[FieldTrip] axes in ft_connectivityplot

[jan-mathijs schoffelen]

Hi Karl,

I looked into ft_topoplotCC and I noticed that you are not using an up-to-date version. The current version does not use strmatch, but uses strcmp. This should not cause a problem.

Best wishes,

Jan-Mathijs


On Jan 25, 2012, at 12:52 AM, Karl Doron wrote:

> Hello,
> 
> Great! That makes sense.
> 
> On my second question for ft_topoplotCC, there is a bug using strmatch on lines 191 and 192. You'll likely encounter an error using horzcat at line 199 if the 'exact' argument is not added due to possible comparison of a vector and a scalar, e.g., begindx will find channel A2* when only A2 is needed.
> 
> begindx = strmatch(beglabel{i}, lay.label,'exact');
> endindx = strmatch(endlabel{i}, lay.label,'exact');
> 
> Thanks!
> 
> karl 
> 
> 
> 
> On Jan 23, 2012, at 11:52 PM, jan-mathijs schoffelen wrote:
> 
>> Hi Karl,
>> 
>> The subplots represent the magnitude of the connectivity metric (which are typically unit-less) as a function of frequency.
>> 
>> Best,
>> 
>> Jan-Mathijs
>> 
>> On Jan 24, 2012, at 1:19 AM, Karl Doron wrote:
>> 
>>> Hello,
>>> 
>>> Just to clarify my first question below. In the context of the tutorial on the fieldtrip website, what do the axes in this figure represent? 
>>> 
>>> Thanks,
>>> karl doron
>>> UC, Santa Barbara
>>> 
>>>> Hello,
>>>> 
>>>> I'm trying to use some of the plot tools for results from ft_connectivityanalysis. Can anyone tell me what the horizontal and vertical axes represent in ft_connectivityplot? The values differ on each plot in the matrix and don't seem to correspond to the data. Also, in ft_topoplotCC, is it possible to weight the line font based on the magnitude of the coherence value?
>>>> 
>>>> %% step 1 | freq analysis
>>>>  
>>>> cfg            = [];
>>>> cfg.channel    = {'A224', 'A188', 'A189', 'A163', 'A184','A162'};
>>>> cfg.method     = 'mtmfft';
>>>> cfg.output     = 'fourier';
>>>> cfg.foilim     = [8 12];
>>>> cfg.toi        = 2.35:0.01:2.65;
>>>> cfg.keeptrials = 'yes';
>>>> cfg.keeptapers = 'yes';
>>>> cfg.tapsmofrq  = 2;
>>>> cfg.taper      = 'dpss';
>>>>  
>>>> freq_alpha     = ft_freqanalysis(cfg, data_spctrm);
>>>>  
>>>>  
>>>> %% step 2 | connectivity analysis
>>>>  
>>>> cfg            = [];
>>>> cfg.method     = 'coh';
>>>>  
>>>> coh            = ft_connectivityanalysis(cfg, freq_alpha);
>>>> 
>>>> 
>>>> 
>>>> Thanks for any feedback,
>>>> karl doron
>>>> UC, Santa Barbara
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>> 
>> Jan-Mathijs Schoffelen, MD PhD 
>> 
>> Donders Institute for Brain, Cognition and Behaviour, 
>> Centre for Cognitive Neuroimaging,
>> Radboud University Nijmegen, The Netherlands
>> 
>> Max Planck Institute for Psycholinguistics,
>> Nijmegen, The Netherlands
>> 
>> J.Schoffelen at donders.ru.nl
>> Telephone: +31-24-3614793
>> 
>> _______________________________________________
>> 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

Jan-Mathijs Schoffelen, MD PhD 

Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands

Max Planck Institute for Psycholinguistics,
Nijmegen, The Netherlands

J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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