[FieldTrip] problem of implementing fieldtrip

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Thu Sep 20 09:59:27 CEST 2012


Dear Jinghao,

you need to specify cfg.avgoverchan='yes' prior to calling 
ft_timelockstatistics to tell fieldtrip that no clustering in space is 
needed. It should work fine then.

Best,
Jörn


On 9/20/2012 12:29 AM, Jinghao Lu wrote:
> 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:
>>
>>     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 ft_checkcoordsys outdated?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 Re: ft_checkcoordsys outdated?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 Re: ft_checkcoordsys outdated?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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>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>> 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
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


-- 
Jörn 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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