[FieldTrip] MEGRealign channel

[jan-mathijs schoffelen]

Hi Jeff,

Thanks for reporting this. We'll look into it as soon as possible.

Best wishes,

Jan-Mathijs


On May 30, 2011, at 11:28 PM, Jeff Stout wrote:

>
> Hi All,
>
> I am having trouble using the ft_megrealign command with a 4D Magnes  
> 3600 system.  I am trying to use this command to interpolate bad  
> channels that have been removed in preprocessing.  When I view the  
> output of megrealign using ft_plot_sens, sensor 'A229' is badly  
> misplaced (approximately 10 cm above the top of the sensor array),  
> but all the other sensors appear appropriate.  In the dataset A229  
> has not been labelled as a bad channel, nor any of its neighboring  
> channels. The location of A229 is significant in that it is the most  
> inferior/anterior channel on the left side.  I am using the original  
> grad file as a template input using ft_read_sens('c,rfDC') and  
> scaling the MEG channels to cm.  I am not sure how helpful the code  
> is - below is my input and some of the output.  I can provide an  
> image if this would be helpful.
>
>
> temp = ft_read_sens(subjectdata.FA_dataset);
> temp.pnt = temp.pnt*100;
> temp.unit  = 'cm';
>
> cfg = [];
> cfg.inwardshift = 1;
> cfg.vol=vol;
> cfg.template{1}= temp;
> cfg.channel={'MEG'};
> con.grad.pnt = con.grad.pnt*100;
> con.grad.unit = 'cm';
> con = ft_megrealign(cfg, con)
>
> computing surface normals
> mean distance towards template gradiometers is 0.00 cm
> creating dipole grid based on inward-shifted brain surface from  
> volume conductor model
> Warning: the normals of the surface triangulation are inward oriented
> > In fieldtrip-20110507/private/headsurface at 211
>   In ft_prepare_sourcemodel at 492
>   In ft_megrealign at 245
> 642 dipoles inside, 0 dipoles outside brain
> computing forward model for 642 dipoles
> pruning 122 from 246, i.e. removing the 122 smallest spatial  
> components
> computing interpolation matrix #1
> computing interpolation matrix #2
> computing interpolation matrix #3
> pruning 124 from 248, i.e. removing the 124 smallest spatial  
> components
> realigning trial 1
> original -> template             RV 14.42 %
> original             -> original RV 14.42 %
> original -> template -> original RV 14.44 % ....................
>
>
> Does anyone know why this would be occurring and how to fix it?
>
> Thanks,
> Jeff Stout
>
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Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: 0031-24-3614793

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