[FieldTrip] one-sample cluster test

Mark Noordenbos mark.noordenbos at gmail.com
Tue Mar 27 15:35:00 CEST 2012


Hi Ulrich,

There is a function 'statfun_actvsblT' to test your activity against the
baseline. However, this function only accepts input with dimord
'chan_freq_time'.
Maybe, you can create your own function based on 'statfun_actvsblT' to test
the activity against zero.

Kind regards,
Mark

Op 27 maart 2012 15:00 schreef <fieldtrip-request at donders.ru.nl> het
volgende:

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> When replying, please edit your Subject line so it is more specific
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> Today's Topics:
>
>   1. Re: Problem with FT_DEFINETRIAL (Jarmo Kontinen)
>   2. Re: Beamforming analysis in frequency band,       concept problem
>      (J?rn M. Horschig)
>   3. one-sample cluster test (Pomper, Ulrich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 27 Mar 2012 13:24:43 +0200 (CEST)
> From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> To: Ivano Triggiani <ivano_triggiani at yahoo.it>, Email discussion list
>        for the FieldTrip project <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> Message-ID:
>        <
> permail-201203271124436509e8c7000033ba-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
> >
>
> Content-Type: text/plain; charset=iso-8859-1
>
>
> Dear Ivano,
> I had some problem with email, so if I am replying to you twice, I
> apologize.
>
>  I was maybe a  bit unclear maybe in my first post. My files already
> contain
>  averaged data.
> Problem is to get the right data-structure to use the existing
> FT-functions to
> do analysis on the data.
>
> Best,
> Jarmo
>
> Ivano Triggiani schrieb am 2012-03-26:
> > Dear Jarmo,
>
> > Filedtrip needs a definition of segments of interest. For example
> > reading a trigger channel or something else to cut the EEG recording
> > into trials. If I have understood what you want to do is to get an
> > average of general EEG (for example resting state EEG closed eyes).
> > But you have to indicate which average you want to obtain, for
> > example you can tell fieldtrip to divide EEG into epochs of 3 seconds
> > and then to make an average of all of them.
> > What you wrote is the request of an average, but you are not
> > specifing of what.
> > Fof example you can write a trial function that provides a trl
> > matrix, i.e.:
> > 0 3 0
>
> > 3 6 0
> > 6 9 0
> > 9 12 0
> > 12 13 0
> > ...
>
> > where first column is the start sample in seconds (you have to
> > multiply it for sample rate), the second column is the end sample and
> > the third is the offset (in this case is always zero), or look at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#use_your_own_function_for_trial_selection
>
> > best wishes,
> > Ivano
>
>
>
> > ------------------------------------------------------------------------
>
>
>
>
> > "No man can wear one face to himself
> > and another to the multitude,
> > without finally getting bewildered
> > as to which one is true."
>
>
> > Nathaniel Hawthorne
>
>
> > ________________________________
> >  Da: "fieldtrip-request at donders.ru.nl"
> >  <fieldtrip-request at donders.ru.nl>
> > A: fieldtrip at donders.ru.nl
> > Inviato: Luned? 26 Marzo 2012 12:00
> > Oggetto: fieldtrip Digest, Vol 16, Issue 33
>
> > Send fieldtrip mailing list submissions to
> > ??? fieldtrip at donders.ru.nl
>
> > To subscribe or unsubscribe via the World Wide Web, visit
> > ??? http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > or, via email, send a message with subject or body 'help' to
> > ??? fieldtrip-request at donders.ru.nl
>
> > You can reach the person managing the list at
> > ??? fieldtrip-owner at donders.ru.nl
>
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of fieldtrip digest..."
>
>
> > Today's Topics:
>
> > ?  1. Re: Problem with FT_DEFINETRIAL (Stephen Politzer-Ahles)
>
>
> > ----------------------------------------------------------------------
>
> > Message: 1
> > Date: Sun, 25 Mar 2012 12:11:28 +0200
> > From: Stephen Politzer-Ahles <politzerahless at gmail.com>
> > To: fieldtrip at donders.ru.nl
