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Merge (i.e. realign) the sensor locations of the MEG recordings with the MRI of the individual subject, create a head model and a grid (aka leadfield matrix) for source analysis.

Step-by-step guide

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rootdir = '/path/to/data';
sujdir = fullfile(rootdir,'/subjectXX');
mkdir(rootdir);mkdir(sujdir);mkdir(fullfile(rootdir,'figures','headmodel');
addpath('/path/to/export_fig'); % https://github.com/altmany/export_fig

1. Load the MRI and "reslice" it

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In this step, we simply put the right side of the MRI up. Skipping this step will result in mixed up slices and/or upside down image. 

Code Block
title ft_volumereslice
mrif = '/path/and/filename/to/T1_mri.mgz'; % the file format could be one of many supported by fieldtrip. Native DICOM format works but is a bit slow to load. % read in the mri mri=ft_read_mri(mrif); % flip image so it looks upright cfg = []; cfg.method = 'flip'; mri_aligned = ft_volumereslice(cfg,mri);

 

 

 

Info
title using freesurfer's orig file
Note that if you have used freesurfer previously to segment your MRI, you can load the original mri stored in your freesurfer subjects' directory under SubjectName/orig/001.mgz

 

 

2. Align the MRI with the fiducial points

This step is just a rough alignment of the MRI fiducial points. The next step will use head shape points to refine this alignment. If no head shape points have been digitized, it is important to point precisely to the fiducial points here. 

% realign with fiducials
cfg             = [];
cfg.method      = 'interactive';
cfg.coordsys    = 'neuromag';
mri_aligned     = ft_volumerealign(cfg, mri_aligned);

3. Refine alignment with head shape points

% headshape should be stored along with the MEG data
headshapef = '/path/to/MEGdata.fif';

cfg             = [];
cfg.method      = 'headshape';
headshape       = ft_read_headshape(headshapef);
headshape       = ft_convert_units(headshape, 'mm');
cfg.headshape.headshape = headshape;
cfg.coordsys    = 'neuromag';
cfg.headshape.interactive = 'no';
mri_aligned     = ft_volumerealign(cfg, mri_aligned);

This step can also be done interactively .to further refine

4. Create a head model (3D surfaces for brain, skull and scalp)

Segment and extract brain, skull and scalp surfaces.

cfg             = [];
cfg.output      = {'brain','skull','scalp'};
mri_seg         = ft_volumesegment(cfg, mri_aligned);

cfg             = [];
cfg.method      = 'singleshell';
cfg.tissue      = {'brain','skull','scalp'};
headmodel       = ft_prepare_headmodel(cfg,mri_seg);

5. Load and align a template grid to the head model

cfg = [];
cfg.grid.warpmni   = 'yes';
cfg.grid.template  = template_grid;
cfg.grid.nonlinear = 'yes';
cfg.grid.unit      = 'mm';
cfg.mri            = mri_aligned;
grid               = ft_prepare_sourcemodel(cfg);

% save the results
save(fullfile(sujdir,'source_head_model.mat'), 'mri', 'mri_aligned','mri_seg','headmodel','grid','headshape');

6. Plot the results and check

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Code Block
title Check results
% make a figure with enough space for 3 panels horizontally p = get(0,'defaultfigureposition'); p(3) = p(3) * 3; figure('name',suj,'numbertitle','off','position',p); % first panel with brain and algned grid subplot(131); hm = headmodel;hm.bnd = hm.bnd(1);% use only the first layer (brain) ft_plot_vol(hm,'vertexcolor','none','facecolor','skin','edgecolor','none','facealpha',.5); ft_plot_mesh(grid.pos(grid.inside,:));% lighting gouraud material shiny camlight view(90,0) rotate3d on drawnow title('brain and source model') % second panel with head shape points, HPI coils, scalp, skull, and brain. subplot(132); ft_plot_vol(headmodel,'vertexcolor','none','facecolor','skin','edgecolor','none','facealpha',.5); ft_plot_headshape(headshape); hpi = find(cellfun(@(x)~isempty(x),regexp(headshape.label,'hpi_.*'))); hold on scatter3(headshape.pos(hpi,1),headshape.pos(hpi,2),headshape.pos(hpi,3),200,'b','.'); text(headshape.pos(hpi,1),headshape.pos(hpi,2),headshape.pos(hpi,3), headshape.label(hpi), 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle', 'Interpreter', 'tex'); lighting gouraud material shiny camlight view(-150,0) rotate3d on drawnow title('head model and head shape') % third panel with head and MEG sensors subplot(133);cla ft_plot_vol(headmodel,'vertexcolor','none','facecolor','skin','edgecolor','none','facealpha',.5); lighting gouraud material shiny camlight view(-180,0) drawnow for i_run = 1:numel(allruns) h = ft_read_header(allruns(i_run).name); h.grad = ft_convert_units(h.grad, 'mm'); ft_plot_sens(h.grad); end rotate3d on drawnow title('head model and sensors') drawnow % save as image and as .fig export_fig(hfig,fullfile(rootdir,'figures','headmodel',['headmodel_' suj '.png']),'-nocrop','-r300'); % https://github.com/altmany/export_fig saveas(hfig,fullfile(rootdir,'figures','headmodel',['headmodel_' suj '.fig']))

 

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