tfanalysis - NaN
Christian Hesse
c.hesse at FCDONDERS.RU.NL
Tue Jun 26 00:19:18 CEST 2007
>> Does the call to FREQANALYSIS produce any (potentially useful)
>> warnings?
>
> All channels, all trials and all samples are correctly reported.
> Using the wavelet analysis, there is no apparent warning.
> Using the multitaper, the warning is that there's only 1 tapper
> (now the problem is that there's 1 tapper only, even when I greatly
> reduce the width of a window and extend the length of the epoch...)
In the configuration options you have specified cfg.taper = 'hanning'
which will apply only one (i.e., the hanning) taper to your data. If
you want to use multitapers you need to set cfg.taper = 'dpss' or
just leave the field it out of the cfg (since multitapers are the
default).
> Are the tf data normalized and how are they normalized?
I'm not really sure what you mean by normalized (the csd is obviously
a density) but if there were any divide by zero issues then matlab
would be chucking warnings. What happens when you set cfg.output =
'pow'; ?
Christian
>>
>>
>>>>>>
>>>>>> Hi Virginie,
>>>>>>
>>>>>> the function freqanalysis will return NaNs when a time
>>>>>> frequency tile extends beyond a corresponding data segment.
>>>>>> One would usually expect a "U" shaped padding of NaNs at the
>>>>>> boundaries of any TFR which has longer time windows for lower
>>>>>> frequencies. From the cfg options you specify below I can see
>>>>>> that you have a data segment of 1.1 seconds length and the
>>>>>> moving windows cfg.t_tfimwin are quite long at the low
>>>>>> ffrequencies, e.g., 1 Hz = 4 s, 6 Hz = 0.6666 s. Hence the
>>>>>> NaNs seem perfectly "normal" in this case. The only way to
>>>>>> avoid NaN in the time window of interest (using this type of
>>>>>> time-frequency tiling) is to make your epochs longer.
>>>>>>
>>>>>> Hope this helps,
>>>>>> Christian
>>>>>>
>>>>>>
>>>>>> On 21 Jun 2007, at 20:44, Virginie van Wassenhove wrote:
>>>>>>
>>>>>>> Hello again.
>>>>>>>
>>>>>>> I am finding NaN whatever method I use (multitaper and
>>>>>>> wavelet analysis), yet using a different analysis tool with
>>>>>>> similar parameters I obtain clean results.
>>>>>>> epoch length = 1.1 s
>>>>>>> baseline length = 0.3 s
>>>>>>> sampling rate = 500Hz
>>>>>>>
>>>>>>> I tried several suggestions listed in the previous message
>>>>>>> list for a similar problem, but none seem to provide
>>>>>>> reasonable results (aka always NaN).
>>>>>>> Also tried with different subjects, no particular error
>>>>>>> otherwise. I am sending a sample script in case someone has a
>>>>>>> suggestion on this...
>>>>>>> Thanks for your help once more!
>>>>>>>
>>>>>>> Virginie
>>>>>>>
>>>>>>> %% ================================================
>>>>>>> % TF analysis - MULTITAPER
>>>>>>> cfg = [];
>>>>>>> cfg.method = 'mtmconvol';
>>>>>>> cfg.taper = 'hanning';
>>>>>>> cfg.output = 'powandcsd';
>>>>>>> %cfg.channel = 'all';
>>>>>>> cfg.channel = 'E75';
>>>>>>>
>>>>>>> %win_length = 0.128;
>>>>>>> %win_n = floor(2.*(1.1./win_length)-1);
>>>>>>>
>>>>>>> cfg.foi = 1:5:45;
>>>>>>> %cfg.t_ftimwin = ones(1,win_n).*win_length;
>>>>>>> cfg.t_ftimwin = 4./cfg.foi;
>>>>>>> %cfg.toi = -0.3:win_length/2:0.8;
