[FieldTrip] potential problem with ft_topoplotER

[jan-mathijs schoffelen]

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

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