[FieldTrip] potential problem with ft_topoplotER

[Stephan Moratti]

I was not aware of that! Thanks for the hint, and sorry for my former  
comment that was kind of useless,

Best,

Stephan

El 04/03/2011, a las 16:13, jan-mathijs schoffelen escribió:

> Hi Stephan,
>
> As a matter of fact, ft_topoplotER can be also used for frequency  
> domain data, when no time axis is present (i.e. non-TFR data).
>
> Best,
>
> Jan-Mathijs
>
> On Mar 4, 2011, at 4:06 PM, Stephan Moratti wrote:
>
>>
>> what if you try topoplotTFR. topoplotER is for time series data,  
>> whereas topoplotTFR is for time-frequ data.
>>
>> Best,
>>
>> Stephan
>>
>> El 04/03/2011, a las 15:27, Jan.Hirschmann at med.uni-duesseldorf.de  
>> escribió:
>>
>>> Dear fieldtrip developers,
>>>
>>> I don’t know whether it is a bug or due to badly chosen settings,  
>>> but I have experienced a problem with ft_topoplotER.  I suspect  
>>> that the function does not plot power values appropriately in the  
>>> presence of labelcmb field. I do frequency analysis with the  
>>> output powandcsd with the newest fieldtrip release:
>>>
>>> cfg=[];
>>>             cfg.method='mtmfft';
>>>             cfg.output='powandcsd';
>>>             cfg.calcdof='yes';
>>>             cfg.taper='hanning';
>>>             cfg.channelcmb={'MEG***2',refchan;'MEG***3',refchan};
>>>             cfg.foilim=[5 90];
>>>             freq1=ft_freqanalysis(cfg,data1);
>>>
>>> What I get is a power spectrum matrix with all the channels of the  
>>> original data and a cross spectrum matrix according to my labelcmb.
>>>
>>> freq1 =
>>>
>>>        label: {320x1 cell}
>>>        dimord: 'chan_freq'
>>>        freq: [1x88 double]
>>>        powspctrm: [320x88 double]
>>>        labelcmb: {204x2 cell}
>>>        crsspctrm: [204x88 double]
>>>        dof: [240x88 double]
>>>        cumtapcnt: [240x1 double]
>>>        grad: [1x1 struct]
>>>        cfg: [1x1 struct]
>>>
>>> After having some doubts about the power topoplots I set all but  
>>> one channel in the .powspctrm field to 0.
>>>
>>>  freq1.powspctrm=zeros(size(freq1.powspctrm));
>>> ind=strmatch('MEG2222',freq1.label);
>>> freq1.powspctrm(ind,:)=1;
>>>
>>> When plotting I don’t see the one channel that has power but  
>>> everything is 0 (see topo1.jpg)
>>>
>>> cfg=[];
>>> cfg.xparam='freq';
>>> cfg.zparam='powspctrm';
>>> cfg.cohrefchannel=refchan;
>>> cfg.layout='/data/apps/fieldtrip/latest/template/ 
>>> neuromag306all.lay';
>>> ft_topoplotER(cfg,freq1)
>>>
>>> Yet, when I remove the labelcmb field from freq1 it works alright  
>>> (topo2.jpg)
>>>
>>> freq1=rmfield(freq1,'labelcmb');
>>>
>>> Likewise, I may get the index ind from freq1.labelcmb(:,1), set it  
>>> to 1, and it works. So it seems that topoplotER plots 204 channel  
>>> values (number of rows in .labelcmb and .crsspctrm) although there  
>>> are 306 MEG channels in the frequency data.  I guess in such a  
>>> situation channel data is neglected in the topoplots without the  
>>> user being aware and the values may not be plotted at the correct  
>>> place. I hope this helps in the development and is not simply a  
>>> user error from my side.
>>>
>>> Best to you,
>>> jan
>>>
>>>
>>>
>>>
>>>
>>> Jan Hirschmann
>>> MSc. Neuroscience
>>> Insititute of Clinical Neuroscience and Medical Psychology
>>> Heinrich Heine University Duesseldorf
>>> Universitaetsstr.  1
>>> 40225  Duesseldorf
>>> Tel: 0049 - (0)211 - 81 - 18415
>>>
>>> <topo1.jpg><topo2.jpg>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>> ________________________________________________________
>> Stephan Moratti, PhD
>>
>> see also: http://web.me.com/smoratti/
>>
>> Department of Basic Psychology
>> Universidad Complutense de Madrid
>>
>> Centro de Tecnología Biomédica CBT,
>> Universidad Politécnica de Madrid,
>>
>> en la actualidad (currently at) en el
>> Centro de Magnetoencefalografía Dr. Perez Modrego,
>> Universidad Complutense de Madrid,
>> Faculdad de Medicina,
>> Pabellón 8,
>> Avda. Complutense, s/n,
>> 28040 Madrid,
>> Spain,
>>
>> email: smoratti at psi.ucm.es
>> Tel.:    +34 91 394 2186
>> Fax.:   +34 91 394 2294
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> Dr. J.M. (Jan-Mathijs) Schoffelen
> Donders Institute for Brain, Cognition and Behaviour,
> Centre for Cognitive Neuroimaging,
> Radboud University Nijmegen, The Netherlands
> J.Schoffelen at donders.ru.nl
> Telephone: 0031-24-3614793
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip


________________________________________________________
Stephan Moratti, PhD

see also: http://web.me.com/smoratti/

Department of Basic Psychology
Universidad Complutense de Madrid

Centro de Tecnología Biomédica CBT,
Universidad Politécnica de Madrid,

en la actualidad (currently at) en el
Centro de Magnetoencefalografía Dr. Perez Modrego,
Universidad Complutense de Madrid,
Faculdad de Medicina,
Pabellón 8,
Avda. Complutense, s/n,
28040 Madrid,
Spain,

email: smoratti at psi.ucm.es
Tel.:    +34 91 394 2186
Fax.:   +34 91 394 2294

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