plots and stats with biosemi128.lay

Katya Vinnik lulswinnik at GMAIL.COM
Wed Apr 8 17:19:19 CEST 2009


Thank you, Robert!


Regards,
Katya

2009/4/8 Robert Oostenveld <r.oostenveld at fcdonders.ru.nl>:
> Dear Katya
>
> If I do
>>> cfg.layout = 'biosemi128.lay'
>>> layoutplot(cfg)
>
> then I get attached figure (which you should be able to reproduce). Looking
> carefully it seems that D39 is lying on top of another channel.
>
> If I then do
> d = dist(lay.pos')
> imagesc(d==0)
>
> then I see that there are multiple off-diagonal elements in the distance
> matrix (i.e. a 128x128 matrix containing the distance bwteen all pairs) that
> are zero.  So there are multiple channels overlapping. I don't know why that
> is and at the moment I don't know where the biosemi layouts were coming
> from. The only information that I have from the log is
>  revision 1.1
>  date: 2005/06/15 08:21:08;  author: roboos;  state: Exp;
>  new layout files, based on excel sheet from biosemi
>
> I don't know the details of this excel sheet any more, but probably the
> excel sheet was already wrong.
>
> But to come to your prime question: does it affect clustering? Yes it will.
> You are using the layout to define neighbours. If the layout is flawed, the
> neighbour definition might also be flawed. Please use the neighbourselection
> function to make a neighbour definition explicitely and check the neighbours
> by looking at the output of the neighbourselection function.
>
>
> best regards,
> Robert
>
> PS it would be nice if you could provide a better layout for the biosemi128
> cap
>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.
>
>
>
>
> On 7 Apr 2009, at 13:56, Katya Vinnik wrote:
>
>> Dear FT users,
>>
>> has anyone of you encountered this warning?
>> Duplicate x-y data points detected: using average of the z values.
>>
>> I'm simply plotting my data with       cfg.layout      = 'biosemi128.lay';
>>
>> and it gives me strange plots  like the one here:
>> picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink
>>
>> basically data from channels B19 and 21 and D22 and 24 are overlayed
>> (circled in red on the pictures).
>> This message appears also with topoplot functions. In the layout file,
>> howether ,positions of this electrodes are different (see below).
>>
>> Do you think it can affect cluster-based multiple comparison correction?
>>
>> For example, if I use
>>
>> cfg.layout      = 'biosemi128.lay';
>> cfg.correctm = 'cluster';
>>  [stat] = freqstatistics(cfg,x,y)
>>
>> does it calculate it properly?
>>
>> Thank you,
>> Best regards,
>> Katya
>>
>> ----------------------------------
>> The aim of this list is to facilitate the discussion between users of the
>> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
>> and EEG analysis. See also
>> http://listserv.surfnet.nl/archives/fieldtrip.html and
>> http://www.ru.nl/neuroimaging/fieldtrip.
>>
>
>
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of the
> FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG
> and EEG analysis. See also
> http://listserv.surfnet.nl/archives/fieldtrip.html and
> http://www.ru.nl/neuroimaging/fieldtrip.
>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.



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