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Bug 716 - ft_megrealign misbehaves when realigning

Reported 2011-05-31 08:59:00 +0200
Modified 2011-06-01 13:43:10 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P1 normal
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Jan-Mathijs Schoffelen - 2011-05-31 08:59:56 +0200

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;{'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

Jan-Mathijs Schoffelen - 2011-05-31 19:48:04 +0200

*** This bug has been marked as a duplicate of bug 719 ***