Hi Ulrich,<br><br>There is a function 'statfun_actvsblT' to test your activity against the baseline. However, this function only accepts input with dimord 'chan_freq_time'.<br>Maybe, you can create your own function based on 'statfun_actvsblT' to test the activity against zero.<br>
<br>Kind regards,<br>Mark<br><br><div class="gmail_quote">Op 27 maart 2012 15:00 schreef <span dir="ltr"><<a href="mailto:fieldtrip-request@donders.ru.nl">fieldtrip-request@donders.ru.nl</a>></span> het volgende:<br>
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Today's Topics:<br>
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1. Re: Problem with FT_DEFINETRIAL (Jarmo Kontinen)<br>
2. Re: Beamforming analysis in frequency band, concept problem<br>
(J?rn M. Horschig)<br>
3. one-sample cluster test (Pomper, Ulrich)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)<br>
From: Jarmo Kontinen <<a href="mailto:Jarmo.Kontinen@ruhr-uni-bochum.de">Jarmo.Kontinen@ruhr-uni-bochum.de</a>><br>
To: Ivano Triggiani <<a href="mailto:ivano_triggiani@yahoo.it">ivano_triggiani@yahoo.it</a>>, Email discussion list<br>
for the FieldTrip project <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL<br>
Message-ID:<br>
<<a href="mailto:permail-201203271124436509e8c7000033ba-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de">permail-201203271124436509e8c7000033ba-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de</a>><br>
<br>
Content-Type: text/plain; charset=iso-8859-1<br>
<br>
<br>
Dear Ivano,<br>
I had some problem with email, so if I am replying to you twice, I apologize.<br>
<br>
I was maybe a bit unclear maybe in my first post. My files already contain<br>
averaged data.<br>
Problem is to get the right data-structure to use the existing FT-functions to<br>
do analysis on the data.<br>
<br>
Best,<br>
Jarmo<br>
<br>
Ivano Triggiani schrieb am 2012-03-26:<br>
> Dear Jarmo,<br>
<br>
> Filedtrip needs a definition of segments of interest. For example<br>
> reading a trigger channel or something else to cut the EEG recording<br>
> into trials. If I have understood what you want to do is to get an<br>
> average of general EEG (for example resting state EEG closed eyes).<br>
> But you have to indicate which average you want to obtain, for<br>
> example you can tell fieldtrip to divide EEG into epochs of 3 seconds<br>
> and then to make an average of all of them.<br>
> What you wrote is the request of an average, but you are not<br>
> specifing of what.<br>
> Fof example you can write a trial function that provides a trl<br>
> matrix, i.e.:<br>
> 0 3 0<br>
<br>
> 3 6 0<br>
> 6 9 0<br>
> 9 12 0<br>
> 12 13 0<br>
> ...<br>
<br>
> where first column is the start sample in seconds (you have to<br>
> multiply it for sample rate), the second column is the end sample and<br>
> the third is the offset (in this case is always zero), or look at<br>
> <a href="http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection</a><br>
<br>
> best wishes,<br>
> Ivano<br>
<br>
<br>
<br>
> ------------------------------------------------------------------------<br>
<br>
<br>
<br>
<br>
> "No man can wear one face to himself<br>
> and another to the multitude,<br>
> without finally getting bewildered<br>
> as to which one is true."<br>
<br>
<br>
> Nathaniel Hawthorne<br>
<br>
<br>
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> Da: "<a href="mailto:fieldtrip-request@donders.ru.nl">fieldtrip-request@donders.ru.nl</a>"<br>
> <<a href="mailto:fieldtrip-request@donders.ru.nl">fieldtrip-request@donders.ru.nl</a>><br>
> A: <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> Inviato: Luned? 26 Marzo 2012 12:00<br>
> Oggetto: fieldtrip Digest, Vol 16, Issue 33<br>
<br>
> Send fieldtrip mailing list submissions to<br>
> ??? <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
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> ? 1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)<br>
<br>
<br>
> ----------------------------------------------------------------------<br>
<br>
> Message: 1<br>
> Date: Sun, 25 Mar 2012 12:11:28 +0200<br>
> From: Stephen Politzer-Ahles <<a href="mailto:politzerahless@gmail.com">politzerahless@gmail.com</a>><br>
> To: <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL<br>
> Message-ID:<br>
> ???<br>
> <<a href="mailto:CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com">CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
<br>
> Hello Jarmo,<br>
<br>
