ft_freqstatistics between two groups

[jan-mathijs schoffelen]

Hi David,

It seems you are averaging both over time and frequency in
ft_freqstatistics. As far as I know, the standard mean-function is
used for that. If there are NaNs in your TFR, which happens now and
then at the edges of the TFR, you get a NaN in the average.

Cheers,

Jan-Mathijs


On Nov 4, 2010, at 8:24 PM, David Ziegler wrote:

> Hi Fieldtrippers,
>
> I am trying to run a comparison between TFRs from two groups of
> subjects and I keep getting some errors that I can't track down
> answers for.  I seem to recall something like this being discussed
> on this list, but I can't for the life of me track down that thread
> at the moment.
>
> I am using data from a neuromag 306 system on which I have
> calculated TFRs on the gradiometer data, then ran ft_combineplanar,
> followed by ft_freqdescriptives, followed by ft_freqgrandaverage for
> each of the two groups with the cfg.keepindividual = 'yes' option.
> I am able to plot the grand averages just fine, so the data seem to
> be ok (and there are fairly striking differences between the two).
>
> When I run a permutation test to quantify the group differences, I
> get the following error messages (although the analysis does run):
>
> computing statistic 500 from 500
> Warning: Not all replications are used for the computation of the
> statistic.
> > > In statfun_indepsamplesT at 57
>   In statistics_montecarlo at 298
>   In fieldtrip-20100617/private/statistics_wrapper at 285
>   In ft_freqstatistics at 105
> Warning: Divide by zero.
>
> When I inspect the output file, the .stat contains a single column
> of NaNs.  Does anyone know what I am doing wrong here?
>
> Here is the actual code I am using to run the statistics:
>
> cfg = [];
> cfg.channel          = {'MEG *3'}; %only combined gradiometer data
> cfg.layout = 'neuromag306cmb_dz.lay';
> cfg.latency     = [0.2 0.8];
> cfg.avgovertime = 'yes';
> cfg.avgoverchan      = 'no';
> cfg.avgoverfreq      = 'yes';
> cfg.parameter   = 'powspctrm';
> cfg.frequency        = [14 26];
> cfg.method           = 'montecarlo';
> cfg.statistic        = 'indepsamplesT';
> cfg.correctm         = 'no';
> cfg.clusteralpha     = 0.05;
> cfg.clusterstatistic = 'maxsum';
> cfg.minnbchan        = 2;
> cfg.tail             = 0;
> cfg.clustertail      = 0;
> cfg.alpha            = 0.05;
> cfg.numrandomization = 500;
>
> cfg.design           = [1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
> 19 20 21 22 23 24 25 ;   % subject number
>                                     1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2
> 2 2 2 2 2 2 2 2 2]; % 12subjs in grp1, 13subjs in grp2
> cfg.uvar = 1;
> cfg.ivar = 2;
>
> GA_low_stat = ft_freqstatistics(cfg, GA_grp1_low, GA_grp2_low)
>
> Thanks,
> David
>
>
> --
> David A. Ziegler
> Department of Brain and Cognitive Sciences
> Massachusetts Institute of Technology
> 43 Vassar St,  46-5121
> Cambridge, MA  02139
> Tel: 617-258-0765
> Fax: 617-253-1504
> daz at mit.edu
>
>
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> and to discuss new ideas for MEG and EEG analysis.
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> ---------------------------------------------------------------------------
>

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793


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