T-4: The MNE command line processing stream

The following processing stream is for processing the SPM dataset using MNE command line tools.

# make sure you've set up your subjects directory and subject
SUBJECTS_DIR = ...
SUBJECT = ...

# setup the mri
mne_setup_mri

# use the watershed method of creating the boundary element model
mne_watershed_bem

# create symbolic links to the surface files
# inner skull
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/SPM_inner_skull_surface \
    $SUBJECTS_DIR/$SUBJECT/bem/SPM-inner_skull.surf
# outer skull
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/SPM_outer_skull_surface \
    $SUBJECTS_DIR/$SUBJECT/bem/SPM-outer_skull.surf
# outer skin
ln -s $SUBJECTS_DIR/$SUBJECT/bem/watershed/SPM_outer_skin_surface \
    $SUBJECTS_DIR/$SUBJECT/bem/SPM-outer_skin.surf

# setup the forward model
mne_setup_forward_model --surf