FieldTrip

This page refers to wiki page headmodels and describes the steps to be done to get a generic head model, with the final aim to calculate the lead fields. Firstly download and unzip the MRI files found in HERE. The following steps are necessary to build a head model in FieldTrip:

The MEG dataset that is used in this demo is available from ftp://ftp.fcdonders.nl/pub/fieldtrip/tutorial/ and is named Subject01.zip.

% load MRI and reslice 
mri = ft_read_mri('Subject01.mri');
 
% Reslicing makes the dimensions of the voxels cubic and
% interpolates/reslices the mri volume according to a given
% grid of points (i.e. in the MEG sensors space). 
% After this transformation the voxel's dimensions are the same.
 
scaling = 1;
cfg = [];
cfg.resolution = scaling;
mri = ft_volumereslice(cfg,mri);

% Coregister the MRI to a 'CTF-like' reference system (head coordinates)
% The cfg.method is 'interactive' so the nasion, 
% left ear and right ear pits have to be marked by pressing the right keys ('n'/'l'/'r')
cfg = [];
cfg.method = 'interactive';
[mri2]     = ft_volumerealign(cfg, mri);

% This may take some time
% (SPM8 is required)
cfg = [];
cfg.smooth = 5;
cfg.threshold = 0.5;
[segment] = ft_volumesegment(cfg, mri2); 

This step is necessary to obtain volumes which are not directly output of the segmentation (skin volume)

% Extract the skin volume:
tmp = double(mri.anatomy);
% 1. get rid of artefacts on the MRI edge
tmp(:,:,175:end)=0; tmp(:,121:end,171:end) = 0;
tmp(:,134:end,168:end) = 0; tmp(139:end,94:end,172:end) = 0;
% 2. smooth and median threshold
spm_smooth(tmp,tmp,3); 
val  = 1.2*median(tmp(:));
tmp  = tmp>val;
% 3.take segmented csf+brain+perimeter
br = imdilate(segment.brainmask,strel_bol(3));
skin = (br | tmp);
 
% Extract the skull volume:
skinshr  = imerode(skin,strel_bol(5));
braindil = imdilate(segment.brainmask,strel_bol(6));
skull =  ~(~braindil & ~skinshr) & ~skin;
 
% Plot all the compartments together with anatomy
% Different compartments are labelled with different integer numbers:
% i.e. 10=brain, 20=skull, 30=skin
mri3=mri;
mri3.seg = 30*skin + 20*skull + 10*brain;
icfg = [];
icfg.interactive  = 'yes';
icfg.funparameter = 'seg';
icfg.funcolormap  = 'jet';
figure,ft_sourceplot(icfg,mri3);

Create a geometrical model of the head surface/surfaces

See also here

% performs an automatic tessellation on the basis of the segmented volume
% intensity value (an integer X) and the number of wanted vertices
cfg = [];
cfg.tissue = [1]; % e.g. skin
cfg.numvertices = [4000];
cfg.sourceunits = 'mm';
cfg.mriunits    = 'mm';
bnd = ft_prepare_mesh(cfg, skin);

Build the method specific Head Model

This step builds the volume conductor structure starting from the information of the head geometry.

It uses ft_prepare_headmodel