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.

SUBJECTS_DIR='</myMRIdirectory/>'


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

        cd ${SUBJECTS_DIR}

        mne_watershed_bem --overwrite --subject $SUBJECT

        rm $SUBJECTS_DIR/$SUBJECT/bem/inner_skull.surf
        rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skull.surf
        rm $SUBJECTS_DIR/$SUBJECT/bem/outer_skin.surf
        rm $SUBJECTS_DIR/$SUBJECT/bem/brain_surface.surf


        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

        mne_setup_mri --overwrite --subject $SUBJECT

        mne_setup_source_space --spacing 5 --overwrite --subject $SUBJECT

        mri_convert -ot cor $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz $SUBJECTS_DIR/$SUBJECT/mri/T1/

        mkheadsurf -subjid $SUBJECT

done