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.

SUBJECTS_DIR='</myMRIdirectory/>'


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).