This is a brief summary of how to align MEG and MRI coordinate systems. For more information see the MNE manual (chapter 12.11).
If you have several fiff-files per participant(e.g. averages for different conditions), and if these files contain the same sensor configuration (e.g. if averages are from the same block, or from different blocks but were interpolated using the -trans option in maxfilter), then this procedure has to be applied only once per subject. If you have different fiff-files per subject with different sensor configurations, then you have to do this for each file separately.
Make sure you've typed
mne_setup_2.6.0 (depending on version, latest version mne_setup_2.7.1_32bit) setenv SUBJECTS_DIR </myMRIdirectory/>
before proceeding.
1) Start mne_analyze ("vglrun mne_analyze").
2) Load a surface file (File -> Load Surface, choose inflated).
3) Load a fiff-file containing digitiser data (raw or averaged file; File -> Load digitizer data).
4) Open the viewer (View -> Show Viewer).
5) Click on "Options". Hide the cortex, make the skin transparent, show the digitiser data.
6) Choose Adjust -> Coordinate Alignment. Define approximate landmarks (LAP, RAP, Nasion) by clicking at their labels, then at their approximate locations in the viewer. The click "Align Using Fiducials".
7) Use the "ICP Align" option multiple times until the transformation matrix doesn't change significantly any more. You can remove outliers using the "Omit/Discard" option (e.g. choose 10 or 5 mm, then ICP align again).
8) When you are happy, click "Save default".
The coordinate transform will automatically be invoked in future operation within MNE.