[FieldTrip] TRENTOOL bad channel combinations

[Patricia Wollstadt]

Hello Tyler,

okay, I'd say the script should run like this (regarding channel
selection). Maybe it's really the data then. If you keep getting errors,
you can send me those as well.

Regarding the number of data points: The error you are getting depends
on a number of parameters TEprepare uses to determine the optimal
embedding dimension and embedding delay. TEprepare checks whether you
have enough samples in one trial after taking into account the ACT,
cfg.actthrvalue, cfg.ragdim, cfg.ragtau and the assumed interaction
delay (these parameters determine the maximum possible length, i.e. the
worst case, of your embedding).

Could you tell me the sampling rate of your data? If your data was
sampled at 1000Hz, 3/9th of 500 ms should give you about 167 sample
points for cfg.repPred, which would be okay.

Otherwise, you may alter the parameters mentioned above, e.g. you can
check whether you could lower the actthrvalue. The actthrvalue is used
to exclude all trials with an ACT higher than the threshold. The value
you put in there should be based on the filtering of the data prior to
TE analysis (e.g. if you highpass filter your data at 10 Hz and have a
sampling rate of 1000Hz, you shouldn't find any autocorrelation above
100 samples. In that case, you may use 100 as a threshold).

What values do you enter for the other parameters (assumed interaction
delay u, specified in cfg.predicttimemin_u/cfg.predicttimemax_u,
embedding parameters to be scanned in cfg.ragdim and cfg.ragtau)? Maybe
you can adjust those as well, to be able to enter a higher value for
.repPred.

Best, Patricia




On 04/11/2014 12:44 PM, Tyler Grummett wrote:
>
> Hello Patricia,
>
>
> I have previously selected the channels that are EEG, I am not
> entering in 'EEG' or anything.
>
>
>             cfgTEP = [];
>             cfgTEP.Path2TSTOOL = fullfile( matlabrootpath, 'Matlab',
> 'OpenTSTOOL'); % dont add this to matlab path
>             cfgTEP.toi = [ min( [vchan.time{ :}]), max( [vchan.time{
> :}])];
>             cfgTEP.channel = vchan.label( comps);
>
>
> After playing around with it for a bit I dont think it is the channel
> combinations, but the data.
>
>
> If I can ask a separate question, what is an optimal length for the
> trials? My trials are about 500 ms long and it gives me the following
> error:
>
>
> Error using TEprepare (line 710)
> TRENTOOL ERROR: Not enough points in timeseries for current analysis
> settings: cfg.repPred too big, or
> max(cfg.ragdim)*max(cfg.ragtaurange) too big, or maximum u to big
>
> It is recommended that the cfgTEP.repPred is size(data.trial{1,1},2)*(3/4)
>
> However it only works for me if it is size(data.trial{1,1},2)*(3/9) .
>
> Then it runs fine, but Im worried about changing this.
>
> Tyler
>
>
>
> *************************
>
> /Tyler Grummett ( BBSc, BSc(Hons I))/
> /PhD Candidate/
> /Brain Signals Laboratory/
> /Flinders University/
> /Rm 5A301/
> /Ext 66124/
> ------------------------------------------------------------------------
> *From:* fieldtrip-bounces at science.ru.nl
> <fieldtrip-bounces at science.ru.nl> on behalf of Patricia Wollstadt
> <Patricia.Wollstadt at gmx.de>
> *Sent:* Friday, 11 April 2014 6:42 PM
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] TRENTOOL bad channel combinations
>  
> Hello Tyler,
>
> TRENTOOL does not support the exclusion of channels like FieldTrip
> does (e.g.  {'all', '-MLx', '-EOG'}), you have to explicitly specify
> channels OR combinations of channels for analysis in the cfg structure
> passed to TEprepare:
>
> %  cfg.sgncmb      = list of channelpairs cell array (Nx(source, target))
> %  or
> %  cfg.channel     = list of channels cell array - testing will be
> done all-by-all
>
> If you provide a list of channel combinations in cfg.sgncmb, TRENTOOL
> will analyze these combinations only; if you provide a list of
> channels in cfg.channel, TEprepare will build all possible channel
> combinations from the list and TRENTOOL will analyze these
> combinations. (Also, channel names have to match the channel labels in
> data.label.)
>
> So, a way to exclude bad channel combinations would be to provide a
> list of all channels that should be included in the analysis in
> cfg.channel and let TEprepare build the channel combinations from that.
>
> I hope this answers your question. Please let me know if you encounter
> any more problems.
>
> Best,
> Patricia
>
>
>
> On 04/11/2014 04:38 AM, Tyler Grummett wrote:
>>
>> Hello fieldtrip,
>>
>>
>> Has anyone worked out how to handle bad channel combinations in
>> TRENTOOL using TEprepare?
>>
>>
>> In my experience it just crashes. I am hoping for a way to calculate
>> the bad channel combinations before running TEprepare.
>>
>>
>> If anyone can help, that will be greatly appreciated!!
>>
>>
>> Tyler
>>
>>
>> *************************
>>
>> /Tyler Grummett ( BBSc, BSc(Hons I))/
>> /PhD Candidate/
>> /Brain Signals Laboratory/
>> /Flinders University/
>> /Rm 5A301/
>> /Ext 66124/
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> ------------------------------------------------------------
>
> Patricia Wollstadt, PhD Student
>
> MEG Unit, Brain Imaging Center
>
> Goethe University, Frankfurt, Germany
>
> Heinrich Hoffmann Strasse 10, Haus 93 B
>
> D - 60528 Frankfurt am Main
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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

Patricia Wollstadt, PhD Student

MEG Unit, Brain Imaging Center

Goethe University, Frankfurt, Germany

Heinrich Hoffmann Strasse 10, Haus 93 B

D - 60528 Frankfurt am Main

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