Computing the Noise Covariance Matrix
The noise covariance matrix is needed for the computation of the inverse operator.
Ingredients for this script are
* raw MEG data files (which are used for averaging, after maxfilter)
* a description file ([#covdescription see below])
The end result is a fiff-file containing the noise covariance matrix, which can be read into Matlab using mne_read_noise_cov.
The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the [http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf MNE manual], [http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers reading papers], and [http://imaging.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup discussions] with more experienced researchers.
#
## Your variables:
datapath='<myrawMEGdatapath>' # 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`
for m in `seq 0 ${lastsubj}`
do
echo " "
echo " Computing covariance matrix for SUBJECT ${subjects[m]}"
echo " "
mne_process_raw \
--raw ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw1.fif \
--raw ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw2.fif \
--raw ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw3.fif \
--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw1-eve.txt \
--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw2-eve.txt \
--eventsout ${datapath}/${subj_pre[m]}/${subj_dir[m]}/rawMEGfile_raw3-eve.txt \
--projoff \
--cov cov_desc1.cov \
--cov cov_desc2.cov \
--cov cov_desc3.cov \
--savecovtag -cov \
--gcov ${datapath}/${subj_pre[m]}/${subj_dir[m]}/covmat-cov.fif
done # subjectsAnchor(covdescription) where the covariance description files cov_desc?.cov are of the form
cov {
gradReject 2000e-13
magReject 3e-12
eegReject 120e-6
eogReject 150e-6
logfile YourLogFileName.txt
def {
event 1
tmin -0.2
tmax 0
basemin -0.2
basemax 0.0
}
def {
event 2
tmin -0.2
tmax 0
basemin -0.2
basemax 0.0
}
def {
event 3
tmin -0.2
tmax 0
basemin -0.2
basemax 0.0
}
}If the parameters are the same for all input files, you only have to specify one description file. For more details and options see the MNE manual.