Analysis with MNE

 For most recent documentation and access, go to 
 /neurospin/local/mne/doc/


 1. Typing mne will return:

   MNE software location set to	 /neurospin/local/mne
   MATLAB sofware location set to /neurospin/local/matlab

   /neurospin/local/mne/bin/mne added to PATH

   Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly.
   Note: Freesurfer environment is needed to run mne_setup_source_space

   When you are finished, type 'exit' to leave the MNE environment

 2. Make your analysis directory
    e.g./neurospin
    >>mkdir /neurospin/meg_tmp/your_folder/MyMNE_dir/

 3. Create a symbolic link to this directory
    e.g.
    >> ln -s /neurospin/unicog/protocols/MEG/MyXPMT_year/MyMNE_dir/ ./myMNE

 4. For each command you send to the MNE suite, specify in your line --digtrig 'STI101'
    e.g.
    $ mne_process_raw --raw <mydata> --digtrig 'STI101' --eventsout <myevents>

 5. Typing mne_browse_raw --digtrig 'STI101' pops up the User Interface and should   
    recognize your triggers

    Typing mne_process_raw –[options] can be used for script/batch analysis

    e.g.to grand average data across multiple runs:
    mne_process_raw --raw myrun1_sss.fif --raw myrun2_sss.fif --filteroff  --projoff --digtrig STI101 --ave myaverage_definition --gave gdav.fif

 This command will grand average the conditions specified in your myaverage_definition across myrun1 and 
 myrun2. The filter setting is off, no projections (e.g. from SSP) will be applied. The resulting fif file 
 is gdav which contains all grand average conditions.