>>>>>>> cfg.toi = -0.3:0.05:0.8;
>>>>>>>
>>>>>>> % cfg.pad = 'maxperlen';
>>>>>>> % cfg.keeptrials = 'no';
>>>>>>> % cfg.keeptapers ='no';
>>>>>>> s08_ill_mult = freqanalysis(cfg,s08_ill);
>>>>>>>
>>>>>>> %% ========================
>>>>>>> % plot freq data
>>>>>>> cfg = [];
>>>>>>> cfg.baseline = [-0.3 0];
>>>>>>> cfg.layout = egilay;
>>>>>>> cfg.zlim = [-0.00001 0.000001]; % a comparer
>>>>>>> entre participants
>>>>>>> % warning off % NaN
>>>>>>> clf
>>>>>>> %multiplotTFR(cfg,s08_ill_mult);
>>>>>>> singleplotTFR(cfg,s08_ill_mult);
>>>>>>>
>>>>>>> %% ================================================
>>>>>>> % TF analysis - wavelet
>>>>>>> cfg = [];
>>>>>>> cfg.method = 'wltconvol';
>>>>>>> cfg.width = 4;
>>>>>>> cfg.output = 'pow';
>>>>>>> cfg.foi = 1:2:30;
>>>>>>> cfg.toi = -0.3:0.05:0.8;
>>>>>>> s14_ill_wvlt = freqanalysis(cfg, s14_ill);
>>>>>>> %% ========================
>>>>>>> cfg = [];
>>>>>>> cfg.baseline = [-0.3 0];
>>>>>>> cfg.zlim = [-1 1];
>>>>>>> cfg.showlabels = 'yes';
>>>>>>> cfg.layout = egilay;
>>>>>>> clf
>>>>>>> multiplotTFR(cfg, s14_ill_wvlt)
>>>>>>>
>>>>>>> %% ================================================
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Virginie van Wassenhove, PhD
>>>>>>>
>>>>>>> :::::::::::: contact info :::::::::::::
>>>>>>> Caltech - Division of Biology
>>>>>>> 1200 E. California Blvd M/C 139-74
>>>>>>> Pasadena CA 91125 USA
>>>>>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>>>>>> <<<mailto:vvw at caltech.edu>mailto:vvw at caltech.edu>mailto:vvw at calt
>>>>>>> ech.edu><<mailto:vvw at caltech.edu>mailto:vvw at caltech.edu><mailto:
>>>>>>> vvw at caltech.edu>vvw at caltech.edu
>>>>>>> <<<mailto:Virginie.van.Wassenhove at gmail.com>mailto:Virginie.van.
>>>>>>> Wassenhove at gmail.com>mailto:Virginie.van.Wassenhove at gmail.com><<
>>>>>>> mailto:Virginie.van.Wassenhove at gmail.com>mailto:Virginie.van.Was
>>>>>>> senhove at gmail.com><mailto:Virginie.van.Wassenhove at gmail.com>Virg
>>>>>>> inie.van.Wassenhove at gmail.com
>>>>>>> W: 626.395.8959
>>>>>>> <<<http://www.its.caltech.edu/~vvw>http://www.its.caltech.edu/
>>>>>>> ~vvw>http://www.its.caltech.edu/~vvw>http://
>>>>>>> www.its.caltech.edu/~vvw
>>>>>>>
>>>>>>> :::::::::::::::::: extras ::::::::::::::::::::
>>>>>>> <<<http://www.kiva.org>http://www.kiva.org>http://
>>>>>>> www.kiva.org>http://www.kiva.org
>>>>>>> <<http://www.thehungersite.com>http://
>>>>>>> www.thehungersite.com>http://www.thehungersite.com/
>>>>>>> <<http://www.agloco.com/r/BBBS1539>http://www.agloco.com/r/
>>>>>>> BBBS1539>http://www.agloco.com/r/BBBS1539
>>>>>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>>>>>>
>>>>>>> ----------------------------------
>>>>>>> The aim of this list is to facilitate the discussion between
>>>>>>> users of the FieldTrip toolbox, to share experiences and to
>>>>>>> discuss new ideas for MEG and EEG analysis. See also
>>>>>>> <<<http://listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>>>> listserv.surfnet.nl/archives/fieldtrip.html and <<<http://
>>>>>>> www.ru.nl/fcdonders/fieldtrip>http://www.ru.nl/fcdonders/
>>>>>>> fieldtrip>http://www.ru.nl/fcdonders/fieldtrip>http://
>>>>>>> www.ru.nl/fcdonders/fieldtrip.
