= 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.


{{{
#!/bin/sh

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
}}}