[FieldTrip] source analysis EEG data without MRI

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Tue Apr 9 08:37:13 CEST 2013

Hi Ingrid,

I just happen to done this a few weeks back, I changed things in the 
meanwhile, but I hope that the below steps are complete:
/% read in the template MRI
     if isunix
       mri = 
     elseif ispc
       mri = ft_read_mri(fullfile('M:', 'FieldTrip', 'trunk', 
'external', 'spm8', 'templates', 'T1.nii'));

% segment the MRI
cfg           = [];
cfg.output    = {'brain'  'skull'  'scalp'};
segmentedmri  = ft_volumesegment(cfg, mris);

% create the headmodel (BEM)
cfg        = [];
%cfg.method ='openmeeg'; % TODO FIXME download openmeeg
if isunix
   cfg.method ='dipoli'; % dipoli only works under linux
   disp('TODO FIXME stick to dipoli for now or download openmeeg\n');
hdm        = ft_prepare_headmodel(cfg, segmentedmri);

elec       = ft_read_sens('standard_1020.elc');
hdm        = ft_convert_units(hdm, elec.unit);

   cfg = [];
   cfg.grid.xgrid  = -125:8:125;
   cfg.grid.ygrid  = -125:8:125;
   cfg.grid.zgrid  = -125:8:125;
   cfg.grid.tight  = 'yes';
   cfg.grid.unit   = hdm.unit;
   cfg.inwardshift = -1.5;
   cfg.vol        = hdm;
   grid  = ft_prepare_sourcemodel(cfg)
   grid        = ft_convert_units(grid, elec.unit);

hold on;
ft_plot_mesh(hdm.bnd(1), 'facecolor',[0.2 0.2 0.2], 'facealpha', 0.3, 
'edgecolor', [1 1 1], 'edgealpha', 0.05);
ft_plot_mesh(grid.pos(grid.inside, :));

% this step is not necessary, cause you will see that everything is 
already aligned
   cfg           = [];
   cfg.method    = 'interactive';
   cfg.elec      = elec;
   cfg.headshape = hdm.bnd(1);
   tmp  = ft_electroderealign(cfg);
   elec = tmp; % I had a bug here that I couldn't assign elec directly

%% verify location of occipital electrodes

occ_elec = elec;
occ_chan = ft_channelselection({'O*', 'PO*', 'Cz*', 'Fz*'}, elec.label);
occ_idx = match_str(elec.label, occ_chan);
occ_elec.chanpos = occ_elec.chanpos(occ_idx, :);
occ_elec.elecpos = occ_elec.elecpos(occ_idx, :);
occ_elec.label = occ_elec.label(occ_idx, :);
hold on;
ft_plot_vol(ft_convert_units(hdm, elec.unit))/

Afair, that's all that is needed. Of course you need to adjust folder 
and file names.


On 4/9/2013 2:04 AM, Ingrid Nieuwenhuis wrote:
> Hi all,
> I'd like to do source analysis (loreta and or DICS) on my EEG data. I 
> don't have anatomical MRIs and I don't have a measurement of the scalp 
> surface. So I'd like to use a template MRI or a template head model 
> that is located in the FieldTrip template directory. I have EGI (128 
> channels) data and electrode positions (not subject specific, just the 
> standard file also available in FieldTrip electrode template, 
> GSN-HydroCel-128.sfp), but I'm kind of stuck how to start. I don't see 
> any examples on the FieldTrip page of how to make a headmodel and 
> volume conduction model giving only this limited data. I'd be happy to 
> make it into a example Matlab script on the FieldTrip page after I got 
> it to work. Would someone be able to give me some pointers, or example 
> code?
> Thanks a lot!
> Ingrid

Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
Tel:    +31-(0)24-36-68493
Web: http://www.ru.nl/donders

Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands

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