AnalyzingData/MNE_Labels - Meg Wiki

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Processing ROIs

ROIs in MNE are defined as "label" files. Freesurfer already creates a parcellation of the cortical surface in various regions of interest (see subdirectory "label" in your subjects' MRI directory). These can be converted to label files for MNE. If you've morphed all your individual STC-files to an average brain (called "average" in the example), you can create MNE-labels from these:

mne_annot2labels --subject average --parc aparc

This will result in files such as "fusiform-lh.label" in the MRI label subdirectory. These are text files that you can read into a text editor etc.

#

## Your variables:

datapath='/myMEGdatapath/'    # root directory for your MEG data

MRIpath='/myMRIdirectory/'    # where your MRI subdirectories are

outpath='/myoutputdirectory'  # where the results should go



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


# subjects names used for MRI data
subjects=(\
        'Subject1' \
        'Subject1' \
        'Subject1' \
)

# 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' \
        )

# labels to be processed        
labels=(\
        'frontalpole'\
        'fusiform'\
        'inferiorparietal'\
        'inferiortemporal'\
        'insula'\
        'lateraloccipital'\
        'lateralorbitofrontal'\
        'lingual'\
        'medialorbitofrontal'\
        'middletemporal'\
        'paracentral'\
        'parahippocampal'\
        'parsopercularis'\
        'parsorbitalis'\
        'parstriangularis'\
        'pericalcarine'\
        'postcentral'\
        'posteriorcingulate'\
        'precentral'\
        'precuneus'\
        'rostralanteriorcingulate'\
        'rostralmiddlefrontal'\
        'superiorfrontal'\
        'superiorparietal'\
        'superiortemporal'\
        'supramarginal'\
        'temporalpole'\
        'transversetemporal'\
        )
        
hemispheres=(\
        'lh' \
        'rh' \
        )
        

#####################
# SCRIPT BEGINS HERE:

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

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

nlabels=${#labels[*]}
lastlabel=`expr $nlabels - 1`

nhemispheres=${#hemispheres[*]}
lasthemisphere=`expr $nhemispheres - 1`



# Processing:

for ss in `seq 0 ${lastsubj}`
do
  echo " "
  echo " Computing movies  for SUBJECT  ${subjects[m]}"
  echo " "
        for cc in `seq 0 ${lastcond}`
        do
          echo " "
          echo " Computing movies for condition  ${conds[c]}"
          echo " "
                        for bb in `seq 0 ${lastlabel}`
                        do
                          echo " "
                          echo " Computing movies  for label  ${labels[b]}"
                          echo " "                      
                                for hh in `seq 0 ${lasthemisphere}`
                                do
                                echo " "
                                echo " Computing movies  for hemisphere  ${hemispheres[h]}"
                                echo " "        
                                                                                        
                                        mne_make_movie \
                                          --subject ${subjects[ss]} \
                                          --stcin ${STCpath}/${subj_pre[m]}_0${subjects[m]}_${conds[c]}_-${hemispheres[h]}.stc \
                                          --label ${MRIpath}/average/label/${labels[b]}-${hemispheres[h]}.label \
                                          --labelverts \
                                          --labeltag -${subjects[m]}_${conds[c]}.amp \
                                          --labeloutdir ${outpath}

                                done # hemispheres
                                
                        done # labels                   
        
        done # conditions

done # subjects