BaMoS_PreprocessingOnly.sh

#!/bin/bash
# set -x

#### WARNING !!!! THIS SCRIPT ASSUMES THAT THE FLAIR IMAGE WILL BE REGISTERED TO THE T1 IMAGE. ALL RESULTS SHOULD BE VISUALISED IN THE T1 SPACE. ALL SCANS ARE PUT IN THE RAS ORIENTATION BY DEFAULT

ArrayModalities=("T1" "T2" "FLAIR" "PD" "SWI")
ListCorr=(102 103 187 188 47 48 49)
AW=0
JC=0
MRE=1
OptSP=0
OptCL=2
OptOL=0
OptWMI=2 # If >0, indicates that a higher level of sensitivity to lesion should be considered from voxels coming from WMI
TVS=1
arrayMod=("T1" "FLAIR" )
arrayModNumber=(1 3)

RuleFileName=/cluster/project0/SegBiASM/DataToTryBaMoS/GenericRule_CSF.txt
NameGMatrix=/cluster/project0/SegBiASM/DataToTryBaMoS/GMatrix4_Low3.txt

Mem=7.9
OW=0.01
JC=1
Opt=${OptCross}
OptVL=1
OptSP=1
OptTA=1
OptTxt=Test
Opt=TA
# Flags for levels of correction
flag_NoCerrebellum=0
flag_furtherCorr=1
flag_corrDGM=1
 
PathReg=/share/apps/cmic/niftyreg-10.4.15/bin
PathReg=/share/apps/cmic/niftyreg_v1.5.43/bin
PathSeg=/home/csudre/NiftySeg_0.9.4/build_comic2/seg-apps
PathFSL=/share/apps/fsl-5.0.8/bin
PathICBM=/cluster/project0/SegBiASM/ICBM_Priors


if [ $# -lt 5 ] || [ $# -gt 10 ]
then
	echo ""
	echo "*******************************************************************************"
	echo "Usage: $0 ID ImageFLAIR ImageT1 GIF_results_path PathResults JUMP_START Opt Mem Space"
	echo "*******************************************************************************"
	echo ""
	exit
fi

ID=$1
ImageFLAIR=$2
ImageT1=$3
GIF_results_path=$4
PathResults=$5
JUMP_START=$6
Opt=$7
Mem=$8
Space=$9
Verbose=$10
PN=${ID}
ModalitiesTot=T1FLAIR
echo ${PathScratch}
PathGIF=${GIF_results_path}

if [ ! -d $PathResults ]
then
    mkdir $PathResults
fi

NameScript=${PathResults}/ScriptBaMoS_${PN}_${Opt}.sh
echo \#\!/bin/sh > ${NameScript}
echo "#$ -S /bin/bash" > ${NameScript}
PathScratch=/scratch0/csudre/${ID}_BaMoSPreProc_${Opt}_${JOB_ID}
echo "mkdir -p ${PathScratch} ">> ${NameScript}
ChangePathString="-inChangePath ${PathScratch}/"

echo "cp ${PathResults}/* ${PathScratch}/." >> ${NameScript}


StringPriorsIO=" "

echo "echo "Reorientation to standard space of T1 image" " >> ${NameScript}
    echo "cp ${ImageT1} ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}
    #echo "${PathFSL}/fslreorient2std ${ImageT1} ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}
    
    echo "${PathSeg}/seg_maths ${PathScratch}/T1_${ID}.nii.gz -odt float ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}

    echo "echo "Alignment of FLAIR image to T1"" >> ${NameScript}
    echo "${PathReg}/reg_aladin -ref ${PathScratch}/T1_${ID}.nii.gz -flo ${ImageFLAIR} -aff ${PathScratch}/Aff_FLAIRtoT1.txt -res ${PathScratch}/FLAIR_${ID}.nii.gz -rigOnly" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/FLAIR_${ID}.nii.gz -odt float ${PathScratch}/FLAIR_${ID}.nii.gz" >> ${NameScript}

