[FieldTrip] channel repair script

Dmitri Filimonov dmitri89 at ut.ee
Thu Sep 20 09:54:59 CEST 2012


Dear Jörn,

Thank you for answering, but unfortunately it doesn't work anyway. I tried
that also. It always gives

"The field cfg.method is required"

I've put several possible cfg.methods = *(like cfg.method = 'mtmfft' (in
case if program wants me to set spectra calculating parameters); or
'nearest' (in case of neighbour selection method). Non of this works, yet
I am trying to deal with it now.

Best wishes,
Dmitri




> Dear Dmitri,
>
> I think you are confusing things here.
> Note that you are calling two FieldTrip functions subsequently. The
> error message you are receiving results from ft_prepare_neighbours.
> ft_prepare_neighbours needs a different cfg than ft_channelrepair. The
> call you are making, does however not make much sense, because you
> already called that function a few lines before. So just drop that
> cfg.neighbours = ft_prepare_neighbours(...) line and replace it by
> cfg.neighbours = neighbours. Thereby, you are removing the function call
> that results in an error (and you already did that call), and I guess
> everything will work fine.
>
> Best,
> Jörn
>
> On 9/18/2012 10:00 AM, Dmitri Filimonov wrote:
>> Dear Sir/Madam,
>>
>> My name is Dmitri Filimonov, I am a master student in University of
>> Tartu
>> (Estonia), using fieldtrip for EEG data analysis. I would like to ask
>> some
>> assistance with fieldtrip script.
>> The task is to repair some EEG channels, so need to use
>> ft_channelrepair.
>> And I tried to do that after artifact rejection, so I could first see,
>> which channels are noisy or disabled. I tried multiple combinations, yet
>> there are still problems with the script.
>> It looks like:
>>
>>>> channels_to_repair={'Fp1', 'Fp2'};
>> layout_file=('C:\ fieldtrip-20120703\template\layout\EEG1010.lay');
>>
>> cfg=[];
>> cfg.layout = 'EEG1010.lay';
>> data.elec = ft_prepare_layout(cfg);
>> neighbours = ft_prepare_neighbours(cfg, good_data)
>> cfg = ft_checkconfig(cfg, 'required', {'method'});
>> cfg.method = 'distance';  (or ‘nearest’)
>> cfg.badchannel=channels_to_repair;
>> cfg.neighbours = ft_prepare_neighbours (cfg, good_data);
>> G_data = ft_channelrepair(cfg, dood_data);
>> (Good_data –is a processed and filtered data, yet containing channels,
>> which have to be repaired.)
>> After processing the program gives me several errors:
>>
>> reading layout from file EEG1010.lay
>> the call to "ft_prepare_layout" took 0 seconds and an estimated NaN MB
>> ??? Error using ==> ft_checkconfig at 151
>> The field cfg.method is required
>> Error in ==> ft_prepare_neighbours at 77
>> cfg = ft_checkconfig(cfg, 'required', {'method'});
>>
>> Other combinations emerge similar errors, or
>>
>> Error in ==> ft_neighbourselection at 30
>> neighbours = ft_prepare_neighbours(varargin{:});
>>
>> Can you give me some help, what kind of ‘method’ exactly program wants
>> me
>> to mention (type)?
>>
>> Yours sincerely,
>> Dmitri
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
> FieldTrip Development Team
>
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>
> Contact:
> E-Mail: jm.horschig at donders.ru.nl
> Tel:    +31-(0)24-36-68493
> Web: http://www.ru.nl/donders
>
> Visiting address:
> Trigon, room 2.30
> Kapittelweg 29
> NL-6525 EN Nijmegen
> The Netherlands
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip





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