> > Subject: Re: [FieldTrip] Problem with FT_DEFINETRIAL
> > Message-ID:
> > ???
> > <CAJT2k__mFC_FxgG2ggt9hJHhNp59DEZgXFMLAQ1BNoErGFJyfg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
>
> > Hello Jarmo,
>
> > I haven't tried importing Brain Vision files into FieldTrip myself,
> > but
> > based on the code you sent it looks like the problem may be that
> > you're
> > missing cfg.trialdef.eventvalue (which is used to tell FieldTrip
> > which
> > triggers to select), cfg.trialdef.prestim, and cfg.trialdef.poststim
> > . See
> > the example at
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing#reading_and_preprocessing_the_interesting_trials
> .
>
> > If what you are trying to do is import all trials from all triggers
> > in the
> > file, I think you have to define your own "trialfun" function to do
> > that
> > (although I haven't tried this myself so I'm not sure).
> > http://fieldtrip.fcdonders.nl/reference/ft_definetrial has some more
> > information.
>
> > Best,
> > Steve Politzer-Ahles
> > University of Kansas
>
>
> > Message: 1
> > > Date: Thu, 22 Mar 2012 17:14:46 +0100 (CET)
> > > From: Jarmo Kontinen <Jarmo.Kontinen at ruhr-uni-bochum.de>
> > > To: <fieldtrip at donders.ru.nl>
> > > Subject: [FieldTrip] Problem with FT_DEFINETRIAL
> > > Message-ID:
> > >? ? ? ? <
> > >
> permail-201203221614466509e8c700002494-Jarmo.Kontinen at msgid.mail.ruhr-uni-bochum.de
>
>
> > > Content-Type: text/plain; charset=us-ascii
>
> > > Dear all,
> > > I am trying to import EEG subject averages into Field Trip. The
> > > files are
> > > exported with the Brainvision Analyzer in binary form
> > > :subject10_konPro2002.dat and subject10_konPro2002.vhdr.
> > > I have a problem with turning the data into the Field Trip
> > > data-structure.
> > > I
> > > am following instructions given on this forum on one similar post.
> > > What I
> > > have
> > > tried is the following:
>
> > > cfg=[];
> > > cfg.trialdef.eventtype='average'
> > > cfg.dataset='subject10_konPro2002.dat'
>
> > >? cfg=ft_definetrial(cfg);
>
> > > Warning: no trialfun was specified, using trialfun_general
> > > > In ft_definetrial at 123
> > > evaluating trialfunction 'trialfun_general'
> > > reading the events from 'subject10_konPro2002.vhdr'
> > > ??? Error using ==> ft_definetrial at 176
> > > no trials were defined, see FT_DEFINETRIAL for help
>
> > > I am grateful for all the help.
> > > Thanks,
> > > Jarmo Kontinen
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 27 Mar 2012 13:27:27 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: fieldtrip at donders.ru.nl
> Subject: Re: [FieldTrip] Beamforming analysis in frequency band,
>        concept problem
> Message-ID: <4F71A41F.4080807 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Ion,
>
> A frequency is by definition at least a peak and a trough(up flank and
> down flank), making it one cycle (think of sinusoid here). Thus, you
> could say that one needs at least one cycle of a certain frequency such
> that it is eligible to talk about a 'frequency'. Just in case you don't
> know it already, you might want to look things up as Rayleigh frequency,
> Nyquist frequency, and I would suggest that you read (or start reading)
> the digitial signal processing book: http://www.dspguide.com/
>
> Note that a true oscillation is usually considered to last at least
> three cycles (of course, opinions differ her - I go with four). The
> length of the window of interest reflects the number of cycles that can
> be estimated. For source reconstruction, make sure cfg.toilim is as long
> as the number of cycles you want to estimate, e.g. when using cfg.foi =
> 10, then cfg.toilim(2)-cfg.toilim(1) should be at least 400ms when you
> want an estimate of 4 cycles.
>
> Hope it helps!
> Best,
> J?rn
>
>
>
> On 3/27/2012 12:46 PM, Ion Lavado wrote:
> > Thank you Stephan, just one thing, why i need a time window big
> > enough? so i'm just studying the frequency.
> >
> > Best,
> >
> > Mikel
> >
> > 2012/3/27 Stephan Moratti <smoratti at psi.ucm.es
> > <mailto:smoratti at psi.ucm.es>>
> >
> >     Dear Mikel,
> >
> >     I understand that you should do a mtmfft with a center frequency
