Overview of MNE Processing Steps and Commands

Pre-processing MRI Data in Freesurfer:

mri_convert
recon-all

Segment Head Surfaces:

mne_watershed_bem

Prepare MRI Data for MNE:

mne_setup_mri

Prepare Source Space (Cortical Surface) for MNE:

mne_setup_source_space

Align MEG and MRI coordinate systems:

mne_analyze

Set Up BEM Information for MNE:

mne_setup_forward_model

Compute Forward Solution:

mne_do_forward_solution

Average MEG Data, Compute Covariance Matrix:

mne_process_raw

Compute Average Cortical Surface:

make_average_subject

Create Inverse Operator (from Forward Solution):

mne_do_inverse_operator

Compute Source Estimates (Apply Inverse Operator to MEG data):

mne_make_movie

Average Source Estimates:

mne_average_estimates

Extract ROI data:

mne_make_movie