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Most difficult is the labeling by other people that models are empty-headed bodies. Boyd Holbrook

Prerequisite

Data with headshape points (3 fiducials, and ~100 head points, optionally 4 HPI coils) should have been digitized before MEG data acquisition.

Individual subject MRI should have been acquired.

Goal of this tutorial

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.

    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);

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

 

  1. Roughly align the MRI with the fiducials.

  2. Improve realignment with headshape points.

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

  4. Load and align a template grid to the headmodel

  5. Plot the results and check

 

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