    # echo "Alignment of T2 image to FLAIR"


    echo "echo "Reorientation of T1 TIV mask and binarisation" " >> ${NameScript}
    echo "cp ${GIF_results_path}/*TIV* ${PathScratch}/Mask_${ID}.nii.gz" >> ${NameScript}
    #echo "${PathFSL}/fslreorient2std ${GIF_results_path}/*TIV* ${PathScratch}/Mask_${ID}.nii.gz" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/Mask_${ID}.nii.gz -bin -odt char ${PathScratch}/GIF_${ID}_B1.nii.gz" >> ${NameScript}

    echo "echo "Reorientation of GIF priors and creation of GIF priors array"" >> ${NameScript}
    echo "cp ${GIF_results_path}/*prior* ${PathScratch}/GIF_prior_${ID}.nii.gz" >> ${NameScript}
    #echo "${PathFSL}/fslreorient2std ${GIF_results_path}/*prior* ${PathScratch}/GIF_prior_${ID}.nii.gz" >> ${NameScript}
    if ((${Space}>1))
then
echo "cp ${ImageFLAIR} ${PathScratch}/FLAIR_${ID}.nii.gz" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/FLAIR_${ID}.nii.gz -odt float ${PathScratch}/FLAIR_${ID}.nii.gz" >> ${NameScript}

echo "echo "Alignment of T1 image to FLAIR"" >> ${NameScript}
    echo "${PathReg}/reg_aladin -ref ${PathScratch}/FLAIR_${ID}.nii.gz -flo ${ImageT1} -aff ${PathScratch}/Aff_T1toFLAIR.txt -res ${PathScratch}/T1_${ID}.nii.gz -rigOnly" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/T1_${ID}.nii.gz -odt float ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}
for p in Segmentation prior TIV	Parcellation
do
echo "${PathReg}/reg_resample -inter 1 -flo  ${PathGIF}/*${p}* -res ${PathScratch}/GIF_${ID}_${p}.nii.gz -ref ${PathScratch}/FLAIR_${ID}.nii.gz -aff ${PathScratch}/Aff_T1toFLAIR.txt" >> ${NameScript}
echo "${PathReg}/reg_resample -inter 1 -flo  ${PathGIF}/*${p}* -res ${PathScratch}/GIF_${p}_${ID}.nii.gz -ref ${PathScratch}/FLAIR_${ID}.nii.gz -aff ${PathScratch}/Aff_T1toFLAIR.txt" >> ${NameScript}
done

else
echo "cp ${ImageT1} ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}
echo "${PathSeg}/seg_maths ${PathScratch}/T1_${ID}.nii.gz -odt float ${PathScratch}/T1_${ID}.nii.gz" >> ${NameScript}
echo "echo "Alignment of FLAIR image to T1"" >> ${NameScript}
    echo "${PathReg}/reg_aladin -ref ${PathScratch}/T1_${ID}.nii.gz -flo ${ImageFLAIR} -aff ${PathScratch}/Aff_FLAIRtoT1.txt -res ${PathScratch}/FLAIR_${ID}.nii.gz -rigOnly" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/FLAIR_${ID}.nii.gz -odt float ${PathScratch}/FLAIR_${ID}.nii.gz" >> ${NameScript}
for p in Segmentation prior TIV Parcellation
do
echo "cp ${PathGIF}/*${p}* ${PathScratch}/GIF_${ID}_${p}.nii.gz" >> ${NameScript}
echo "cp ${PathGIF}/*${p}* ${PathScratch}/GIF_${p}_${ID}.nii.gz" >> ${NameScript}
done



echo "${PathSeg}/seg_maths ${PathScratch}/GIF_${ID}_TIV.nii.gz -odt char ${PathScratch}/GIF_${ID}_B1.nii.gz" >>${NameScript}
echo "${PathSeg}/seg_maths ${PathScratch}/GIF_${ID}_TIV.nii.gz -odt char ${PathScratch}/GIF_B1_${ID}.nii.gz" >> ${NameScript}

