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= Forward Solution = {{{ #!/bin/sh # ## 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 }}} |
You should now realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set). |
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 scripts.
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
doneYou should now realign the MRI and MEG coordinate systems, otherwise the following analyses (forward solution, inverse operator etc.) won't make sense. The procedure is described in the MNE manual, e.g. chapter 12.11. (sample data set).