[FieldTrip] ICA problem
Sylvana
sylvana.schister at utah.edu
Thu Jul 7 18:07:48 CEST 2011
Hi all,
Thank you so much for your quick reply. This is all very helpful. I am
using tsss filtered data. After thinking it through all day, I
understood that I have a dimensionality problem.
Anyway, thanks again!
Cheers,
Sylvana
On Wed, 2011-07-06 at 22:18 -0600, Sheraz Khan wrote:
> Hi Joseph,
>
> Most likely cause of ill-conditioned in neuromag data is maxfilter
> (signal space separation) which reduces the dimensionality from 306
> (Channels in neuromag machine) to 64 (Spherical harmonics Multipolar
> expansion of order 8). Also neuromag is consist of two different type
> of sensors (Planar Gradiometer and magnetometer) having different
> sensitivities, so either ica needs to run separately on them or
> combined by making them equal through normalization.
>
> Sheraz Khan
> Martinos Center
> Boston, USA
>
>
>
> On Wed, Jul 6, 2011 at 9:27 PM, Joseph Dien <jdien07 at mac.com> wrote:
> I've had this same problem with EEGlab's runICA implementation
> when the rank of the data was less than the number of
> variables (i.e., it's an ill-conditioned matrix, which is to
> say it has multicolinearity). Including the reference channel
> can do this (since it's just zeroes). Using PCA to reduce the
> data to a subspace can help as well since the rank will now
> equal the number of variables (namely the number of factor
> scores will equal the number of retained factors). Before you
> go the PCA route, it's worth trying to figure out why the data
> is ill-conditioned. There is likely to be something wrong
> with one of your channels. Maybe two of them are shorted
> together or something along those lines. Or if you used mean
> mastoid reference and included both mastoids, that can do it
> too (since they will be exactly inversely correlated, one of
> them is statistically redundant, reducing the rank by one).
> My EP Toolkit artifact correction routine
> (http://sourceforge.net/projects/erppcatoolkit/) takes all
> these sorts of things into account when performing eyeblink
> correction.
>
>
> Cheers!
>
>
> Joe
>
>
>
>
> On Jul 6, 2011, at 8:44 PM, Sheraz Khan wrote:
>
> > Hi Sylvana,
> >
> > Is the data SSS (maxfilter), I normally have this problem
> > when data is SSS, try doing ICA with PCA (set at 64
> > components).
> >
> > Sheraz Khan
> > Martinos Center
> > Boston, USA
> >
> > On Wed, Jul 6, 2011 at 2:09 PM, Stephen Whitmarsh
> > <stephen.whitmarsh at gmail.com> wrote:
> > Dear Sylvana,
> >
> > >From the top op my head: When running the ICA, try
> > only computing it
> > for the MEG or EEG channels. (cfg.channel = 'MEG';),
> > so it doesn't run
> > on reference sensors in case of MEG.
> > I have hunch that might help out.
> >
> > Cheers,
> > Stephen
> >
> >
> >
> > On 6 July 2011 19:37, Sylvana
> > <sylvana.schister at utah.edu> wrote:
> > > Hi all,
> > >
> > > I am trying to use ICA to clean EOG and ECG
> > artifacts of neuromag data.
> > > I am running ft_topoplotIC(cfg, comp), where
> > 'comp' is the output of
> > > ft_componentanalysis.
> > >
> > > I get the following error message:
> > >
> > >
> > > ??? Error using ==> surf at 74
> > > X, Y, Z, and C cannot be complex.
> > >
> > > Error in ==> ft_plot_topo at 184
> > > h = surf(Xi-deltax/2,Yi-deltay/2,zeros(size(Zi)),
> > Zi, 'EdgeColor',
> > > 'none', 'FaceColor', shading);
> > >
> > > Error in ==> ft_topoplotER at 753
> > >
> > ft_plot_topo(chanX,chanY,datavector,'interpmethod',cfg.interpolation,...
> > >
> > > Error in ==> ft_topoplotIC at 116
> > > ft_topoplotER(cfg, varargin{:});
> > >
> > >
> > > The complex variable is 'Zi', which is taken from
> > 'comp'. I can modify
> > > the function to take the real part of the variable
> > (or the absolute
> > > value), but I am not sure if this would be the
> > correct thing to do. In
> > > case this is a bug, I thought I should report it.
> > Any comments?
> > >
> > > Thanks for your help,
> > >
> > > Sylvana Schister
> > > Univ. of Utah
> > > Dept. of Bioengineering
> > >
> > > _______________________________________________
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> > > fieldtrip at donders.ru.nl
> > >
> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> > >
> >
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>
>
> --------------------------------------------------------------------------------
>
>
> Joseph Dien,
> Senior Research Scientist
> University of Maryland
>
>
> E-mail: jdien07 at mac.com
> Phone: 301-226-8848
> Fax: 301-226-8811
> http://homepage.mac.com/jdien07/
>
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