[FieldTrip] ICA problem
Sheraz Khan
sherrykhan78 at gmail.com
Thu Jul 7 18:32:57 CEST 2011
Hi,
tsss is more tricky, if uses default 4 sec window then you different
dimensionality every 4 sec.
Sheraz
On Thu, Jul 7, 2011 at 12:07 PM, Sylvana <sylvana.schister at utah.edu> wrote:
> 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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> >
> --------------------------------------------------------------------------------
> >
> >
> > 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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