>>>>>>
>>>>>> -----------------------------------------------------------------
>>>>>> -----
>>>>>> Christian Hesse, PhD, MIEEE
>>>>>>
>>>>>> F.C. Donders Centre for Cognitive Neuroimaging
>>>>>> P.O. Box 9101
>>>>>> NL-6500 HB Nijmegen
>>>>>> The Netherlands
>>>>>>
>>>>>> Tel.: +31 (0)24 36 68293
>>>>>> Fax: +31 (0)24 36 10989
>>>>>>
>>>>>> Email:
>>>>>> <<<mailto:c.hesse at fcdonders.ru.nl>mailto:c.hesse at fcdonders.ru.nl>
>>>>>> mailto:c.hesse at fcdonders.ru.nl><<mailto:c.hesse at fcdonders.ru.nl>m
>>>>>> ailto:c.hesse at fcdonders.ru.nl><mailto:c.hesse at fcdonders.ru.nl>c.h
>>>>>> esse at fcdonders.ru.nl
>>>>>> Web: <<<http://www.fcdonders.ru.nl>http://
>>>>>> www.fcdonders.ru.nl>http://
>>>>>> www.fcdonders.ru.nl>www.fcdonders.ru.nl
>>>>>> -----------------------------------------------------------------
>>>>>> -----
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----------------------------------
>>>>>>
>>>>>> The aim of this list is to facilitate the discussion between
>>>>>> users of the FieldTrip toolbox, to share experiences and to
>>>>>> discuss new ideas for MEG and EEG analysis.
>>>>>>
>>>>>> <<http://listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>>> listserv.surfnet.nl/archives/fieldtrip.html
>>>>>>
>>>>>> <http://www.ru.nl/fcdonders/fieldtrip/>http://www.ru.nl/
>>>>>> fcdonders/fieldtrip/
>>>>>
>>>>> Virginie van Wassenhove, PhD
>>>>>
>>>>> :::::::::::: contact info :::::::::::::
>>>>> Caltech - Division of Biology
>>>>> 1200 E. California Blvd M/C 139-74
>>>>> Pasadena CA 91125 USA
>>>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>>>> <<mailto:vvw at caltech.edu>mailto:vvw at caltech.edu><mailto:vvw at caltec
>>>>> h.edu>vvw at caltech.edu
>>>>> <<mailto:Virginie.van.Wassenhove at gmail.com>mailto:Virginie.van.Was
>>>>> senhove at gmail.com><mailto:Virginie.van.Wassenhove at gmail.com>Virgin
>>>>> ie.van.Wassenhove at gmail.com
>>>>> W: 626.395.8959
>>>>> <<http://www.its.caltech.edu/~vvw>http://www.its.caltech.edu/
>>>>> ~vvw>http://www.its.caltech.edu/~vvw
>>>>>
>>>>> :::::::::::::::::: extras ::::::::::::::::::::
>>>>> <<http://www.kiva.org>http://www.kiva.org>http://www.kiva.org
>>>>> <http://www.thehungersite.com>http://www.thehungersite.com/
>>>>> <http://www.agloco.com/r/BBBS1539>http://www.agloco.com/r/BBBS1539
>>>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>>>>
>>>>> ----------------------------------
>>>>> The aim of this list is to facilitate the discussion between
>>>>> users of the FieldTrip toolbox, to share experiences and to
>>>>> discuss new ideas for MEG and EEG analysis. See also <<http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>>> listserv.surfnet.nl/archives/fieldtrip.html and <<http://
>>>>> www.ru.nl/fcdonders/fieldtrip>http://www.ru.nl/fcdonders/
>>>>> fieldtrip>http://www.ru.nl/fcdonders/fieldtrip.
>>>>
>>>> -------------------------------------------------------------------
>>>> ---
>>>> Christian Hesse, PhD, MIEEE
>>>>
>>>> F.C. Donders Centre for Cognitive Neuroimaging
>>>> P.O. Box 9101
>>>> NL-6500 HB Nijmegen
>>>> The Netherlands
>>>>
>>>> Tel.: +31 (0)24 36 68293
>>>> Fax: +31 (0)24 36 10989
>>>>
>>>> Email:
>>>> <<mailto:c.hesse at fcdonders.ru.nl>mailto:c.hesse at fcdonders.ru.nl><ma
>>>> ilto:c.hesse at fcdonders.ru.nl>c.hesse at fcdonders.ru.nl
>>>> Web: <<http://www.fcdonders.ru.nl>http://
>>>> www.fcdonders.ru.nl>www.fcdonders.ru.nl
>>>> -------------------------------------------------------------------
>>>> ---
>>>>
>>>>
>>>>
>>>>
>>>> ----------------------------------
>>>>
>>>> The aim of this list is to facilitate the discussion between
>>>> users of the FieldTrip toolbox, to share experiences and to
>>>> discuss new ideas for MEG and EEG analysis.
