[FieldTrip] problem with surface Laplacian

Max Cantor mcantor at umich.edu
Wed Dec 17 15:30:31 CET 2014


Why were you not able to repair them? Is it that they are neighbors, so
linear interpolation won't work? I can't speak to this too much as I
haven't tried it, but I've been looking into spline and if this is your
problem spline could work.

Otherwise I imagine you could manually edit / create a new elec or layout
file (in matlab or in a text editor), which wouldn't be a bad idea anyway.
I did this for our system as we could not find a premade one, but we use
equidistant caps so it was pretty straightforward. However, I don't know if
there would be any negative implications with removing the electrodes from
the layout/elec file(s) altogether.

On Wed, Dec 17, 2014 at 9:25 AM, Hwee Ling Lee <hweeling.lee at gmail.com>
wrote:
>
> Hi,
>
> Would it possible to change the number of channels in the sensor
> description? There are some channels that I cannot repair, hence, I decided
> to discard them completely from the analyses.
>
> Cheers,
> Hweeling
>
>
> On 17 December 2014 at 15:07, Max Cantor <mcantor at umich.edu> wrote:
>>
>> It seems like the issue is between the number of channels in your input
>> (48) is different from the number of channels in the sensor description
>> (60). You should use ft_channelrepair to interpolate the removed channels,
>> and then it should work barring any other issues.
>>
>> On Wed, Dec 17, 2014 at 5:45 AM, Hwee Ling Lee <hweeling.lee at gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I have 60 channel EEG resting state data, and after discarding bad
>>> channels, I am left with 48 channels common to all subjects.
>>>
>>> I applied scalp current density to my data before extracting power
>>> information from my EEG data. The EEG cap that I used was in a 10-10
>>> system, and I don't have the electrode position file. Hence, I used the
>>> default electrode position file named 'standard_1005.elc' for the purpose.
>>>
>>> Here's the part of my script for the surface Laplacian:
>>>
>>>
>>>     cfg_neighb.method = 'template';
>>>     cfg_neighb.layout = 'EEG1010.lay';
>>>     cfg_neighb.channel = 'all';
>>>     cfg_neighb.feedback = 'no';
>>>
>>>     neighbours = ft_prepare_neighbours(cfg_neighb, data7);
>>>
>>>     cfg                 = [];
>>>     cfg.method          = 'finite';
>>>     cfg.elecfile        = 'standard_1005.elc';
>>>     cfg.elec            = ft_read_sens(cfg.elecfile);
>>>     cfg.trials          = 'all';
>>>     cfg.neighbours      = neighbours;
>>>     cfg.conductivity    = 0.33;
>>>
>>>     data8               = ft_scalpcurrentdensity(cfg, data7);
>>>
>>> When I tried to extract power from data8 (after surface Laplacian), I
>>> keep getting an error message (see below). I'm not sure why this would be
>>> the case, and would appreciate very much if someone could help me resolve
>>> the error!
>>>
>>> Thank you!
>>>
>>> Here's my script for extracting the power:
>>>  cfg                 = [];
>>>     cfg.output          = 'pow';
>>>     cfg.channel         = {'all'};
>>>     cfg.method          = 'mtmfft';
>>>     cfg.keeptrials      = 'no';
>>>     cfg.tapsmofrq       = 5;
>>>     cfg.layout          = 'EEG1010.lay';
>>>
>>>     % for frequencies up to 30 Hz
>>>     cfg.foilim          = [1 30]; % either the full range of frequencies
>>> (data2.hdr.Fs/2) or up to 100 Hz
>>>     cfg.taper           = 'hanning';
>>>
>>>     % find the index for the c200 condition
>>>     pre_c200_idx = find(data8.trialinfo == 200);
>>>     cfg.trials          = pre_c200_idx;
>>>     LF_pre_c200        = ft_freqanalysis(cfg, data8);
>>>
>>> Here's the output plus error message:
>>>
>>> the input is raw data with 48 channels and 343 trials
>>> Error using ft_datatype_sens (line 375)
>>> inconsistent number of channels in sensor description
>>>
>>> Error in ft_datatype_raw (line 138)
>>>       data.elec = ft_datatype_sens(data.elec);
>>>
>>> Error in ft_checkdata (line 223)
>>>   data = ft_datatype_raw(data, 'hassampleinfo', hassampleinfo);
>>>
>>> Error in ft_freqanalysis (line 209)
>>> data = ft_checkdata(data, 'datatype', {'raw', 'raw+comp', 'mvar'},
>>> 'feedback',
>>> cfg.feedback, 'hassampleinfo', 'yes');
>>>
>>> Best regards,
>>> Hweeling
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> --
>> Max Cantor
>> Lab Manager
>> Computational Neurolinguistics Lab
>> University of Michigan
>>
>
>
> --
> =================================================
> Dr. rer. nat. Lee, Hwee Ling
> Postdoc
> German Center for Neurodegenerative Diseases (DZNE) Bonn
>
> Email 1: hwee-ling.lee<at>dzne.de
> Email 2: hweeling.lee<at>gmail.com
>
> https://sites.google.com/site/hweelinglee/home
>
> Correspondence Address:
> Ernst-Robert-Curtius Strasse 12, 53117, Bonn, Germany
> =================================================
>


-- 
Max Cantor
Lab Manager
Computational Neurolinguistics Lab
University of Michigan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20141217/90e5fe72/attachment.html>


More information about the fieldtrip mailing list