Reading a csv file into FieldTrip, calculating power and coherence between channels...

[jan-mathijs schoffelen]

Dear W.Saad,

Could it be that there is a typo in how you define data.time? You
define it in sample numbers but it should be in seconds: data.time{1}
= [1:filelength]./daga.fsample;

I guess this may help.

Best,

Jan-Mathijs

On May 26, 2010, at 12:09 PM, W. Saad wrote:

> Hi,
>
> I am new to matlab and FieldTrip - so bare with me and thanks for
> your feedback in advance :)
>
> I have a csv file containing readings for 25 electrode EEG trial.
> There are 129,908 readings in
> the file (sampling rate is 256 - approx. 507 seconds) The file is 25
> columns by 129,908 rows.
>
> I would like to calculate power for each of the 5 wave types for
> each channel. Also, I would
> like to find the coherence for all intra-hemispheric and inter-
> hemispheric pairwise
> combination of the 25 channels (300 in total).
>
> I am trying the following code but getting a memory error and other
> errors (code is mostly based
> on the samples I have found in FieldTrip website).
>
>
> %--------------------------------------------------------------
>
> fieldtripdefs;
>
> filename='recall.dat';
> filelength=129908;
> rdata=csvread(filename);
> rdata=rdata';
>
> % cell-array containing strings, Nchan X 1
> data.label = {'E2' 'E3' 'E4' 'E5' 'E6' 'E7' 'E8' 'E9' 'E10' 'E11'
> 'E12' 'E13' 'E14' 'E15' 'E16' 'E17' 'E18' 'E19' 'E20' 'E21' 'E22'
> 'E23' 'E24' 'E25' 'E26'};
>
> % sampling frequency in Hz, single number
> data.fsample = 256;
>
> % cell-array containing a data matrix for each trial (1 X Ntrial),
> each data matrix is Nchan X Nsamples
> data.trial = {rdata};
>
> % cell-array containing a time axis for each trial (1 X Ntrial),
> each time axis is a 1 X Nsamples vector
> timevector = [1:filelength];
> data.time = { timevector };
>
> cfg            = [];
> cfg.output     = 'powandcsd';
> cfg.method     = 'mtmfft';
> cfg.foilim     = [0.5 50];
> cfg.tapsmofrq  = 5;
> cfg.keeptrials = 'yes';
> cfg.channel    = {'all' };
> cfg.channelcmb = {'all' 'all'};
> freq           = ft_freqanalysis(cfg, data);
>
> cfg            = [];
> cfg.method     = 'coh';
> cfg.channelcmb = {'all' 'all'};
> fd             = ft_connectivityanalysis(cfg, freq);
>
> % Let us not draw for now..
> %cfg                  = [];
> %cfg.xparam           = 'freq';
> %cfg.zparam           = 'cohspctrm';
> %cfg.xlim             = [5 80];
> %cfg.cohrefchannel    = 'EMGlft';
> %cfg.layout           = 'CTF151.lay';
> %cfg.showlabels       = 'yes';
> %figure; ft_multiplotER(cfg, fd)
>
> -----------------------------------------------------------------
>
> The messages/error I get is:
>
> the input is raw data with 25 channels and 1 trials
> ??? Maximum variable size allowed by the program is exceeded.
>
> Error in ==> dpss>dpsscalc at 127
> E = zeros(N,k(2)-k(1)+1);
>
> Error in ==> dpss at 54
>    [E,V] = dpsscalc(N,NW,k);
>
> Error in ==> ft_freqanalysis_mtmfft>double_dpss at 423
> tap = dpss(double(a), double(b), varargin{:});
>
> Error in ==> ft_freqanalysis_mtmfft at 249
>     tap = double_dpss(numdatbns,numdatbns*(cfg.tapsmofrq./
> data.fsample))';
>
> Error in ==> ft_freqanalysis at 75
>   [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)),
> cfg, data);
>
> Error in ==> saad_fieldtrip at 29
> freq           = ft_freqanalysis(cfg, data);
>
> -----------------------------------------------------------------
>
> I have been looking around in the discussion board trying to find
> how to read a csv file with no success (though it looks to me it
> was read successfully since Fieldtrip detected it has 25 channels).
>
> Also, I am worried about the message
> ??? Maximum variable size allowed by the program is exceeded.
> Because most of my trials are huge in size, in fact the biggest file
> size I have is 25 columns x 250,000 rows (~60MB).
>
> Your input is highly appreciated.
>
> Thanks.
> 30 days of prizes: Hotmail makes your day easier! Enter now
> ----------------------------------
> 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/

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: 0031-24-3668063


----------------------------------
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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