[FieldTrip] Problem plotting independent components

[Dave Deriso]

I should also note that when I tried the *ft_databrowser* function it was
unable to plot the component topographies because there weren't enough grid
points. Have you encountered this before? Thanks again for all of your
great help!!

My code:

cfg = [];
cfg.viewmode = 'component'
ft_databrowser(cfg, comp);


Output:

creating layout from cfg.grad
creating layout for neuromag306alt system
the input is component data with 306 components and 306 original channels
detected   0 visual artifacts
redrawing with viewmode component
fetching data... done
fetching artifacts... done
preprocessing data... done
plotting artifacts...
plotting events...
plotting data...

Warning: Imaginary parts of complex X and/or Y arguments ignored
> In ft_plot_vector at 191
  In ft_databrowser>redraw_cb at 1309
  In ft_databrowser at 508
Warning: Imaginary parts of complex X and/or Y arguments ignored
> In ft_plot_vector at 191
  In ft_databrowser>redraw_cb at 1309
  In ft_databrowser at 508
                                          ****** these errors repeat about
10 times, then:
plotting component topographies...
Error using griddata (line 79)
Not enough unique sample points specified.

Error in ft_plot_topo (line 153)
[Xi,Yi,Zi] = griddata(chanX', chanY, dat, xi', yi, interpmethod); %
interpolate the topographic data

Error in ft_databrowser>redraw_cb (line 1377)
      ft_plot_topo(chanx, chany, chanz, 'mask', laychan.mask, 'interplim',
'mask', 'outline', laychan.outline, 'tag', 'topography',
      ...

Error in ft_databrowser (line 508)
redraw_cb(h);





Cheers,
Dave


On Tue, Dec 6, 2011 at 11:17 AM, Dave Deriso <dderiso at ucsd.edu> wrote:

> Dear JM and Jörn,
>
> Thank you so much for your helpful suggestions. Matlab could not find/open
> layout file: *NM306.lay* with both *ft_topoplotTFR* and* ft_topoplotIC*.
> I have also tried each of the following layouts without success:
>
> cfg.layout    =3D data.grad;
> cfg.layout    =3D 'neuromag306all.lay';
> cfg.layout    =3D 'neuromag306cmb.lay';
> cfg.layout    =3D 'neuromag306mag.lay';
> cfg.layout    =3D 'neuromag306planar.lay';
> (and no layout cfg, as prescribed by the bottom of
> http://fieldtrip.fcdonders.nl/reference/ft_topoplotic)
>
>
> As Jörn mentioned, the IC and sensor labels are different and,
> therefore, doing a string comparison will return an error. The question is
> then, how can I project the ICs back into sensor space and plot them
> topographically using the pre-existing sensor layouts? If this accomplished
> by the *ft_topoplotIC* function, shouldn't it expect the IC labels to be
> different from the layout labels?
>
> Thanks again for all of your help!
>
> Cheers,
> Dave Deriso
>
> --
> UCSD Institute for Neural Computation
> UCSD Department of Neurosurgery
>
>
>
>
> On Tue, Dec 6, 2011 at 3:55 AM, "Jörn M. Horschig" <
> jm.horschig at donders.ru.nl> wrote:
>
>>  Dear Dave,
>>
>> the labels do not match indeed, because ICs do not correspond to single
>> channel (obviously). I am not exactly sure how ft_topoplotIC is built, but
>> you could try using ft_databrowser instead, with cfg.viewmode = 'component'
>> Hope that at least circumvents your problem.
>>
>> Best,
>> Jörn
>>
>>
>> On 12/6/2011 2:45 AM, Dave Deriso wrote:
>>
>> Dear Fieldtrip Users,
>>
>>  I am trying to implement the tutorial on using ICA to extract eyeblink
>> artifacts (
>> http://fieldtrip.fcdonders.nl/example/use_independent_component_analysis_ica_to_remove_eog_artifacts).
>> Everything works, except that the labels from the IC data do not match the
>> labels from the layout file, causing an error in the topoplotIC
>> function. Your help in solving this is most appreciated.
>>
>>
>>  Layout labels (I am using a Neuromag 306 MEG):
>>  'MEG0113'
>> 'MEG0112'
>> 'MEG0111'
>> 'MEG0122'
>> 'MEG0123'
>>
>>  IC labels:
>>  'runica001'
>> 'runica002'
>> 'runica003'
>> 'runica004'
>> 'runica005'
>>
>>   Matlab Output:
>>  ft_topoplotIC(cfg, comp);
>> creating layout from data.grad
>> creating layout for neuromag306alt system
>> Error using ft_topoplotTFR (line 659)
>> labels in data and labels in layout do not match
>> Error in ft_topoplotIC (line 122)
>> ft_topoplotTFR(cfg, varargin{:});
>>
>>
>>
>>  Cheers,
>> Dave Deriso
>>
>> --
>> UCSD Institute for Neural Computation
>> UCSD Department of Neurosurgery
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> --
>> Jörn M. Horschig
>> PhD Student
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Neuronal Oscillations Group
>>
>> 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
>> Kapittelweg 29
>> NL-6525 EN Nijmegen
>> The Netherlands
>>
>>
>> _______________________________________________
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>>
>
>
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