft_componentanalysis(cfg,data);"<br>><br>> It seems there's here a bad use of function toc.m<br>><br>> It should be : "fprintf('total time in componentanalysis %.1f seconds<br>> \n',<br>> toc(stopwatch));"<br>> I tried it and it worked fine.<br>><br>> Please let me know if I'm wrong.<br>><br>> Cheers,<br>><br>> Baptiste gauthier<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110211/87187478/attachment.html">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20110211/87187478/attachment.html</a><br>> ><br>><br>> ------------------------------<br>><br>> _______________________________________________<br>> fieldtrip mailing list<br>> fieldtrip@donders.ru.nl<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 3, Issue 17<br>> ****************************************<br><br><br><br><br><br><br><br>_______________________________________________<br>fieldtrip mailing list<br>fieldtrip@donders.ru.nl<br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
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