[FieldTrip] problem of implementing fieldtrip
Jinghao Lu
jhlu at ucdavis.edu
Thu Sep 20 00:29:25 CEST 2012
Hi Roemer,
the more exact problem may be like this:
1. I used eeglab to do all the erps and time-frequency and then used
'eeglab2fieldtrip(preprocessing, which seems the only way)'
2. then ran ft_timelockanalysis to generate erps, with cfg.channel =
{'naLeft1'}(only one channel)
3. ran permutation with cfg.correctm = 'cluster' and subsequent cfg
settings. However, an error message came out saying:
"Error using ==> statistics_wrapper at 249
You need to specify a neighbourstructure"
Which part did I set wrong?
Best,
Jinghao
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> Today's Topics:
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> 1. Re: Question of implementing Fieldtrip (Roemer van der Meij)
> 2. Re: Problems plotting TFR with different frequency sacle
> (J?rn M. Horschig)
> 3. ft_checkcoordsys outdated? (Markus Butz)
> 4. Re: ft_checkcoordsys outdated? (Johanna Zumer)
> 5. Re: ft_checkcoordsys outdated? (jan-mathijs schoffelen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 19 Sep 2012 16:04:19 +0200
> From: Roemer van der Meij <r.vandermeij at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
> <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Question of implementing Fieldtrip
> Message-ID:
> <CA+WpQ35nN-cDKQAX807aJ4RMQOTUCio1-
XXYb5Wb0vcyG_j=8g at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Jinghao,
>
> If you are talking about only looking at a single channel and using those
> for analyses, you can use cfg.channel for this purpose. It might be a
> good
> idea as well to run through the respective tutorial, which can be found
> at: http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock.
> My previous suggestion will also aid in reducing small clusters popping
> up.
>
> Best,
> Roemer
>
>
>
> On Wed, Sep 19, 2012 at 1:50 PM, Jinghao Lu <jhlu at ucdavis.edu> wrote:
>
> >
> >
> > As for my question, what I mean is that I want to apply the
> cluster-based
> > permutation on the data from a single intracranial electrode just like
> what
> > Maris did in his paper 'Nonparametric statistical testing of EEG- and
> MEG-
> > data'. In this way, the scattered clusters will reduce to only several.
> > Some discrete sample with significant difference may disappear as well.
> >
> > In Fieldtrip, if I choose cfg.correctm = 'cluster', then a neighborhood
> is
> > required. However, I only have one electrode and want to apply it on
> > time(or further frequency). How can I set cfg?
> >
> >
> --
> Roemer van der Meij M.Sc.
> PhD student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognition
> P.O. Box 9104
> 6500 HE Nijmegen
> The Netherlands
> Tel: +31(0)24 3655932
> E-mail: r.vandermeij at donders.ru.nl
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> ------------------------------
>
> Message: 2
> Date: Wed, 19 Sep 2012 16:07:09 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Problems plotting TFR with different
> frequency sacle
> Message-ID: <5059D18D.4070705 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Haiteng,
>
> I'm gonna drop by since you are in the office next door ;)
>
> Best,
> J?rn
>
> On 9/19/2012 3:39 PM, Haiteng Jiang wrote:
> > Dear Fieldtripers ,
> > I try to plot the TFR with Fieldtrip , but I find the frequency
> > shift in the plotting when I use different frequency scale. Please
> > see the attached two examples (4-30Hz versus 4-100Hz). The TFR within
> > 4-30Hz is centered in alpha band while it is switched to beta band
> > with the 4-100Hz. scale . Regarding to the TFR, I calculate it by
> > using an adaptive sliding time window of four cycles length (?t = 4/f)
> > and a Hanning taper for lower frequencies (4--30 Hz), and a sliding
> > time window of fixed length (200ms) and three orthogonal Slepian
> > tapers resulting in ?10 Hz smoothing (29) for higher frequencies
> > (30--100 Hz).
> > Any suggestion ?
