[FieldTrip] stats on planar gradient topographies

[Luisa Frei]

Thanks for all the answers, I'll try Julian's suggestion and let you  
know what happens.

Luisa

On 16 May 2011, at 13:58, Julian Keil wrote:

> Hi all,
>
> sorry, I thought the answer would only go to Luisa.
>
> Apologies,
> Julian
>
> Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig:
>
>> Hi all,
>>
>> First of all, @julian: It would be nice if you wrote in English so  
>> that all people can understand what you are saying :)
>>
>> Second, I would like to mention ft_neighbourplot, which is a  
>> relative new function and plots sensors and its' neighbours in 2D  
>> or 3D, depending on whether you got 2D or 3D coordinates. Using  
>> that function, you can verify whether your neighbourselection  
>> looks meaningful and makes sense.
>>
>> Finally, we are currently working on changing/improving the  
>> neighbourselecion function. There will be different methods to  
>> choose from, and we (me) will create templates for the most common  
>> systems that can be used instead of relying on a particular  
>> mathematical selection method. We will announce this when it's  
>> done (probably soon).
>>
>> Maybe Julian is right and Luisa's problem is due to a 'wrong'  
>> neighbourselection. Given that cfg.minnbhchan is set to 4, this  
>> might be likely, because not all of the found clusters consist of  
>> 4 or more channels. What system are you using?
>>
>> Best,
>> Jörn
>>
>>
>> On 5/16/2011 2:32 PM, Julian Keil wrote:
>>>
>>> Hi Luisa,
>>>
>>> schnell from the top of my head: wie definierst du denn deine  
>>> neighbors?
>>> Ich seh nirgendwo ein Feld cfg.neighbors....
>>> Ich muss das bei unserem 4D-System immer angeben....
>>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen  
>>> sind falsch definierst, so könntest du zu deinen "random"  
>>> Clustern kommen.
>>>
>>> Ich mache diese Neighbor-Struktur folgendermaßen:
>>>
>>> cfg=[];
>>> cfg.neighbourdist=0.1;
>>> %cfg.grad=Comb_AV1_1{1}.grad;
>>> cfg.layout='4D148.lay';
>>> cfg.channel={'all'};
>>> %cfg.grad.pnt=cfg.grad.pnt*100;
>>> dummy=neighbourselection(cfg);
>>>
>>> Da bekomme ich auch immer einen Output, wie viele Channels so in  
>>> der Umgebung sind (sollten in etwa 5 sein).
>>>
>>> Hoffe das hilft dir weiter
>>>
>>> Viele Grüße
>>>
>>> Julian
>>>
>>> Am 14.05.2011 um 22:37 schrieb Luisa Frei:
>>>
>>>> Hi there,
>>>> I am trying to compute a simple cluster-based statistic in a  
>>>> between subjects design. I have followed the steps in the  
>>>> respective tutorial very closely.
>>>> This the code I used:
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> cfg = [];
>>>> cfg.method = 'montecarlo';
>>>> cfg.statistic = 'indepsamplesT';
>>>>
>>>> cfg.correctm = 'cluster';
>>>> cfg.clusteralpha = 0.001;
>>>> cfg.clusterstatistic = 'maxsize';
>>>> cfg.minnbchan = 4;
>>>>
>>>> cfg.tail = 0;
>>>> cfg.clustertail = 0;
>>>> cfg.alpha = 0.005;
>>>> cfg.numrandomization = 500;
>>>>
>>>> design = [ones(1,13) ones(1,13)+1];
>>>>
>>>> cfg.design = design;
>>>> cfg.ivar  = 1;
>>>>
>>>> cfg.channel = {'MEG',sub(1).allbadchan{:}};
>>>> cfg.latency = [.15 .2];
>>>>
>>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); %  
>>>> individuals kept
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>>
>>>> My problem is, that I'm not sure which time resolution to use. I  
>>>> would like to use a small resolution of 10 ms, but this leads to  
>>>> a fairly random pattern of significant sensors (see attached  
>>>> figure, on the right). Of course, the more time points I  
>>>> include, the less significant sensors are left over. However,  
>>>> another problem is, that the ones that are left (figure, left),  
>>>> are not related to big differences in the activation pattern at  
>>>> all. How is it possible that my significant sensors end up being  
>>>> so randomly distributed? Also, ft_timelockstatistics only comes  
>>>> up with one positive and one negative cluster., but the sign.  
>>>> sensors are not always connected. Could anyone give some helpful  
>>>> input here?
>>>>
>>>> Thanks,
>>>> Luisa
>>>>
>>>> Fyi: I have tried different thresholds and different numbers of  
>>>> neighbourhood channels, but there's not much of a change.
>>>> <Picture 2.png>_______________________________________________
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>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>>
>>> _______________________________________________
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>>
>>
>> -- 
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>>
>> 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
>> Kapitelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
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>
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