Average Thickness and Surface Area from AAL atlas CIVET

CIVET 1.1.12

Method

• You need to specify in CIVET the use of the AAL Atlas as such:

-surface-atlas ${QUARANTINE_PATH}/CIVET/1.1.12/build/CIVET-1.1.12/models/AAL_atlas_left.txt ${QUARANTINE_PATH}/CIVET/1.1.12/build/CIVET-1.1.12/models/AAL_atlas_right.txt

If you don't there will be no atlas files to process.

When CIVET is complete and all files have successfully processed, run this script:

#!/bin/bash

output=$1

if [[ -s $output ]]
then
  echo "Output file $output exists"
  exit 1
fi

echo "subject,PreCG.L_SA,SFGdor.L_SA,ORBsup.L_SA,MFG.L_SA,ORBmid.L_SA,IFGoperc.L_SA,IFGtriang.L_SA,ORBinf.L_SA,ROL.L_SA,SMA.L_SA,OLF.L_SA,SFGmed.L_SA,ORBsupmed.L_SA,REC.L_SA,INS.L_SA,ACG.L_SA,DCG.L_SA,PCG.L_SA,PHG.L_SA,CAL.L_SA,CUN.L_SA,LING.L_SA,SOG.L_SA,MOG.L_SA,IOG.L_SA,FFG.L_SA,PoCG.L_SA,SPG.L_SA,IPL.L_SA,SMG.L_SA,ANG.L_SA,PCUN.L_SA,PCL.L_SA,HES.L_SA,STG.L_SA,TPOsup.L_SA,MTG.L_SA,TPOmid.L_SA,ITG.L_SA,Total.L_SA,PreCG.R_SA,SFGdor.R_SA,ORBsup.R_SA,MFG.R_SA,ORBmid.R_SA,IFGoperc.R_SA,IFGtriang.R_SA,ORBinf.R_SA,ROL.R_SA,SMA.R_SA,OLF.R_SA,SFGmed.R_SA,ORBsupmed.R_SA,REC.R_SA,INS.R_SA,ACG.R_SA,DCG.R_SA,PCG.R_SA,PHG.R_SA,CAL.R_SA,CUN.R_SA,LING.R_SA,SOG.R_SA,MOG.R_SA,IOG.R_SA,FFG.R_SA,PoCG.R_SA,SPG.R_SA,IPL.R_SA,SMG.R_SA,ANG.R_SA,PCUN.R_SA,PCL.R_SA,HES.R_SA,STG.R_SA,TPOsup.R_SA,MTG.R_SA,TPOmid.R_SA,ITG.R_SA,Total.R_SA,PreCG.L_CT,SFGdor.L_CT,ORBsup.L_CT,MFG.L_CT,ORBmid.L_CT,IFGoperc.L_CT,IFGtriang.L_CT,ORBinf.L_CT,ROL.L_CT,SMA.L_CT,OLF.L_CT,SFGmed.L_CT,ORBsupmed.L_CT,REC.L_CT,INS.L_CT,ACG.L_CT,DCG.L_CT,PCG.L_CT,PHG.L_CT,CAL.L_CT,CUN.L_CT,LING.L_CT,SOG.L_CT,MOG.L_CT,IOG.L_CT,FFG.L_CT,PoCG.L_CT,SPG.L_CT,IPL.L_CT,SMG.L_CT,ANG.L_CT,PCUN.L_CT,PCL.L_CT,HES.L_CT,STG.L_CT,TPOsup.L_CT,MTG.L_CT,TPOmid.L_CT,ITG.L_CT,Mean.L_CT,PreCG.R_CT,SFGdor.R_CT,ORBsup.R_CT,MFG.R_CT,ORBmid.R_CT,IFGoperc.R_CT,IFGtriang.R_CT,ORBinf.R_CT,ROL.R_CT,SMA.R_CT,OLF.R_CT,SFGmed.R_CT,ORBsupmed.R_CT,REC.R_CT,INS.R_CT,ACG.R_CT,DCG.R_CT,PCG.R_CT,PHG.R_CT,CAL.R_CT,CUN.R_CT,LING.R_CT,SOG.R_CT,MOG.R_CT,IOG.R_CT,FFG.R_CT,PoCG.R_CT,SPG.R_CT,IPL.R_CT,SMG.R_CT,ANG.R_CT,PCUN.R_CT,PCL.R_CT,HES.R_CT,STG.R_CT,TPOsup.R_CT,MTG.R_CT,TPOmid.R_CT,ITG.R_CT,Mean.R_CT,PreCG.L_CV,SFGdor.L_CV,ORBsup.L_CV,MFG.L_CV,ORBmid.L_CV,IFGoperc.L_CV,IFGtriang.L_CV,ORBinf.L_CV,ROL.L_CV,SMA.L_CV,OLF.L_CV,SFGmed.L_CV,ORBsupmed.L_CV,REC.L_CV,INS.L_CV,ACG.L_CV,DCG.L_CV,PCG.L_CV,PHG.L_CV,CAL.L_CV,CUN.L_CV,LING.L_CV,SOG.L_CV,MOG.L_CV,IOG.L_CV,FFG.L_CV,PoCG.L_CV,SPG.L_CV,IPL.L_CV,SMG.L_CV,ANG.L_CV,PCUN.L_CV,PCL.L_CV,HES.L_CV,STG.L_CV,TPOsup.L_CV,MTG.L_CV,TPOmid.L_CV,ITG.L_CV,Total.L_CV,PreCG.R_CV,SFGdor.R_CV,ORBsup.R_CV,MFG.R_CV,ORBmid.R_CV,IFGoperc.R_CV,IFGtriang.R_CV,ORBinf.R_CV,ROL.R_CV,SMA.R_CV,OLF.R_CV,SFGmed.R_CV,ORBsupmed.R_CV,REC.R_CV,INS.R_CV,ACG.R_CV,DCG.R_CV,PCG.R_CV,PHG.R_CV,CAL.R_CV,CUN.R_CV,LING.R_CV,SOG.R_CV,MOG.R_CV,IOG.R_CV,FFG.R_CV,PoCG.R_CV,SPG.R_CV,IPL.R_CV,SMG.R_CV,ANG.R_CV,PCUN.R_CV,PCL.R_CV,HES.R_CV,STG.R_CV,TPOsup.R_CV,MTG.R_CV,TPOmid.R_CV,ITG.R_CV,Total.R_CV" > $output


