[FieldTrip] align MRI- headmodel- EEG electrodes problem

[Konstantina Kalogianni]

Dear fieldtrippers,

I am struggling with aligning the individual MRI, the headmodel and electrode positions(EEG) for some days now, without any success.
I would appreciate some help.

To begin with,  as an input I have the subject specific MRI which was segmented with the use of freesurfer and MNE software.
I load first the MRI ,the triangulated meshes for brain skull and skin, and the electrodes positions of 65-channel EEG.
I am then computing the bem headmodel from the brain skull skin (computed with the use of MNE software)
Afterwards I am aligning the MRI to my headmodel (ft_volumerealign) and then I identify the fiducials with the interactive mode (ft_volumerealign).
I do the transformation of the fiducial points  with ft_warp_apply to the coordinates specified at the alignment.
Then I call the  ft_electroderealign to align my electrodes to the mri's fiducial points.
And then I realign  my electrodes manually.

The problem is that no matter how much rotation translation scaling I do, it's IMPOSSIBLE TO FIT THE ELECTRODES TO THE HEADMODEL!

I tried the volume_realign with ctf coordinates as well and I tried the ft_electroderalign with the interactive mode only(without matching the fiducials), it doesn't work.

Below you can find the code that I used.
Any ideas on this issue would be of great help!


%% READ
% read mri
mri=ft_read_mri([freesurferDir 'mri\orig.mgz']);
mri.coordsys='neuromag';

% read surfaces

brain=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_brain_surface']);

skull=ft_read_headshape([freesurferDir 'bem\brain.surf\Pilot08_inner_skull_surface' ]);
skin=ft_read_headshape([freesurferDir 'bem\brain.surfilot08_outer_skin_surface' ]);

% read electrodes positions
elec_file=[datadir '\raw\M10.elc'];
elec=ft_read_sens(elec_file );
elec.coordsys='neuromag';
elec.label=upper(elec.label);

%% HEADMODEL
%assign values of segmented surfaces
geom(1).tri=brain.tri;
geom(2).tri=skull.tri;
geom(3).tri=skin.tri;

geom(1).pnt=brain.pnt;
geom(2).pnt=skull.pnt;
geom(3).pnt=skin.pnt;
% compute headmodel
vol=ft_headmodel_bemcp(geom);
vol=ft_convert_units(vol, 'mm');
vol.coordsys='neuromag';

%% ALIGNMENTS
%align mri and headshape
mri_coord=ft_determine_coordsys(mri, 'interactive', 'yes');
vol_coord=ft_determine_coordsys(vol, 'interactive', 'yes');

cfg=[];
cfg.method = 'headshape';
cfg.headshape=vol_coord.bnd(3);
mri_headshape=ft_volumerealign(cfg,mri_coord);

%find fiducials
cfg=[];
cfg.method='interactive';
cfg.coordsys='neuromag';
mri_fid=ft_volumerealign(cfg,mri_headshape);


%% APPLY TRANSFORMATIONS ON FIDUCIALS

transm=mri_fid.transform;
nas=ft_warp_apply(transm,mri_fid.cfg.fiducial.nas, 'homogenous');
lpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.rpa, 'homogenous');
rpa=ft_warp_apply(transm,mri_fid.cfg.fiducial.lpa, 'homogenous');



fid.chanpos       = [nas;  rpa; lpa];
fid.elecpos       =fid.chanpos;
fid.label         = {'NASION',  'RIGHTEAR','LEFTEAR'}; % same labels as in elec
fid.unit          = 'mm';            % same units as mri
% Automatic electrode alignment using the fiducials
cfg               = [];
cfg.method        = 'fiducial';
cfg.template      = fid;
cfg.elec          = elec;
cfg.fiducial      = {'NASION',  'RIGHTEAR','LEFTEAR'};  % labels of fiducials in fid and in sens
cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape
elec_aligned_fid      = ft_electroderealign(cfg);


%% Interactive alignment of electrodes to fix some misalignment

cfg=[];
cfg.method='interactive';
cfg.elec=elec_aligned_fid;
cfg.headshape=vol_coord.bnd(3); % use the scalp as headshape
elec_aligned=ft_electroderealign(cfg);



Best Regards,

K. (Nadia) Kalogianni
PhD candidate

TU Delft /Department of Biomechanical Engneering
Neuromuscular Control Laboratory

Mekelweg 2
2628 CD Delft
Room: F-1-320
T +31 15-27 84230
E  k.kalogianni at tudelft.nl

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