freqstastics script

Thu Sep 17 16:59:03 CEST 2009

Hi everyone. I am trying to use Fieldtrip and the function freqstatistics to run the kruskalwallis test across subjects after doing the grandaverage. The grandaverage works but I am confused about some of the arguments for the freqstatistics function. I have pasted in the lines from my script below.  I am particularly wondering if anyone has used this successfully before and if so what is the cfg.design command asking for and am I missing any other command/inputs for the kruskalwallis/freqstatistics function?
Any comments would be much appreciated.
claudia bonin 

[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));

________________________________________
From: FieldTrip discussion list [FIELDTRIP at NIC.SURFNET.NL] On Behalf Of P. Toffanin [P.Toffanin at RUG.NL]
Sent: Wednesday, September 16, 2009 4:27 PM
To: FIELDTRIP at NIC.SURFNET.NL
Subject: Re: [FIELDTRIP] freqstastics script

Dear Claudia,

the first error message seems a 'matlab-related error', it does not have anything to do with fieldtrip, but just with the way you use matlab. Basically matlab is complaining because the function you are using is not defined to use cell types. I believe that data.time is probably containing something like

data.time = {1,2,3};

then, what you should do, is to use the function like this:

isnan(data.time{:}) % this will show the content of data.time "ignoring" that it is a cell
rather than
isnan(data.time) % this will feed a cell to the isnan function, which uses arrays of numbers

About the warning message you get I cannot help you with that one, I'm sorry.

The best of luck!

Paolo

On 16/09/09, "Bonin, Claudia (NIH/NINDS) [F]" <boninc at NINDS.NIH.GOV> wrote:
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

-----Ursprüngliche 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{:});
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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.

http://listserv.surfnet.nl/archives/fieldtrip.html

http://www.ru.nl/fcdonders/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.