tfanalysis - NaN
Christian Hesse
c.hesse at FCDONDERS.RU.NL
Mon Jun 25 23:30:48 CEST 2007
Hi Virginie,
>> If the NaNs occur also at other points in the TFR then there may
>> be something else going on ... is it the case that the NaNs are
>> confined to the edges (edge regions) of your TFR?
>
> The entire matrices (cfg.powspctrm) return NaN whether for
> (i)1.1 secs or 2.4 secs epochs
> (ii) narrow (25-50) or wide (2-50) bandwidth
> (iii) short or large cfg. toi (then would expect U shape)
>
That's not good! Does the call to FREQANALYSIS produce any
(potentially useful) warnings?
Regards,
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 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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