Forward Solution and BEM

The following script creates the forward model and BEM, from which the inverse operator will be computed. It is essential that you have created the [http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing source space and head surfaces, and realigned your MRI and MEG coordinate systems].

The script creates two forward solutions: One for MEG only (using only the inner skull surface), and one for combined EEG and MEG analysis (using inner skull, out skull and skin surfaces). If you only have MEG data, you can skip the latter. The main ingredients for this step are

* the source space (cortical surface)

* the BEM model (surfaces describing boundaries of different electrical conductivity)

* the MEG data (at this stage only sensor/electrode positions and MRI-MEG realignment)

The end product will be the forward solution file (something ending in *fwd.fif), which can be read into Matlab using mne_read_forward_solution. The BEM surfaces can be read using mne_read_bem_surfaces.

For more details and further options see the MNE manual.

#

## 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 (your directory structure may differ)
subj_pre=(\
        'meg10_0001' \
        'meg10_0002' \
        'meg10_0003' \
        )

# MEG subdirectories (your directory structure may differ)      
subj_dir=(\
         '100001' \
         '100002' \
         '100003' \
        )
        

## Processing:

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

for m in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Computing forward solution for SUBJECT  ${subjects[m]}"
  echo " "
  
  ## setup model 3 layers (EEG+MEG)
  mne_setup_forward_model --overwrite  --subject ${subjects[m}} --surf --ico 4
 
  mne_do_forward_solution \
                        --overwrite \
                        --subject ${subjects[m}} \
                        --mindist 5 \
                        --spacing 5 \
                        --bem ${MRIpath}/${subjects[m}}/bem/${subject}-5120-5120-5120-bem-sol.fif \
                        --src ${MRIpath}/${subjects[m}}/bem/${subject}-5-src.fif \
                        --meas ${path}/${subj_pre[m]}/${subj_dir[m]}/YourMEGfile.fif  \
                        --fwd ${path}/${subj_pre[m]}/${subj_dir[m]}/YourName_5-3L-EMEG-fwd.fif



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

  mne_do_forward_solution \
                        --overwrite \
                        --subject ${subjects[m}} \
                        --mindist 5 \
                        --spacing 5 \
                        --megonly \
                        --bem ${MRIpath}/${subjects[m}}/bem/${subject}-5120-bem-sol.fif \
                        --src ${MRIpath}/${subjects[m}}/bem/${subject}-5-src.fif \
                        --meas ${path}/${subj_pre[m]}/${subj_dir[m]}/YourMEGfile.fif \
                        --fwd ${path}/${subj_pre[m]}/${subj_dir[m]}/YourName_5-1L-MEG-fwd.fif

done # subjects