<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>AnalyzingData/MNE_InverseOperator</title><revhistory><revision><revnumber>16</revnumber><date>2013-03-08 10:02:47</date><authorinitials>localhost</authorinitials><revremark>converted to 1.6 markup</revremark></revision><revision><revnumber>15</revnumber><date>2012-04-16 16:53:27</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>14</revnumber><date>2010-07-22 15:34:10</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>13</revnumber><date>2010-06-17 11:28:32</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>12</revnumber><date>2010-06-17 11:27:05</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>11</revnumber><date>2010-06-15 14:37:56</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>10</revnumber><date>2010-06-10 13:12:36</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>9</revnumber><date>2010-06-10 13:04:51</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>8</revnumber><date>2010-06-10 12:06:33</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>7</revnumber><date>2010-06-09 16:40:49</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>6</revnumber><date>2010-06-09 15:58:46</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>5</revnumber><date>2010-06-09 15:57:30</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>4</revnumber><date>2010-06-09 15:57:10</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>3</revnumber><date>2010-06-09 15:53:09</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>2</revnumber><date>2010-06-09 15:52:20</date><authorinitials>YaaraErez</authorinitials></revision><revision><revnumber>1</revnumber><date>2010-06-09 15:45:06</date><authorinitials>YaaraErez</authorinitials></revision></revhistory></articleinfo><para>The following script computes the inverse operator, which will later be applied to your MEG data to compute the source estimates. You must have created a <ulink url="https://lsr-wiki-02.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_InverseOperator/meg/AnalyzingData/MNE_ForwardSolution#">forward solution</ulink> already. Just as for the forward solution, two inverse operators will be created: One for MEG only, and one for combined EEG and MEG. If you only have MEG data, you can skip the latter. </para><para>The main ingredients for this script are </para><para>* the forward solution </para><para>* the noise covariance matrix </para><para>The end product will be the inverse operator (something ending in *-inv.fif), which can be read into Matlab using mne_read_inverse_operator.  </para><para>The inverse operators will be computed using the loose orientation constraint and without depth weighting (see MNE manual for details and more options). </para><para>The parameters below are reasonable choices for standard analyses. However, these Wiki pages are not supposed to substitute the <ulink url="http://www.nmr.mgh.harvard.edu/meg/manuals/MNE-manual-2.6.pdf">MNE manual</ulink>, <ulink url="http://imaging.mrc-cbu.cam.ac.uk/meg/MEGpapers">reading papers</ulink>, and <ulink url="http://wiki.mrc-cbu.cam.ac.uk/imaging/ImagersInterestGroup#">discussions</ulink> with more experienced researchers. </para><screen><![CDATA[#
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## Your variables:
]]><![CDATA[
datapath='<myMEGdatapath>'    # root directory for your MEG data
]]><![CDATA[
MRIpath='/myMRIdirectory/'    # where your MRI subdirectories are
]]><![CDATA[
# subjects names used for MRI data
subjects=(\
        'Subject1' \
        'Subject2' \
        'Subject3' \
)
]]><![CDATA[
# MEG IDs (your directory structure may differ)
subj_pre=(\
        'meg10_0001' \
        'meg10_0002' \
        'meg10_0003' \
        )
]]><![CDATA[
# MEG subdirectories (your directory structure may differ)      
subj_dir=(\
         '100001' \
         '100002' \
         '100003' \
        )
]]><![CDATA[
]]><![CDATA[
]]><![CDATA[
## Processing:
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nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`
]]><![CDATA[
]]><![CDATA[
for m in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Computing inverse operator for SUBJECT  ${subjects[m]}"
  echo " "
]]><![CDATA[
# MEG only (forward solution based on 1-layer BEM required)
]]><![CDATA[
mne_do_inverse_operator \
                  --fwd ${datapath}/${subj_pre[m]}/${subj_dir[m]}/${subjects[m]}_5-1L-MEG-fwd.fif \
                  --meg \
                  --loose 0.2 \
                  --senscov ${datapath}/${subj_pre[m]}/${subj_dir[m]}/YourCovName-cov.fif \
                  --megreg 0.1 \
                  --inv ${datapath}/${subj_pre[m]}/${subj_dir[m]}/YourName_1L-MEG-loose0.2-inv.fif
]]><![CDATA[
]]><![CDATA[
# MEG and EEG (forward solution based on 3-layer BEM required)
]]><![CDATA[
mne_do_inverse_operator \
                  --fwd ${datapath}/${subj_pre[m]}/${subj_dir[m]}/${subjects[m]}_5-3L-EMEG-fwd.fif \
                  --meg \
                  --eeg \
                  --loose 0.2 \
                  --senscov ${datapath}/${subj_pre[m]}/${subj_dir[m]}/YourCovName-cov.fif \
                  --megreg 0.1 \
                  --eegreg 0.1 \
                  --inv ${datapath}/${subj_pre[m]}/${subj_dir[m]}/YourName_3L-EMEG-loose0.2-inv.fif     
]]><![CDATA[
done # subjects]]></screen><para>The --loose option requires dipoles to be almost perpendicular to the cortical surface, with some variation in the tangential plane (0.2 means that variation in the tangential dimension is one-fifth of the radial dimension). </para><para>The --megreg/eegreg option are &quot;regularization parameters&quot; for the covariance matrices. </para></article>