[FieldTrip] single subject headmodel and mni-transformed grid doesn't fit

Yuka Okazaki yukaokazaki at gmail.com
Fri May 31 08:21:56 CEST 2013

Dear all

I have a problem that single subject headmodel and the warped its grid to
template grid do not fit, as attached figure. I expected they are exactly
fit each other but it seems not.

I generated this figure by following steps. MEG system is yokogawa.
Any advices I should check will be very helpful and appreciated.


template_grid  = sourcemodel;

% Read mri data
mri2nifti('subject.mri', 'mri.nii');
mri_nifti = ft_read_mri('mri.nii');

% Define fiducial position in MRI coordinate
cfg = [];
cfg.method = 'interactive';
mri = ft_volumerealign(cfg, mri_nifti);

% segment the anatomical MRI
cfg = [];
cfg.coordsys = 'ctf';
seg = ft_volumesegment(cfg, mri);

% construct volume conductor model (i.e. head model) for each subject
cfg = [];
cfg.method = 'singleshell';
vol = ft_prepare_headmodel(cfg, seg);
vol = ft_convert_units(vol, 'cm');

% create the subject specific grid, using the template grid that has just
been created
cfg = [];
cfg.grid.warpmni   = 'yes';
cfg.grid.template  =  template_grid; %sourcemodel%
cfg.grid.nonlinear = 'yes'; % use non-linear normalization
cfg.mri            = mri;
grid               = ft_prepare_sourcemodel(cfg);

% make a figure of the single subject headmodel, and grid positions
ft_plot_vol(vol, 'edgecolor', 'none'); alpha 0.4;
ft_plot_mesh(grid.pos(grid.inside,:),'vertexcolor','r');[image: Inline
image 1]
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