{{attachment:mrclogo.gif}}

= Overview of MNE Processing Steps and Commands =
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_preprocessing|Pre-processing MRI Data in Freesurfer]]:'''

 * mri_convert
 * recon-all
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing|Segment Head Surfaces]]:'''

 * mne_watershed_bem
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing|Prepare MRI Data for MNE]]:'''

 * mne_setup_mri
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing|Prepare Source Space (Cortical Surface) for MNE]]:'''

 * mne_setup_source_space
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_MRI_processing|Align MEG and MRI coordinate systems]]:'''

 * mne_analyze
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution|Set Up BEM Information for MNE]]:'''

 * mne_setup_forward_model
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ForwardSolution|Compute Forward Solution]]:'''

 * mne_do_forward_solution
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Averaging|Average MEG Data]], [[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_CovarianceMatrix|Compute Covariance Matrix]]:'''

 * mne_process_raw
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates|Compute Average Cortical Surface]]:'''

 * make_average_subject
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator|Create Inverse Operator (from Forward Solution)]]:'''

 * mne_do_inverse_operator
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates|Compute Source Estimates (Apply Inverse Operator to MEG data)]]:'''

 * mne_make_movie
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_ComputeEstimates|Average Source Estimates]]:'''

 * mne_average_estimates
'''[[http://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_Labels|Extract ROI data]]:'''

 * mne_make_movie