> >     of interest (in your case cfg.foil = [11 11]) and then you do a
> >     frequency smoothing of 3 Hz (cfg.tapsmofrq = 3). Of course you
> >     need a time window big enough to allow such a smoothing. The CSD
> >     should represent a frequency window of 8 to 14 Hz then. Then you
> >     put the result of the mtmfft into the dics beamformer.
> >
> >     Best,
> >
> >     Stephan
> >
> >     El 27/03/2012, a las 11:19, Ion Lavado escribi?:
> >
> >>     Hello, i'm having problems trying the beamformer analysis with a
> >>     frequency band of interest. I would like to have for example an
> >>     interval like [8 14] Hz. My concept problem is about the
> >>     cfg.frequency and cfg.tapsmofrq  values. (it must be a escalar,
> >>     but i want a frequency band).
> >>
> >>     %FREQ ANALYSIS
> >>     cfg = [];
> >>     cfg.method    = 'mtmfft';
> >>     cfg.output    = 'powandcsd';
> >>     cfg.tapsmofrq = 5;
> >>     cfg.foilim    = [8 14];
> >>     freq_words_alpha = ft_freqanalysis(cfg, words);
> >>
> >>
> >>     %SOURCE ANALYSIS
> >>     cfg              = [];
> >>     cfg.frequency    = 11;
> >>     cfg.lambda=0;
> >>     cfg.method       = 'dics';
> >>     cfg.coordsys       = 'neuromag';
> >>     cfg.projectnoise = 'yes';
> >>     cfg.grad            =  freq_words_alpha.grad;
> >>     cfg.channel   = {'MEG'};
> >>     cfg.grid         = grid;
> >>     cfg.reducerank      = 2;
> >>     cfg.vol          = vol02;
> >>     vol02=ft_convert_units(vol02,'cm');
> >>     source_pre11  = ft_sourceanalysis(cfg,  freq_words_alpha );
> >>
> >>
> >>     I use a cfg.frequency of 11 but i don't have really clear what
> >>     i'm doing as a get the same result using cfg.frequency=11 but a
> >>     freqanalysis in [10 12]. I would be very grateful if someone
> >>     could solve my doubt.
> >>
> >>     Best wishes,
> >>
> >>     Mikel
> >>     _______________________________________________
> >>     fieldtrip mailing list
> >>     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >>     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >     ________________________________________________________
> >     Stephan Moratti, PhD
> >
> >     see also: http://web.me.com/smoratti/
> >
> >     Universidad Complutense de Madrid
> >     Facultad de Psicolog?a
> >     Departamento de Psicolog?a B?sica I
> >     Campus de Somosaguas
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >     and
> >
> >     Center for Biomedical Technology
> >     Laboratory for Cognitive and Computational Neuroscience
> >     Parque Cient?fico y Tecnol?gico de la Universidad Politecnica de
> >     Madrid
> >     Campus Montegancedo
> >     28223 Pozuelo de Alarc?n (Madrid)
> >     Spain
> >
> >
> >     email: smoratti at psi.ucm.es <mailto:smoratti at psi.ucm.es>
> >     Tel.: +34 679219982 <tel:%2B34%20679219982>
> >
> >
> >
> >     _______________________________________________
> >     fieldtrip mailing list
> >     fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >     http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
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> ------------------------------
>
> Message: 3
> Date: Tue, 27 Mar 2012 15:00:32 +0200
> From: "Pomper, Ulrich" <Ulrich.Pomper at charite.de>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: [FieldTrip] one-sample cluster test
> Message-ID: <4F71B9F0.8080106 at charite.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear list members,
>
> this topic was discussed some time in 2008, but it seems to me no
> conclusion was found.
>
> I would like to find source activity that differs significantly from
> zero. I could run a one sample t-test for every voxel and end up having
> a huge MC problem, or (preferably) use some kind of cluster based
> permutation statistics. However, the option for a one sample cluster
> test is not implemented in FT.
>
> Would it be correct to test the data from my experimental condition
> against a set of data containing all zeros using a cluster based
> permutation test?
>
> Any help is very much appreciated!
> Best, Ulrich
>
>
>
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