AnalyzingData/MNE_Averaging - Meg Wiki

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Averaging data in MNE

The following script is an example for a standard averaging procedure. Obviously, you may want to use different parameters - have a look at the manual for details and more options.

You should have processed your raw data using [http://imaging.mrc-cbu.cam.ac.uk/meg/Maxfilter Maxfilter].

Note that MNE will not process EEG data from the CBU correctly unless you apply "mne_check_eeg_locations" to your files ([#checkeeglocs see below]).

You can [#markbadchannels mark bad channels] in your fif-files using mne_mark_bad_channels. These bad channels will be excluded from further MNE operations (forward solution, inverse operator etc.).

The end result will be fiff-files with averages for each condition defined in the specification file (see below). They can be read into Matlab using fiff_read_evoked. 


## Your variables

datapath='<myMEGdatapath>'       # root directory for your MEG data

# MEG IDs (your directory structure may differ)
subj_pre=(\
        'meg10_0001' \
        'meg10_0002' \
        'meg10_0003' \
        )

# MEG subdirectories (your directory structure may differ)      
subj_dir=(\
         '100001' \
         '100002' \
         '100003' \
        )
        

## Processing:

nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`


# REPORT number of files to be processed:

for m in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Averaging SUBJECT  ${subjects[m]}"
  echo " "
 
  inpath=${path}'/'${subj_dir[m]}'/'${subjects[m]}
  
  echo ${inpath}

  mne_process_raw \
        --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1.fif \
        --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2.fif \
        --raw ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3.fif \
        --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile1-eve.txt \
        --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile2-eve.txt \
        --eventsout ${datapath}/${subj_dir[m]}/${subjects[m]}/yourrawMEGfile3-eve.txt \
        --ave YourSpecificationFile.ave \
        --gave ${datapath}/${subj_dir[m]}/${subjects[m]}/gave.fif \
        --saveavetag _avg \
        --highpass 0.1 \
        --projoff 

done # subjects

Note: You can modify the event information in the eve.txt-files, and read the modified information later using the --events option. This is useful when you want to average with respect to trigger combinations (e.g. correct responses only) etc.

The specification file YourSpecificationFile.ave should be of the form: 

average {
#       Rejection values
#
        gradReject      20e-15                # artefact rejection thresholds
        magReject       3e-12
        eegReject       120e-6
        eogReject       150e-6
        logfile         ave_logfile.txt       # log-file for some useful information

#       Category specifications
#
        category {
                name    "Cond1"               # name of condition
                event   1                     # trigger/event code for condition
                tmin    -0.1                  # duration of epochs with respect to trigger
                tmax    1.0
                bmin    -0.1                  # interval for baseline correction
                bmax    0.0
        }
        category {
                name    "Cond2"
                event   2
                tmin    -0.1
                tmax    1.0
                bmin    -0.1
                bmax    0.0
        }       
}

Anchor(checkeeglocs)

Fixing EEG electrode positions

Unless you apply mne_check_eeg_locations to your data, MNE will get confused with the EEG electrode digitisation used at the CBU, and e.g. the creation of the forward solution for EEG will fail. 


# Your variables

datapath='<myMEGdatapath>'       # root directory for your MEG data

# MEG IDs (your directory structure may differ)
subj_pre=(\
        'meg10_0001' \
        'meg10_0002' \
        'meg10_0003' \
        )

# MEG subdirectories (your directory structure may differ)      
subj_dir=(\
         '100001' \
         '100002' \
         '100003' \
        )

#condition names as used in file names
conds=('cond1' 'cond2' 'cond3')
        

# Processing:

nsubjects=${#subj_pre[*]}
lastsubj=`expr $nsubjects - 1`

nconds=${#conds[*]}
lastcond=`expr $nconds - 1`


for m in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Fixing electrodes for SUBJECT  ${subjects[m]}"
  echo " "
        for c in `seq 0 ${lastcond}`
        do
        
                mne_check_eeg_locations \
                        --file ${datapath}/${subj_pre[m]}/${subj_dir[m]}/${conds[c]}.fif \
                        --fix                           
                
        done # conditions

done # subjects

Anchor(markbadchannels)

Marking Bad Channels

You can mark channels already for raw MEG data files - these channels will then be excluded from artefact rejection during averaging. 

datapath='<myMEGdatapath>'       # root directory for your MEG data

mne_mark_bad_channels \
        --bad yoursubjectbads.txt \      # File with bad channel information
        ${datapath}/YourSubjectDir/YourSubjectFile1.fif \
        ${datapath}/YourSubjectDir/YourSubjectFile2.fif \
        ${datapath}/YourSubjectDir/YourSubjectFile3.fif \

where yoursubjectbads.txt could look like this 

EEG001
EEG044

if EEG channels 1 and 44 are bad. I had problems when I created these text files in Windows - if in doubt, open the file under Linux (e.g. using nedit), use "save as" and make sure it's in Linux (not Dos) format.