Head Model and Source Space Creation in MNE
Make sure you've typed
mne_setup_2.6.0
and
setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
Then run the following script.
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