[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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>         
>         --------------------------------------------------------------------------------
>         
>         
>         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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