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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

1. Load the MRI and "reslice" it

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.

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);

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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.

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Improve realignment with headshape points.

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.

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

1. Load and align a template grid to the headmodel

2. Plot the results and check

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