Head Model and Source Space Creation in MNE

Make sure you've typed

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

done }}} You've got to create the links ("ln -s..."), such that MNE uses the newly created surfaces in the following analyses.