<div>Hi Robert</div>
<div> </div>
<div>Thanks for your kind reply. </div>
<div> </div>
<div>Best Regards,</div>
<div>Ayda<br></div>
<div class="gmail_quote">On Fri, Jan 20, 2012 at 6:00 AM, <span dir="ltr"><<a href="mailto:fieldtrip-request@donders.ru.nl">fieldtrip-request@donders.ru.nl</a>></span> wrote:<br>
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<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: ft_definetrial with .nex files (J?rn M. Horschig)<br>
2. Re: ft_definetrial with .nex files (Robert Oostenveld)<br> 3. Re: A problem (Robert Oostenveld)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 20 Jan 2012 09:48:18 +0100<br>
From: "J?rn M. Horschig" <<a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>><br>To: Email discussion list for the FieldTrip project<br> <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] ft_definetrial with .nex files<br>Message-ID: <<a href="mailto:4F192A52.2050808@donders.ru.nl">4F192A52.2050808@donders.ru.nl</a>><br>Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>Dear Tara,<br><br>you define cfg.trialdef.triallength prior to calling ft_definetrial.<br>This will cause the trialfunction to not look for events, but cut your<br>recorded data into chunks of 3 seconds, independently of the eventtype<br>
and -value that you specified. The parameters you probably want to use<br>instead are cfg.trialdef.poststim and .prestim. Triallength is supposed<br>for continuous data without events, e.g. resting state data.<br><br>Btw, if you specifiy cfg.trialdef.eventtype='?' you will get a list with<br>
all events in your data - that way you can make sure that you are<br>specifying the correct types or values (alternatively, you could also<br>use ft_read_event).<br><br>Hope it helps!<br>Best,<br>J?rn<br><br>On 1/19/2012 10:12 PM, Tara Jacobson wrote:<br>
> Hello,<br>><br>> Does anyone have experience with .nex files? It seems straight<br>> forward to be able to define trials using events in the .nex, but<br>> ft_definetrial is not recognizing them as events.<br>
><br>> filename =('11-087_12292011.nex')<br>><br>><br>> stim30Hz=[27.25275159.26715258.277925357.2887489.303075522.306625621.317425786.335425885.3462984.3569751083.367751149.37491281.38931347.3964251446.407251578.42161644.42881776.4431751875.453951974.464725];<br>
><br>> cfg = [];<br>> cfg.dataset = filename;<br>><br>> cfg.trialdef.triallength=3;<br>> cfg.trialdef.eventtype=('Event007');<br>> cfg.trialdef.eventvalue=stim30Hz;<br>><br>> cfg=ft_definetrial(cfg);<br>
><br>> filename =<br>> 11-087_12292011.nex<br>> Warning: no trialfun was specified, using trialfun_general<br>> > In ft_definetrial at 95<br>> evaluating trialfunction 'trialfun_general'<br>> reading the events from '11-087_12292011.nex'<br>
> found 0 events<br>> created 676 trials<br>><br>> My question is what are the 676 trials if it found no events?<br>><br>> Can anyone give me some advice?<br>><br>><br>> Thanks very much.<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" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
<br><br>--<br>J?rn M. Horschig<br>PhD Student<br>Donders Institute for Brain, Cognition and Behaviour<br>Centre for Cognitive Neuroimaging<br>Radboud University Nijmegen<br>Neuronal Oscillations Group<br><br>P.O. Box 9101<br>
NL-6500 HB Nijmegen<br>The Netherlands<br><br>Contact:<br>E-Mail: <a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a><br>Tel: <a href="tel:%2B31-%280%2924-36-68493" value="+31243668493">+31-(0)24-36-68493</a><br>
Web: <a href="http://www.ru.nl/donders" target="_blank">http://www.ru.nl/donders</a><br><br>Visiting address:<br>Trigon, room 2.30<br>Kapittelweg 29<br>NL-6525 EN Nijmegen<br>The Netherlands<br><br>-------------- next part --------------<br>
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<br>------------------------------<br><br>Message: 2<br>Date: Fri, 20 Jan 2012 10:43:36 +0100<br>From: Robert Oostenveld <<a href="mailto:r.oostenveld@donders.ru.nl">r.oostenveld@donders.ru.nl</a>><br>To: Email discussion list for the FieldTrip project<br>
<<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>Subject: Re: [FieldTrip] ft_definetrial with .nex files<br>Message-ID: <<a href="mailto:895F6559-E5B6-410F-B6AA-F8407C73E30F@donders.ru.nl">895F6559-E5B6-410F-B6AA-F8407C73E30F@donders.ru.nl</a>><br>
Content-Type: text/plain; charset=us-ascii<br><br>Dear Tara,<br><br>To add to Jorns suggestion<br><br>On 19 Jan 2012, at 22:12, Tara Jacobson wrote:<br><br>> ...<br>> cfg=ft_definetrial(cfg);<br>><br>> filename =<br>
> 11-087_12292011.nex<br>> Warning: no trialfun was specified, using trialfun_general<br>> > In ft_definetrial at 95<br>> evaluating trialfunction 'trialfun_general'<br>> reading the events from '11-087_12292011.nex'<br>
> found 0 events<br>> created 676 trials<br><br>The line "found 0 events" suggests that ft_read_event (which is called in ft_definetrial) did not find any events in your nex file. I suggest you look into the ft_read_event MATLAB code (and the underlying nex functions) to figure out why it does not detect the triggers in the nex file.<br>
<br>best<br>Robert<br><br><br><br><br><br>------------------------------<br><br>Message: 3<br>Date: Fri, 20 Jan 2012 10:49:59 +0100<br>From: Robert Oostenveld <<a href="mailto:r.oostenveld@donders.ru.nl">r.oostenveld@donders.ru.nl</a>><br>
To: Email discussion list for the FieldTrip project<br> <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>Subject: Re: [FieldTrip] A problem<br>Message-ID: <<a href="mailto:F6708862-5D39-4EBD-A9E5-9CC276910812@donders.ru.nl">F6708862-5D39-4EBD-A9E5-9CC276910812@donders.ru.nl</a>><br>
Content-Type: text/plain; charset=us-ascii<br><br>Dear Ayda<br><br>On 19 Jan 2012, at 20:01, aida ghahremani wrote:<br>> I have the coordinates of the cortex. Would you please help me to locates the sources (dipoles) which best explain the EEG?<br>
<br>You can pass the cortical sheet to the ft_sourceanalysis function (or to the ft_prepare_leadfield function) to use all vertices of the cortical sheet as dipole locations. This is also the approach used in <a href="http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#source_model" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate#source_model</a>. The vertex positions should be specified as cfg.grid.pos.<br>
<br>> How I can make their orientations normal to the cortex?<br><br>You'll have to determine the dipole orientation at each vertex outside of fieldtrip, but you can use the fieldtrip/forward/private/normals.m to help you with it. If you specify the dipole orientations as cfg.grid.mom, then the leadfield will computed for a dipole in that direction. See line 227 in ft_prepare_leadfield.<br>
<br>best<br>Robert<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" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br><br>End of fieldtrip Digest, Vol 14, Issue 31<br>*****************************************<br>
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