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

Forward Solution

#

## Your variables:

path='<myMEGdatapath>'    # where your MEG fiff-files are
MRIpath='/myMRIdirectory/'    # where your MRI subdirectories are

# subjects names used for MRI data
subjects=(\
        'Subject1' \
        'Subject1' \
        'Subject1' \
)

# MEG IDs
subj_pre=(\
        'meg10_0001' \
        'meg10_0002' \
        'meg10_0003' \
        )

# MEG subdirectories    
subj_dir=(\
         '100001' \
         '100002' \
         '100003' \
        )
        
dirbem='subject'


## Processing:

nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`


# REPORT number of files to be processed:

for m in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Computing forward & inverse solution for SUBJECT  ${subjects[m]}"
  echo " "
  
  subject=Subject${subjects[m]}


## setup model 3 layers (EEG+MEG)
mne_setup_forward_model --overwrite  --subject ${subject} --surf --ico 4
 
mne_do_forward_solution \
                        --overwrite \
                        --subject ${subject} \
                        --mindist 5 \
                        --spacing 5 \
                        --bem ${MRIpath}/${subject}/bem/${subject}-5120-5120-5120-bem-sol.fif \
                        --src ${MRIpath}/${subject}/bem/${subject}-5-src.fif \
                        --meas ${path}/${subj_pre[m]}/${subj_dir[m]}/MEGfile.fif  \
                        --fwd ${path}/${subj_pre[m]}/${subj_dir[m]}/lex_go_5-3L-EMEG-fwd.fif



## setup model 1 layer (MEG only)
mne_setup_forward_model --overwrite  --subject ${subject} --surf --homog --ico 4

mne_do_forward_solution \
                        --overwrite \
                        --subject ${subject} \
                        --mindist 5 \
                        --spacing 5 \
                        --megonly \
                        --bem ${MRIpath}/${subject}/bem/${subject}-5120-bem-sol.fif \
                        --src ${MRIpath}/${subject}/bem/${subject}-5-src.fif \
                        --meas ${path}/${subj_pre[m]}/${subj_dir[m]}/MEGfile.fif \
                        --fwd ${path}/${subj_pre[m]}/${subj_dir[m]}/lex_go_5-1L-MEG-fwd.fif



done # subject loop