for subject in $(ls -d output/* | grep -v References.txt | grep -v QC)
do
    echo $(basename $subject)
    echo -n $(basename $subject), >> $output
    for datatype in $subject/surfaces/*lobe_areas*dat $subject/surfaces/*lobe_thickness*dat $subject/surfaces/*lobe_volumes*dat
    do
      tr -s ' ' < $datatype | tail -n +4 | cut -d " " -f3 | tr '\n' ','
    done | sed 's/,$//g' >> $output
    echo "" >> $output
done

> bash get-AAL-values.sh outputfile.csv

CIVET 2.1.0

Run CIVET with the option -surface-atlas AAL

#!/bin/bash

output=$1

if [[ -s $output ]]
then
  echo "Output file $output exists"
  exit 1
fi

echo "subject,PreCG.L_SA,SFGdor.L_SA,ORBsup.L_SA,MFG.L_SA,ORBmid.L_SA,IFGoperc.L_SA,IFGtriang.L_SA,ORBinf.L_SA,ROL.L_SA,SMA.L_SA,OLF.L_SA,SFGmed.L_SA,ORBsupmed.L_SA,REC.L_SA,INS.L_SA,ACG.L_SA,DCG.L_SA,PCG.L_SA,PHG.L_SA,CAL.L_SA,CUN.L_SA,LING.L_SA,SOG.L_SA,MOG.L_SA,IOG.L_SA,FFG.L_SA,PoCG.L_SA,SPG.L_SA,SMG.L_SA,ANG.L_SA,PCUN.L_SA,PCL.L_SA,HES.L_SA,STG.L_SA,TPOsup.L_SA,MTG.L_SA,TPOmid.L_SA,ITG.L_SA,Total.L_SA,PreCG.R_SA,SFGdor.R_SA,ORBsup.R_SA,MFG.R_SA,ORBmid.R_SA,IFGoperc.R_SA,IFGtriang.R_SA,ORBinf.R_SA,ROL.R_SA,SMA.R_SA,OLF.R_SA,SFGmed.R_SA,ORBsupmed.R_SA,REC.R_SA,INS.R_SA,ACG.R_SA,DCG.R_SA,PCG.R_SA,PHG.R_SA,CAL.R_SA,CUN.R_SA,LING.R_SA,SOG.R_SA,MOG.R_SA,IOG.R_SA,FFG.R_SA,PoCG.R_SA,SPG.R_SA,SMG.R_SA,ANG.R_SA,PCUN.R_SA,PCL.R_SA,HES.R_SA,STG.R_SA,TPOsup.R_SA,MTG.R_SA,TPOmid.R_SA,ITG.R_SA,Total.R_SA,PreCG.L_CT,SFGdor.L_CT,ORBsup.L_CT,MFG.L_CT,ORBmid.L_CT,IFGoperc.L_CT,IFGtriang.L_CT,ORBinf.L_CT,ROL.L_CT,SMA.L_CT,OLF.L_CT,SFGmed.L_CT,ORBsupmed.L_CT,REC.L_CT,INS.L_CT,ACG.L_CT,DCG.L_CT,PCG.L_CT,PHG.L_CT,CAL.L_CT,CUN.L_CT,LING.L_CT,SOG.L_CT,MOG.L_CT,IOG.L_CT,FFG.L_CT,PoCG.L_CT,SPG.L_CT,SMG.L_CT,ANG.L_CT,PCUN.L_CT,PCL.L_CT,