> I haven't tried importing Brain Vision files into FieldTrip myself,<br>
> but<br>
> based on the code you sent it looks like the problem may be that<br>
> you're<br>
> missing cfg.trialdef.eventvalue (which is used to tell FieldTrip<br>
> which<br>
> triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim<br>
> . See<br>
> the example at<br>
> <a href="http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials" target="_blank">http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials</a>.<br>
<br>
> If what you are trying to do is import all trials from all triggers<br>
> in the<br>
> file, I think you have to define your own "trialfun" function to do<br>
> that<br>
> (although I haven't tried this myself so I'm not sure).<br>
> <a href="http://fieldtrip.fcdonders.nl/reference/ft_definetrial" target="_blank">http://fieldtrip.fcdonders.nl/reference/ft_definetrial</a> has some more<br>
> information.<br>
<br>
> Best,<br>
> Steve Politzer-Ahles<br>
> University of Kansas<br>
<br>
<br>
> Message: 1<br>
> > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)<br>
> > From: Jarmo Kontinen <<a href="mailto:Jarmo.Kontinen@ruhr-uni-bochum.de">Jarmo.Kontinen@ruhr-uni-bochum.de</a>><br>
> > To: <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
> > Subject: [FieldTrip] Problem with FT_DEFINETRIAL<br>
> > Message-ID:<br>
> >? ? ? ? <<br>
> > <a href="mailto:permail-201203221614466509e8c700002494-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de">permail-201203221614466509e8c700002494-Jarmo.Kontinen@msgid.mail.ruhr-uni-bochum.de</a><br>
<br>
<br>
> > Content-Type: text/plain; charset=us-ascii<br>
<br>
> > Dear all,<br>
> > I am trying to import EEG subject averages into Field Trip. The<br>
> > files are<br>
> > exported with the Brainvision Analyzer in binary form<br>
> > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.<br>
> > I have a problem with turning the data into the Field Trip<br>
> > data-structure.<br>
> > I<br>
> > am following instructions given on this forum on one similar post.<br>
> > What I<br>
> > have<br>
> > tried is the following:<br>
<br>
> > cfg=[];<br>
> > cfg.trialdef.eventtype='average'<br>
> > cfg.dataset='subject10_konPro2002.dat'<br>
<br>
> >? cfg=ft_definetrial(cfg);<br>
<br>
> > Warning: no trialfun was specified, using trialfun_general<br>
> > > In ft_definetrial at 123<br>
> > evaluating trialfunction 'trialfun_general'<br>
> > reading the events from 'subject10_konPro2002.vhdr'<br>
> > ??? Error using ==> ft_definetrial at 176<br>
> > no trials were defined, see FT_DEFINETRIAL for help<br>
<br>
> > I am grateful for all the help.<br>
> > Thanks,<br>
> > Jarmo Kontinen<br>
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------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 27 Mar 2012 13:27:27 +0200<br>
From: "J?rn M. Horschig" <<a href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>><br>
To: <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
Subject: Re: [FieldTrip] Beamforming analysis in frequency band,<br>
concept problem<br>
Message-ID: <<a href="mailto:4F71A41F.4080807@donders.ru.nl">4F71A41F.4080807@donders.ru.nl</a>><br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"<br>
<br>
Hi Ion,<br>
<br>
A frequency is by definition at least a peak and a trough(up flank and<br>
down flank), making it one cycle (think of sinusoid here). Thus, you<br>
could say that one needs at least one cycle of a certain frequency such<br>
that it is eligible to talk about a 'frequency'. Just in case you don't<br>
know it already, you might want to look things up as Rayleigh frequency,<br>
Nyquist frequency, and I would suggest that you read (or start reading)<br>
the digitial signal processing book: <a href="http://www.dspguide.com/" target="_blank">http://www.dspguide.com/</a><br>
<br>
Note that a true oscillation is usually considered to last at least<br>
three cycles (of course, opinions differ her - I go with four). The<br>
length of the window of interest reflects the number of cycles that can<br>
be estimated. For source reconstruction, make sure cfg.toilim is as long<br>
as the number of cycles you want to estimate, e.g. when using cfg.foi =<br>
10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you<br>
want an estimate of 4 cycles.<br>
<br>
Hope it helps!<br>
Best,<br>
J?rn<br>
<br>
<br>
<br>
On 3/27/2012 12:46 PM, Ion Lavado wrote:<br>
> Thank you Stephan, just one thing, why i need a time window big<br>
> enough? so i'm just studying the frequency.<br>