>>>>
>>>> <http://listserv.surfnet.nl/archives/fieldtrip.html>http://
>>>> listserv.surfnet.nl/archives/fieldtrip.html
>>>>
>>>> http://www.ru.nl/fcdonders/fieldtrip/
>>>
>>> Virginie van Wassenhove, PhD
>>>
>>> :::::::::::: contact info :::::::::::::
>>> Caltech - Division of Biology
>>> 1200 E. California Blvd M/C 139-74
>>> Pasadena CA 91125 USA
>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>> <mailto:vvw at caltech.edu>vvw at caltech.edu
>>> <mailto:Virginie.van.Wassenhove at gmail.com>Virginie.van.Wassenhove at gm
>>> ail.com
>>> W: 626.395.8959
>>> <http://www.its.caltech.edu/~vvw>http://www.its.caltech.edu/~vvw
>>>
>>> :::::::::::::::::: extras ::::::::::::::::::::
>>> <http://www.kiva.org>http://www.kiva.org
>>> http://www.thehungersite.com/
>>> <http://www.agloco.com/r/BBBS1539>http://www.agloco.com/r/BBBS1539
>>> :::::::::::::::::::::::::::::::::::::::::::::::::
>>>
>>> ----------------------------------
>>> The aim of this list is to facilitate the discussion between
>>> users of the FieldTrip toolbox, to share experiences and to
>>> discuss new ideas for MEG and EEG analysis. See also <http://
>>> listserv.surfnet.nl/archives/fieldtrip.html>http://
>>> listserv.surfnet.nl/archives/fieldtrip.html and <http://www.ru.nl/
>>> fcdonders/fieldtrip>http://www.ru.nl/fcdonders/fieldtrip.
>>
>> ---------------------------------------------------------------------
>> -
>> Christian Hesse, PhD, MIEEE
>>
>> F.C. Donders Centre for Cognitive Neuroimaging
>> P.O. Box 9101
>> NL-6500 HB Nijmegen
>> The Netherlands
>>
>> Tel.: +31 (0)24 36 68293
>> Fax: +31 (0)24 36 10989
>>
>> Email: <mailto:c.hesse at fcdonders.ru.nl>c.hesse at fcdonders.ru.nl
>> Web: <http://www.fcdonders.ru.nl>www.fcdonders.ru.nl
>> ---------------------------------------------------------------------
>> -
>>
>>
>>
>>
>> ----------------------------------
>>
>> The aim of this list is to facilitate the discussion between users
>> of the FieldTrip toolbox, to share experiences and to discuss new
>> ideas for MEG and EEG analysis.
>>
>> http://listserv.surfnet.nl/archives/fieldtrip.html
>>
>> http://www.ru.nl/fcdonders/fieldtrip/
>
> Virginie van Wassenhove, PhD
>
> :::::::::::: contact info :::::::::::::
> Caltech - Division of Biology
> 1200 E. California Blvd M/C 139-74
> Pasadena CA 91125 USA
> :::::::::::::::::::::::::::::::::::::::::::::::::
> vvw at caltech.edu
> Virginie.van.Wassenhove at gmail.com
> W: 626.395.8959
> http://www.its.caltech.edu/~vvw
>
> :::::::::::::::::: extras ::::::::::::::::::::
> http://www.kiva.org
> http://www.thehungersite.com/
> http://www.agloco.com/r/BBBS1539
> :::::::::::::::::::::::::::::::::::::::::::::::::
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users
> of the FieldTrip toolbox, to share experiences and to discuss new
> ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/
> archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
>
----------------------------------------------------------------------
Christian Hesse, PhD, MIEEE
F.C. Donders Centre for Cognitive Neuroimaging
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Tel.: +31 (0)24 36 68293
Fax: +31 (0)24 36 10989
Email: c.hesse at fcdonders.ru.nl
Web: www.fcdonders.ru.nl
----------------------------------------------------------------------
----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.
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