[FieldTrip] ft_prepare_neighbours
Beom Jun Min
mbj0310 at gmail.com
Fri Mar 7 01:41:58 CET 2014
Dear Jörn and Max
Thank you for your help.
However, another error occurred.
>>>
cfg = [];
cfg.method = 'triangulation'; %'distance', 'triangulation' or
'template' (default = 'distance')
cfg.layout = lay;
cfg.channel = {'all',
'-VEOG','-HEOG','-EKG','-EMG','-COMNT','-SCALE'};
cfg.feedback = 'yes';
neighbours = ft_prepare_neighbours(cfg);
>>>
These work successfully.
But
>>>
cfg = [];
cfg.neighbours = neighbours;
cfg.enableedit = 'yes';
neighbours = ft_neighbourplot(cfg);
>>>
??? Error using ==> ft_fetch_sens at 179
no electrodes or gradiometers specified.
Error in ==> ft_neighbourplot at 85
sens = ft_fetch_sens(cfg);
In addition,
>>>
cfg = [];
cfg.method = 'spline'; %'nearest', 'spline' or 'slap'
(default='nearest')
cfg.missingchannel = 'T7'; % cell-array, see FT_CHANNELSELECTION for details
cfg.neighbours = neighbours;
cfg.trials = 'all';
% cfg.lambda = % regularisation parameter (default = 1e-5, not for
method 'distance')
% cfg.order = % order of the polynomial interpolation (default =
4, not for method 'distance')
interpolated = ft_channelrepair(cfg, final)
>>>
??? Error using ==> ft_fetch_sens at 179
no electrodes or gradiometers specified.
Error in ==> ft_channelrepair at 112
sens = ft_fetch_sens(cfg, data);
It seems the problem is associated with position of electrode. But I do not
have manufacture's file.
Do I have to make the positions of electrodes manually?
Actually, I do not understand the information from help* ft_datatype_sens,
and ft_read_sens.*
With regards
2014-03-06 23:19 GMT+09:00 Max Cantor <mcantor at umich.edu>:
> Alternatively, you could create a .sfp file for cfg.elecfile of the
> ft_channelrepair. If your channels are equidistant the equation for
> determining the neighbours should be fairly straightforward, as long as you
> have at least the phi and theta coordinates.
>
> I talk about it in this thread:
> http://mailman.science.ru.nl/pipermail/fieldtrip/2013-November/007213.html
>
> Here is the conclusion I came to:
>
> "For future reference, because I don't remember seeing anything on the
> fieldtrip FAQ about this and it may be useful to somebody else, the
> important thing is to turn the phi/theta from degrees into radians, and
> then applying a trigonometric function to get the X, Y, and Z coordinates.
>
> You can do all of these steps in 3 excel functions:
>
> X = COS(RADIANS(Phi))*SIN(RADIANS(Theta))
> Y = SIN(RADIANS(Theta))*SIN(RADIANS(Phi))
> Z = =COS(RADIANS(Theta))
>
> This link on the easycap website (http://www.easycap.de/easycap/e/downloads/how_to_read_3d.htm) explains the
> coordinate system.
>
> I then typed up the channel name, x, y, and z coordinates in a four column
> notepad document saved as a .sfp file, and used that as my cfg.elecfile."
>
> I'm not sure if this is your problem, but I didn't see a cfg.elecfile
> parameter in your code, so hopefully this helps.
>
>
> On Thu, Mar 6, 2014 at 5:24 AM, "Jörn M. Horschig" <
> jm.horschig at donders.ru.nl> wrote:
>
>> Hi Beom,
>>
>> did your code produce an error?
