freqstastics script

Hanneke van Dijk hanneke.p.van.dijk at GMAIL.COM
Wed Sep 23 09:10:12 CEST 2009


Hi Claudia,

I think that if you want to do non-parametric tests using fieldtrip the
cluster randomization statistics routines would help you a great deal. I
think a lot of people using fieldtrip are using this method. You could have
a look at this site:

http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq

and the paper:

*Eric Maris, Robert Oostenveld, Nonparametric statistical testing of
EEG- and MEG-data, Journal of Neuroscience Methods, Volume 164, Issue
1, 15 August 2007, Pages 177-190, ISSN 0165-0270, DOI:
10.1016/j.jneumeth.2007.03.024.
(http://www.sciencedirect.com/science/article/B6T04-4NFXDDW-1/2/ebd219fd45cb52bf39c710fe25635040)
Keywords: Nonparametric statistical testing; Hypothesis testing; EEG;
MEG; Multiple comparisons problem*


Also, this mailing list is not a help desk but is read by fellow researchers
also using fieldtrip. And I would like to say that although it sometimes
takes a little while before you get your answer, that is because everybody
is busy and I am impressed and happy with the way everybody on this list is
nice enough to take the time to help eachother!

Best,

Hanneke

On Fri, Sep 18, 2009 at 9:15 PM, Bonin, Claudia (NIH/NINDS) [F] <
boninc at ninds.nih.gov> wrote:

> DOES ANYONE KNOW HOW TO USE THE FIELDTRIP FUNCTION FREQSTATISTICS TO RUN A
> KRUSKALWALLIS TEST?
>
> -----Original Message-----
> From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On
> Behalf Of Bonin, Claudia (NIH/NINDS) [F]
> Sent: Wednesday, September 16, 2009 1:06 PM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: Re: [FIELDTRIP] freqstastics script
>
> Hi. I am having trouble getting a freqstastics script to run to do a
> Kruskalwallis test. Thre freqgrandaverage works but I am having trouble with
> the arguments for the Kruskalwallis. I have pasted in the script and the
> error message in this email.  Has anyone written a script using
> freqsstatistics to do Kruskalwallis? I would love to see it or get some
> direction on the arguments that need to be assigned....Also I made up an
> argument for cfg.design but I don't really understand what this assignment
> is. Could anyone elaborate?
> Thank you!
> claudia Bonin
>
>
>
>
>
> here's the error message
>
>  isnan(data.time)
> ??? Undefined function or method 'isnan' for input arguments of type
> 'cell'.
>
> computing average power over 21 subjects
> Warning: discarding gradiometer information
> > In freqgrandaverage at 121
>  In tf2_virt_all_plot at 11
>
> here's the script.....
>
>
> Nsubj = 21;
>
> for subj = 1:Nsubj
>    fname = ['/home/boninc/tfresults/subj' 64 + subj];
>    clear fr
>    load(fname);
>    frs(subj) = fr;
> end
>
> cfg = [];
> [gr] = freqgrandaverage(cfg, frs(1), frs(2), frs(3), frs(4), frs(5),
> frs(6), frs(7), frs(8), frs(9), frs(10), frs(11), frs(12), frs(13), frs(14),
> frs(15), frs(16), frs(17), frs(18), frs(19), frs(20), frs(21));
>
> %cfg = [];
> %cfg.alpha = .05;
> %cfg.method = 'stats';
> %cfg.design = 1:21;
> %cfg.statistic = 'kruskalwallis';
> %[stat] = freqstatistics(cfg, frs(1), frs(2), frs(3), frs(4), frs(5),
> frs(6), frs(7), frs(8), frs(9), frs(10), frs(11), frs(12), frs(13), frs(14),
> frs(15), frs(16), frs(17), frs(18), frs(19), frs(20), frs(21));
>
> clf
> contourf(gr.time, gr.freq, squeeze(sum(gr.powspctrm))); colorbar
> %contourf(gr.time, gr.freq, gr.powspctrm); colorbar
>
> title '21 Subjects, RandL, RIGHT Central Motor'
> xlabel 'time, sec'
> ylabel 'frequency, Hz'
>
>
> ________________________________________
> From: FieldTrip discussion list [FIELDTRIP at NIC.SURFNET.NL] On Behalf Of
> Hanneke Van Dijk [Hanneke.vanDijk at MED.UNI-DUESSELDORF.DE]
> Sent: Thursday, September 10, 2009 7:21 AM
> To: FIELDTRIP at NIC.SURFNET.NL
> Subject: [FIELDTRIP] AW: [FIELDTRIP] freqstastics script
>
> Dear Claudia,
>
> Normally when matlab says 'undefined function for input of type ....' it
> means it cannot find the specific function in the paths you have defined.
> You can check whether neighbourselection.m is in your fieldtrip folder, if
> not I have attached it (version 20090428) so you can put it there. If this
> doesn't fix it please let me know!
>
> Groetjes Hanneke
>
>
> -----Urspr√ľngliche Nachricht-----
> Von: FieldTrip discussion list im Auftrag von Bonin, Claudia (NIH/NINDS)
> [F]
> Gesendet: Mi 09.09.2009 18:26
> An: FIELDTRIP at NIC.SURFNET.NL
> Betreff: [FIELDTRIP] freqstastics script
>
> I am trying to do statistics on time-frequency data across 16 subjects,
> averaging over channels. I received back the following error about
> 'neighbourselection' which means nothing to me.....Does anyone have any idea
> what might be wrong here? I have pasted in the exact message below.
> thanks!
> claudia
>
>
> >> cfg.statistic = 'kruskalwallis';
> >> cfg.method = 'stats';
> >> [s] = freqstatistics(cfg, fr, fr);
> averaging over 3 channels
> selected 50 time bins
> selected 41 frequency bins
> Warning: PACK can only be used from the MATLAB command line.
> > In fieldtrip/private/prepare_timefreq_data at 305
>  In fieldtrip/private/statistics_wrapper at 167
>  In freqstatistics at 44
> ??? Undefined function or method 'neighbourselection' for input arguments
> of type
> 'struct'.
>
> Error in ==> statistics_wrapper at 181
>    cfg = neighbourselection(cfg,varargin{1});
>
> Error in ==> freqstatistics at 44
> [stat] = statistics_wrapper(cfg, varargin{:});
> ----------------------------------
> 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/neuroimaging/fieldtrip.
>
>
>
> ----------------------------------
> 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/neuroimaging/fieldtrip.
>
> ----------------------------------
> 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/neuroimaging/fieldtrip.
>
> ----------------------------------
> 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/neuroimaging/fieldtrip.
>

----------------------------------
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/neuroimaging/fieldtrip.
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