= 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 [#readwritesubtract read into Matlab] using fiff_read_evoked.

The following script requires a [#avgspecfile specification file] with averaging parameters (thresholds etc.).

{{{
#!/bin/sh


## 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=${#subj_pre[*]}
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_pre[m]}/${subj_dir[m]}/yourrawMEGfile1.fif \
        --raw ${datapath}/${subj_pre[m]}/${subj_dir[m]}/yourrawMEGfile2.fif \
        --raw ${datapath}/${subj_pre[m]}/${subj_dir[m]}/yourrawMEGfile3.fif \
  	--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/yourrawMEGfile1-eve.txt \
  	--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/yourrawMEGfile2-eve.txt \
  	--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/yourrawMEGfile3-eve.txt \
  	--ave YourSpecificationFile.ave \
  	--gave ${datapath}/${subj_pre[m]}/${subj_dir[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.

[[Anchor(avgspecfile)]]
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. 

{{{

#!/bin/sh


# 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. 

{{{
#!/bin/sh

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.

[[Anchor(readwritesubtract)]]
== Reading, Writing, Subtracting Fiff-files ==
This is a simple example of how you can read and write fiff-files, e.g. for subtracting conditions etc. Note that if you apply an inverse operator with the --dSPM option to subtracted data, you may have to adjust the number of effective averages (see manual).

{{{

data1 = fiff_read_evoked( fiff_file1 );  % Read file 1
data2 = fiff_read_evoked( fiff_file2 );  % Read file 2
        
data3 = data2;  % data3 will contain the subtracted data, plus other information from file 2

data3.evoked.epochs = data2.evoked.epochs - data1.evoked.epochs;  % subtract file 1 from file 2

fiff_write_evoked(out_fiff_file, data3);  % write subtracted data to fiff-file  

}}}