><br>
> Best,<br>
><br>
> Mikel<br>
><br>
> 2012/3/27 Stephan Moratti <<a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a><br>
> <mailto:<a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a>>><br>
><br>
> Dear Mikel,<br>
><br>
> I understand that you should do a mtmfft with a center frequency<br>
> of interest (in your case cfg.foil = [11 11]) and then you do a<br>
> frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you<br>
> need a time window big enough to allow such a smoothing. The CSD<br>
> should represent a frequency window of 8 to 14 Hz then. Then you<br>
> put the result of the mtmfft into the dics beamformer.<br>
><br>
> Best,<br>
><br>
> Stephan<br>
><br>
> El 27/03/2012, a las 11:19, Ion Lavado escribi?:<br>
><br>
>> Hello, i'm having problems trying the beamformer analysis with a<br>
>> frequency band of interest. I would like to have for example an<br>
>> interval like [8 14] Hz. My concept problem is about the<br>
>> cfg.frequency and cfg.tapsmofrq values. (it must be a escalar,<br>
>> but i want a frequency band).<br>
>><br>
>> %FREQ ANALYSIS<br>
>> cfg = [];<br>
>> cfg.method = 'mtmfft';<br>
>> cfg.output = 'powandcsd';<br>
>> cfg.tapsmofrq = 5;<br>
>> cfg.foilim = [8 14];<br>
>> freq_words_alpha = ft_freqanalysis(cfg, words);<br>
>><br>
>><br>
>> %SOURCE ANALYSIS<br>
>> cfg = [];<br>
>> cfg.frequency = 11;<br>
>> cfg.lambda=0;<br>
>> cfg.method = 'dics';<br>
>> cfg.coordsys = 'neuromag';<br>
>> cfg.projectnoise = 'yes';<br>
>> cfg.grad = freq_words_alpha.grad;<br>
>> cfg.channel = {'MEG'};<br>
>> cfg.grid = grid;<br>
>> cfg.reducerank = 2;<br>
>> cfg.vol = vol02;<br>
>> vol02=ft_convert_units(vol02,'cm');<br>
>> source_pre11 = ft_sourceanalysis(cfg, freq_words_alpha );<br>
>><br>
>><br>
>> I use a cfg.frequency of 11 but i don't have really clear what<br>
>> i'm doing as a get the same result using cfg.frequency=11 but a<br>
>> freqanalysis in [10 12]. I would be very grateful if someone<br>
>> could solve my doubt.<br>
>><br>
>> Best wishes,<br>
>><br>
>> Mikel<br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a> <mailto:<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>
> Stephan Moratti, PhD<br>
><br>
> see also: <a href="http://web.me.com/smoratti/" target="_blank">http://web.me.com/smoratti/</a><br>
><br>
> Universidad Complutense de Madrid<br>
> Facultad de Psicolog?a<br>
> Departamento de Psicolog?a B?sica I<br>
> Campus de Somosaguas<br>
> 28223 Pozuelo de Alarc?n (Madrid)<br>
> Spain<br>
><br>
> and<br>
><br>
> Center for Biomedical Technology<br>
> Laboratory for Cognitive and Computational Neuroscience<br>
> Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de<br>
> Madrid<br>
> Campus Montegancedo<br>
> 28223 Pozuelo de Alarc?n (Madrid)<br>
> Spain<br>
><br>
><br>
> email: <a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a> <mailto:<a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a>><br>
> Tel.: <a href="tel:%2B34%20679219982" value="+34679219982">+34 679219982</a> <tel:%2B34%20679219982><br>
><br>
><br>
><br>
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> _______________________________________________<br>
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<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>
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<br>
Message: 3<br>
Date: Tue, 27 Mar 2012 15:00:32 +0200<br>
From: "Pomper, Ulrich" <<a href="mailto:Ulrich.Pomper@charite.de">Ulrich.Pomper@charite.de</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: [FieldTrip] one-sample cluster test<br>
Message-ID: <<a href="mailto:4F71B9F0.8080106@charite.de">4F71B9F0.8080106@charite.de</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear list members,<br>
<br>
this topic was discussed some time in 2008, but it seems to me no<br>
conclusion was found.<br>
<br>
I would like to find source activity that differs significantly from<br>
zero. I could run a one sample t-test for every voxel and end up having<br>
a huge MC problem, or (preferably) use some kind of cluster based<br>
permutation statistics. However, the option for a one sample cluster<br>
test is not implemented in FT.<br>
<br>
Would it be correct to test the data from my experimental condition<br>
against a set of data containing all zeros using a cluster based<br>
permutation test?<br>
<br>
Any help is very much appreciated!<br>
Best, Ulrich<br>
<br>
<br>
<br>
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</blockquote></div>