HES.L_CT,STG.L_CT,TPOsup.L_CT,MTG.L_CT,TPOmid.L_CT,ITG.L_CT,Mean.L_CT,PreCG.R_CT,SFGdor.R_CT,ORBsup.R_CT,MFG.R_CT,ORBmid.R_CT,IFGoperc.R_CT,IFGtriang.R_CT,ORBinf.R_CT,ROL.R_CT,SMA.R_CT,OLF.R_CT,SFGmed.R_CT,ORBsupmed.R_CT,REC.R_CT,INS.R_CT,ACG.R_CT,DCG.R_CT,PCG.R_CT,PHG.R_CT,CAL.R_CT,CUN.R_CT,LING.R_CT,SOG.R_CT,MOG.R_CT,IOG.R_CT,FFG.R_CT,PoCG.R_CT,SPG.R_CT,SMG.R_CT,ANG.R_CT,PCUN.R_CT,PCL.R_CT,HES.R_CT,STG.R_CT,TPOsup.R_CT,MTG.R_CT,TPOmid.R_CT,ITG.R_CT,Mean.R_CT,PreCG.L_CV,SFGdor.L_CV,ORBsup.L_CV,MFG.L_CV,ORBmid.L_CV,IFGoperc.L_CV,IFGtriang.L_CV,ORBinf.L_CV,ROL.L_CV,SMA.L_CV,OLF.L_CV,SFGmed.L_CV,ORBsupmed.L_CV,REC.L_CV,INS.L_CV,ACG.L_CV,DCG.L_CV,PCG.L_CV,PHG.L_CV,CAL.L_CV,CUN.L_CV,LING.L_CV,SOG.L_CV,MOG.L_CV,IOG.L_CV,FFG.L_CV,PoCG.L_CV,SPG.L_CV,SMG.L_CV,ANG.L_CV,PCUN.L_CV,PCL.L_CV,HES.L_CV,STG.L_CV,TPOsup.L_CV,MTG.L_CV,TPOmid.L_CV,ITG.L_CV,Total.L_CV,PreCG.R_CV,SFGdor.R_CV,ORBsup.R_CV,MFG.R_CV,ORBmid.R_CV,IFGoperc.R_CV,IFGtriang.R_CV,ORBinf.R_CV,ROL.R_CV,SMA.R_CV,OLF.R_CV,SFGmed.R_CV,ORBsupmed.R_CV,REC.R_CV,INS.R_CV,ACG.R_CV,DCG.R_CV,PCG.R_CV,PHG.R_CV,CAL.R_CV,CUN.R_CV,LING.R_CV,SOG.R_CV,MOG.R_CV,IOG.R_CV,FFG.R_CV,PoCG.R_CV,SPG.R_CV,SMG.R_CV,ANG.R_CV,PCUN.R_CV,PCL.R_CV,HES.R_CV,STG.R_CV,TPOsup.R_CV,MTG.R_CV,TPOmid.R_CV,ITG.R_CV,Total.R_CV" > $output


for subject in $(ls -d output/* | grep -v References.txt | grep -v QC)
do
    echo $(basename $subject)
    echo -n $(basename $subject), >> $output
    for datatype in $subject/surfaces/*lobe_areas_0mm*dat $subject/surfaces/*lobe_thickness*tlaplace_0mm*dat $subject/surfaces/*lobe_volumes_0mm*dat
    do
      tr -s ' ' < $datatype | tail -n +4 | cut -d " " -f3 | tr '\n' ','
    done | sed 's/,$//g' >> $output
    echo "" >> $output
done

> bash get-AAL-values.sh outputfile.csv