[FieldTrip] ft_prepare_neighbours

[Max Cantor]

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
>
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