tfanalysis - NaN

Virginie van Wassenhove vvw at CALTECH.EDU
Mon Jun 25 23:11:45 CEST 2007


Hi Christian

>>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.

Yes, I do realize that.


>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)

Virginie

>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 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>Virginie.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><mailto: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 gmail.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.



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