Make sure you've typed
mne_setup_2.6.1_32bit (depending on version, latest version mne_setup_2.7.1_32bit) freesurfer_4.3.0 (depending on version, latest version freesurfer_5.1.0) setenv SUBJECTS_DIR </myMRIdirectory/>
in your Linux command window.
The following script will produce the source space (downsampled version of the cortical surface in Freesurfer), which will be saved in a file ending in *-src.fif, which can be read into Matlab using mne_read_source_spaces.
After this step, you should 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). It is briefly described below.
The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the MNE manual, reading papers, and discussions with more experienced researchers.
SUBJECTS_DIR='</myMRIdirectory/>' # root directory for MRI data
for SUBJECT in Subject1 Subject2 Subject3 # use your list of subject names here do
- # 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 }}} You've got to create the links ("ln -s..."), such that MNE uses the newly created surfaces in the following analyses.