[FieldTrip] Problem plotting independent components
Dave Deriso
dderiso at ucsd.edu
Wed Dec 7 23:34:48 CET 2011
Hi Johanna,
Thanks for taking a look. I could not find a method inside *
ft_componentanalysis* that extracts real values (although using real()
could also accomplish this), however the warning seems to indicate that the
complex values are ignored. Do you think this is still an issue? The error
with *ft_databrowser* indicates a lack of "unique sample points" from some
kind of grid, which is perhaps a bigger problem. Any thoughts? Thanks again!
Cheers,
Dave
On Wed, Dec 7, 2011 at 3:59 AM, Johanna Zumer
<johanna.zumer at donders.ru.nl>wrote:
> Hi Dave,
> Perhaps this error is due to the complex data that ft_databrowser cannot
> plot? If you re-calculate the components and get out real-only values, do
> you still get this error?
>
> Best,
> Johanna
>
>
> On 7 December 2011 02:07, Dave Deriso <dderiso at ucsd.edu> wrote:
>
>> 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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