[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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