= Head Model and Source Space Creation in MNE =

Make sure you've typed
   '''mne_setup_2.6.0'''

   '''freesurfer_4.3.0'''

   '''setenv SUBJECTS_DIR </myMRIdirectory/>'''
in your Linux command window.

The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces.

{{{
#!/bin/sh

SUBJECTS_DIR='</myMRIdirectory/>'    # root directory for MRI data


for SUBJECT in Subject1 Subject2Subject3  # use your subject names here
do 

	cd ${SUBJECTS_DIR}

        # creates surfaces necessary for BEM head models
	mne_watershed_bem --overwrite --subject $SUBJECT

	ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_inner_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf
	ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skull_surface' $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf
	ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_outer_skin_surface'  $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf
	ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/$SUBJECT'_brain_surface'       $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf

        # creates fiff-files for MNE describing MRI data
	mne_setup_mri --overwrite --subject $SUBJECT

        # create a source space from the cortical surface created in Freesurfer
	mne_setup_source_space --spacing 5 --overwrite --subject $SUBJECT

done
}}}

You should now realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set).