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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 }}} |
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
done