[FieldTrip] Problem with EEG channels in ft_neighborselection when running cluster statistics

Mon Sep 19 16:43:15 CEST 2011

Jörn,

Thanks lot for this information. I tried specifying cfg.layout and got a new
error message:

??? Error using ==> ft_neighbourselection at 130
Sensor distance is measured in an unknown unit type

Error in ==> statistics_wrapper at 241
    cfg.neighbours = ft_neighbourselection(cfg,varargin{1});

Error in ==> ft_timelockstatistics at 123
[stat, cfg] = statistics_wrapper(cfg, varargin{:});

(I get the same message when trying to run
neighbours=ft_neighbourselection(cfg,data) with that layout file specified.)
The layout file I was using is based directly on EEG1010.lay which is
included in fieldtrip, and it works fine when I use it for topoplotting and
multiplotting, so I'm not sure why it's causing errors when fed to
ft_neighbourselection.

As for the version, I actually am using the most recent version (which I
downloaded yesterday before trying to run cluster statistics, and updated my
path accordingly), but still getting these errors. The code I've been trying
to run, though, is based on the sample code on the wiki page
http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_timelock, which
may be out of date.

Is there perhaps anyone on the list who has run cluster statistics on EEG
data and would be willing to share a sample of their code?

Best,
Steve

> Message: 1
> Date: Mon, 19 Sep 2011 09:12:32 +0200
> From: "J?rn M. Horschig" <jm.horschig at donders.ru.nl>
> To: Email discussion list for the FieldTrip project
>        <fieldtrip at donders.ru.nl>
> Subject: Re: [FieldTrip] Problem with EEG channels in
>        ft_neighborselection when running cluster statistics
> Message-ID: <4E76EB60.9080801 at donders.ru.nl>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hey Stephen,
>
> You need to specify the position of your electrodes, which are mostly
> stored in an 'elec' structure. If you do not have that available, you
> can circumvent the problem by defining a cfg.layout. In that case,
> neighbouring sensors will be selected according to how they are placed
> in that layout-file you specify. That's not 100% correct of course, but
> at least an estimate how the sensors are positioned (note that a layout
> has only 2D coordinates). For example, you could use cfg.layout =
> 'EEG1010.lay' as a start.
>
> Anyway, could you try using a more recent version of FieldTrip? A few
> months ago, we changed the way the neighbourselection works (actually,
> you have to call cfg.neighbours = ft_neighbourselection manually, now).
> You can then also check with cfg.feedback = 'yes' whether the
> neighbourselection looks alright to you (that's the same as calling
> ft_neighbourplot)
>
> Hope it helps! Best regards,
> J?rn
>
>
>
> On 9/17/2011 6:42 PM, Stephen Politzer-Ahles wrote:
> > When attempting to run cluster statistics on my EEG data (originally
> > from Neuroscan .CNT, then processed in EEGLAB and finally imported to
> > fieldtrip) using ft_timelockstatistics(), I receive the following
> > error message:
> >
> > ??? Error using ==> ft_neighbourselection at 114
> > Did not find gradiometer or electrode information.
> >
> > Error in ==> statistics_wrapper at 241
> >     cfg.neighbours = ft_neighbourselection(cfg,varargin{1});
> >
> > Error in ==> ft_timelockstatistics at 123
> > [stat, cfg] = statistics_wrapper(cfg, varargin{:});
> >
> > This seems to be because when I use cfg.channel = {'EEG'}; with my
> > data, the channel information (the variable "sens" used in
> > ft_neighbourselection) consists only of the list of channel labels:
> >
> > sens =  {'FPZ'    'CPZ'    'FP2'    'F7' .........}
> >
> > On the other hand, when I run timelockstatistics on the sample data
> > from the wiki, "sens" includes much more information:
> >
> > sens =
> >
> >       pnt: [151x3 double]
> >       ori: [356x3 double]
> >       tra: [184x356 double]
> >     label: {151x1 cell}
> >      unit: 'cm'
> >
> > I think most of that extra information is planar gradient data (i.e.,
> > it comes from GA_FIC.grad). Since my data are EEG data, I assume it
> > wouldn't make sense to use ft_megplanar on them. So, assuming that I
> > need to get the extra channel location information into my EEG data,
> > does anyone have any ideas on how to do that?
> >
> > Best,
> > Steve Politzer-Ahles
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://www.linguistics.ku.edu/
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
> --
> J?rn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Neuronal Oscillations Group
>
> 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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-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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