echo "echo "Reorientation of GIF segmentation"" >> ${NameScript}

    echo "cp ${PathScratch}/* ${PathResults}/." >> ${NameScript}

    PriorsArray=("Out" "CSF" "CGM" "WMI" "DGM" "Brainstem")
    array_Priors=()

    for ((p=0;p<6;p++))
    do
       echo " ${PathSeg}/seg_maths ${PathScratch}/GIF_prior* -tp ${p} ${PathScratch}/GIF_${PriorsArray[p]}_${ID}.nii.gz" >> ${NameScript}
    done


    echo "echo "Registration of ICBM template and creation of ICBM atlases"" >> ${NameScript}
    echo "${PathReg}/reg_aladin -ref ${PathScratch}/T1_${ID}.nii.gz -flo ${PathICBM}/ICBM_Template.nii.gz -aff ${PathScratch}/${ID}_AffTransf.txt" >> ${NameScript}
    echo "${PathReg}/reg_f3d -ref ${PathScratch}/T1_${ID}.nii.gz -flo ${PathICBM}/ICBM_Template.nii.gz -aff ${PathScratch}/${ID}_AffTransf.txt -cpp ${PathScratch}/${ID}_cpp.nii.gz" >> ${NameScript}

    echo "cp ${PathScratch}/*cpp* ${PathResults}/." >> ${NameScript} 

    for p in CGM DGM ECSF ICSF Out WM
    do
        echo "${PathReg}/reg_resample -ref ${PathScratch}/T1_${ID}.nii.gz -flo ${PathICBM}/ICBM_${p}.nii.gz -cpp ${PathScratch}/${ID}_cpp.nii.gz -res ${PathScratch}/ICBM_${p}_${ID}.nii.gz" >> ${NameScript}
    done

    echo "${PathSeg}/seg_maths ${PathScratch}/ICBM_DGM_${ID}.nii.gz -add ${PathScratch}/ICBM_CGM_${ID}.nii.gz ${PathScratch}/ICBM_GM_${ID}.nii.gz" >> ${NameScript}

    echo "${PathSeg}/seg_maths ${PathScratch}/ICBM_ICSF_${ID}.nii.gz -add ${PathScratch}/ICBM_ECSF_${ID}.nii.gz ${PathScratch}/ICBM_CSFs_${ID}.nii.gz" >> ${NameScript}

    echo "${PathSeg}/seg_maths ${PathScratch}/ICBM_DGM_${ID}.nii.gz -bin -mul ${PathScratch}/GIF_DGM_${ID}.nii.gz ${PathScratch}/GIF_DGM_${ID}_bis.nii.gz" >> ${NameScript}
    
echo "${PathSeg}/seg_maths ${PathScratch}/GIF_CGM_${ID}.nii.gz -add ${PathScratch}/GIF_DGM_${ID}_bis.nii.gz ${PathScratch}/GIF_GM_${ID}.nii.gz" >> ${NameScript}
    echo "${PathSeg}/seg_maths ${PathScratch}/GIF_DGM_${ID}.nii.gz -sub ${PathScratch}/GIF_DGM_${ID}_bis.nii.gz -add ${PathScratch}/GIF_WMI_${ID}.nii.gz ${PathScratch}/GIF_WMI_${ID}_bis.nii.gz" >> ${NameScript}

    echo "${PathSeg}/seg_maths ${PathScratch}/GIF_WMI_${ID}_bis.nii.gz -add ${PathScratch}/GIF_Brainstem_${ID}.nii.gz ${PathScratch}/GIF_WM_${ID}.nii.gz" >> ${NameScript}

