tfanalysis - NaN

Christian Hesse c.hesse at FCDONDERS.RU.NL
Mon Jun 25 21:49:16 CEST 2007


Hi Virginie,

> thanks for your inputs. Actually, I have tried different window
> sizes and frequency parameters (and wavelet, tf tiling,...). I
> would not expect to obtain NaN for a narrow band in higher
> frequencies (say 35-45Hz) with 2Hz and 4 cycles resolution with the
> same epoch but I still do.
>
> I'll try with a longer epoch, but I find puzzling that I should
> still get NaN when the resolution should be sufficient for the
> computations.

If these NaNs occur at the edges of the TFR then that could still be
explained by the fact that the analysis time windows have been placed
in such a way that some of them do not overlap 100% with the signal
time axis. The time points in cfg.toi actually specify the middle of
the time interval over which the spectral analysis is carried out.
Therefore, if the extremes of cfg.toi coincide with the extremes of
your epoch time axis then there will always be NaNs in at least the
first and last windows at all frequencies.

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?

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>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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