>>
>> Generally, the 'template' method tries to look for already defined
>> 'template' neighbours. However, as far as I understoog you only created a
>> 'layout', which define where electrodes are placed, but not whether they
>> are neighbours or not. I would advice you to use these settings:
>>
>> cfg = [];
>> cfg.method = 'triangulation';
>> cfg.layout = lay;
>> cfg.channel = 'all'; % that way you only need to run this once for
>> *all* your subjects
>> cfg.feedback = 'yes';
>> neighbours = ft_prepare_neighbours(cfg);
>>
>> Then, if you are unhappy with the result, for modifcation you can use
>> cfg = [];
>> cfg.neighbours = neighbours;
>> cfg.enableedit = 'yes';
>> neighbours = ft_neighboursplot(cfg);
>>
>> in that plot, you can click around to mark channels as being neighbours
>> or not. When you are happy, save that neighbour structure and make sure to
>> use it for all your subjects, so that there is no bias for individual
>> subjects.
>>
>> Note that the data variable is used nowhere now, because that would cause
>> missing sensors to be removed from the neighbour structure, but you
>> probably do not want that (or if you do, then use it).
>>
>> And finally, yes, using preprocessed data is possible.
>>
>> Should you have any other questions, feel free to ask.
>>
>> Best,
>> Jörn
>>
>>
>>
>> On 3/6/2014 2:09 AM, Beom Jun Min wrote:
>>
>>>
>>> Hello
>>>
>>> I have a problem with channel repair.
>>>
>>> Firstly, I created my own layout because I cannot apply my data into the
>>> offered layout files.
>>> As far as I know, my EEG data was acquired through SynAmps 2 system with
>>> 128 electrodes, but I cannot find a suitable layout files.
>>> QuikCap_NSL_128 does not match either.
>>>
>>> Anyway, I created own customized layout, and usual preprocessing steps
>>> were done.
>>> However, there were some bad recording channels so I removed them during
>>> preprocessing.
>>> Moreover, the removed channels are different among the subjects, and now
>>> it becomes a big problem for analyzing the data.
>>>
>>> So I tried channel repair process, but encountered with errors.
>>>
>>> >>>
>>> cfg = [];
>>> cfg.method = 'template';
>>> cfg.template = 'bj_plot.mat';
>>> cfg.layout = lay;
>>> cfg.channel = 'T7'; % channels for which neighbours should be found
>>> cfg.feedback = 'yes';
>>> neighbours = ft_prepare_neighbours(cfg, data);
>>> >>>
>>>
>>> I think I have to use 'template' method because, there are some missing
>>> channels serially.
>>> And here are my question.
>>> Is it possible to assign my own layout in the cfg.template or
>>> cfg.layout? Actually at this step, I do not understand how to proceed.
>>> Also, there are many missing channels differ from each subject, but I am
>>> not sure which channels should be placed in the cfg.channel. (T7 is one of
>>> the missing channel in a subject in my case.)
>>> Finally, at 'data' field, is it possible to assign a finalized
>>> preprocessed data?
>>>
>>> And after ft_prepare_neighbours,
>>>
>>> >>>
>>> cfg = [];
>>> cfg.method = 'spline'
>>> % cfg.badchannel = 'T7';
>>> cfg.missingchannel = 'T7';
>>> cfg.neighbours = neighbours;
>>> cfg.trials = 'all'
>>> interpolated = ft_channelrepair(cfg, data)
>>>
>>> Is that right?
>>>
>>>
>>> --
>>> BeomJun Min, M.D.
>>>
>>> Department of Medical System Engineering (DMSE)
>>> Gwangju Institute of Science and Technology (GIST)
>>> 261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
>>> 500-712, Republic of Korea (South)
>>> Phone: +82-62-715-3266 / Fax: +82-62-715-3244
>>> E-mail: mbj0310 at gmail.com <mailto:mbj0310 at gmail.com>,
>>> http://bmssa.gist.ac.kr <http://bmssa.gist.ac.kr/>
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
BeomJun Min, M.D.
Department of Medical System Engineering (DMSE)
Gwangju Institute of Science and Technology (GIST)
261 Cheomdan-gwagiro(Oryong-dong), Buk-gu, Gwangju
500-712, Republic of Korea (South)
Phone: +82-62-715-3266 / Fax: +82-62-715-3244
E-mail: mbj0310 at gmail.com, http://bmssa.gist.ac.kr
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