> > All the best,
> > Haiteng
> > --
> > Haiteng Jiang
> > PhD candidate
> > Neuronal Oscillations Group
> > Donders Institute for Brain, Cognition and Behaviour
> > Centre for Cognitive Neuroimaging
> > Radboud University Nijmegen
> >
> > Visiting address
> > Room 2.32
> > Donders Centre for Cognitive Neuroimaging
> > Kapittelweg 29
> > 6525 EN Nijmegen
> > the Netherlands
> >
> > Tel.: +31 (0)243668291 <tel:%2B31%20%280%29243668291>
> > Web: https://sites.google.com/site/haitengjiang/
> >
> >
> >
> > _______________________________________________
> > 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
> FieldTrip Development Team
>
> 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: Wed, 19 Sep 2012 15:25:33 +0100
> From: Markus Butz <Markus.Butz at uni-duesseldorf.de>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] ft_checkcoordsys outdated?
> Message-ID: <7630d250a5f1.5059e3ed at uni-duesseldorf.de>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear list
>
> the headmodel tutorial
> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the
> function ft_checkcoordsys.
> This function is also explained here
> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys.
> However, as far as I can see it is not existent in the fieldtrip version
I
> am using right now, ie 20111101.
> How come? Is it outdated or do I miss something here?
>
> Best wishes
> Markus
>
>
>
>
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> ------------------------------
>
> Message: 4
> Date: Wed, 19 Sep 2012 18:17:43 +0200
> From: Johanna Zumer <johanna.zumer at donders.ru.nl>
> To: Markus.Butz at uni-duesseldorf.de, FieldTrip discussion list
> <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ft_checkcoordsys outdated?
> Message-ID:
> <CAL4kA6c3tFJm+=7ijBEKyLaSH1G0ns-
8FHxUvcAhG0Or35B=Ow at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Markus,
>
> Indeed it is outdated. It has been renamed to ft_determine_coordsys and
> moved to utilities:
> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219
> Thanks for spotting that on the tutorial, as it should be updated.
>
> Cheers,
> Johanna
>
> 2012/9/19 Markus Butz <Markus.Butz at uni-duesseldorf.de>
>
> > Dear list
> >
> > the headmodel tutorial (
> > http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the
> > function ft_checkcoordsys.
> > This function is also explained here
> > http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys.
> > However, as far as I can see it is not existent in the fieldtrip
version
> I
> > am using right now, ie 20111101.
> > How come? Is it outdated or do I miss something here?
> >
> > Best wishes
> > Markus
> >
> >
> >
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
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> ------------------------------
>
> Message: 5
> Date: Wed, 19 Sep 2012 19:06:12 +0200
> From: jan-mathijs schoffelen <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] ft_checkcoordsys outdated?
> Message-ID: <B0578539-7D16-4A7B-BA98-538614977F2D at donders.ru.nl>
> Content-Type: text/plain; charset="us-ascii"
>
> ...and the good thing about a wiki is: anybody can update it! ;-)
>
> Best,
> Jan-Mathijs
>
>
> On Sep 19, 2012, at 6:17 PM, Johanna Zumer wrote:
>
> > Hi Markus,
> >
> > Indeed it is outdated. It has been renamed to ft_determine_coordsys
and
> moved to utilities:
> http://code.google.com/p/fieldtrip/source/detail?spec=svn3219&r=3219
> > Thanks for spotting that on the tutorial, as it should be updated.
> >
> > Cheers,
> > Johanna
> >
> > 2012/9/19 Markus Butz <Markus.Butz at uni-duesseldorf.de>
> > Dear list
> >
> > the headmodel tutorial
> (http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg) refers to the
> function ft_checkcoordsys.
> > This function is also explained here
> http://fieldtrip.fcdonders.nl/reference/ft_checkcoordsys.
> > However, as far as I can see it is not existent in the fieldtrip
version
> I am using right now, ie 20111101.
> > How come? Is it outdated or do I miss something here?
> >
> > Best wishes
> > Markus
> >
> >
> >
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > 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
>
> Jan-Mathijs Schoffelen, MD PhD
>
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
>
> Max Planck Institute for Psycholinguistics,
> Nijmegen, The Netherlands
>
> J.Schoffelen at donders.ru.nl
> Telephone: +31-24-3614793
>
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>
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>
> End of fieldtrip Digest, Vol 22, Issue 37
> *****************************************
>
Jinghao Lu
Dept. of Physics
Zhejiang University
866 Yuhangtang Road
Hangzhou
310058 ZHEJIANG
CHINA
Temporary Affiliate
Dynamic Memory Lab
UC Davis
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