[FieldTrip] MEGRealign channel

[Jeff Stout]

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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