    

    arrayImage=()
    arrayModNumber=()
    echo "echo "Modalities to put are ${arrayMod[0]}"" >> ${NameScript}
    for ((m=0;m<${#arrayMod[@]};m++))
    do
        for ((pos=0;pos<${#ArrayModalities[@]};pos++))
        do
            TmpModa=${ArrayModalities[pos]}
            TmptestModa=${arrayMod[m]}
            Subtracted="${TmptestModa/$TmpModa}"
    #echo ${#Subtracted}
            if ((${#Subtracted}<${#TmptestModa}))
            then
    # echo "Testing between $TmptestModa $TmpModa"
                FinModa=$((pos+1))
                arrayModNumber=(${arrayModNumber[*]} $FinModa)
            fi
        done
        arrayImage=( "${arrayImage[*]}" "${PathScratch}/${arrayMod[m]}_${ID}.nii.gz" )
    done

array_Priors=("${PathScratch}/GIF_GM_${ID}.nii.gz" "${PathScratch}/GIF_WM_${ID}.nii.gz" "${PathScratch}/GIF_CSF_${ID}.nii.gz" "${PathScratch}/GIF_Out_${ID}.nii.gz")
    echo "echo "Segmentation SegBiASM"" >> ${NameScript}
    #${PathSeg}/Seg_BiASM -in 2 ${arrayImage[0]} ${arrayImage[1]} -priors 4 ${array_Priors[*]} -mask ${PathScratch}/GIF_${ID}_B1.nii.gz -out 2 ${PathScratch}/${arrayMod[0]}${arrayMod[1]}_BiASM_${ID}_${Opt}.nii.gz ${PathScratch}/${arrayMod[0]}${arrayMod[1]}_BiASMG_${ID}.nii.gz -txt_out ${PathScratch}/${arrayMod[0]}${arrayMod[1]}_BiASM_${ID}_${Opt}.txt -bc_order 3 -CovPriors 8 -BFP 1 -maxRunEM ${MRE} -AtlasSmoothing 1 1 -AtlasWeight 1 ${AW}  -SMOrder 0 -KernelSize 3 -PriorsKept 5 -VLkappa 1.5 -unifSplitW 0.5 -varInitUnif 1 -uniformTC 4 -deleteUW 1 -outliersM 3 -outliersW ${OW} -init_splitUnif 0 -splitAccept 0 -unifTot 1 -MRF 1 -GMRF ${NameGMatrix} -juxtaCorr ${JC} -progMod 0 -priorDGM ${PathScratch}/ICBM_DGM_${ID}.nii.gz -TypicalityAtlas ${OptTA} ${StringPriorsIO}




echo "${PathSeg}/Seg_BiASM -VLkappa 3 -in 2 ${arrayImage[*]} -priors 4 ${array_Priors[*]} -mask ${PathScratch}/GIF_${ID}_B1.nii.gz -out 2 ${PathScratch}/${ModalitiesTot}_BiASM_${ID}_${Opt}.nii.gz ${PathScratch}/${ModalitiesTot}_BiASMG_${ID}.nii.gz -txt_out ${PathScratch}/${ModalitiesTot}_BiASM_${ID}_${Opt}.txt -bc_order 3 -CovPriors 8 -BFP 1 -maxRunEM ${MRE} -AtlasSmoothing 1 1 -AtlasWeight 1 ${AW}  -SMOrder 0 -KernelSize 3 -PriorsKept 5 -unifSplitW 0.5 -varInitUnif 1 -uniformTC 4 -deleteUW 1 -outliersM 3 -outliersW ${OW} -init_splitUnif 0 -splitAccept 0 -unifTot 1 -MRF 1 -GMRF ${NameGMatrix} -juxtaCorr ${JC} -progMod 0 -priorDGM ${PathScratch}/ICBM_DGM_${ID}.nii.gz -TypicalityAtlas ${OptTA}" >> ${NameScript}

echo "rm ${PathScratch}/BG* ${PathScratch}/MRF*" >> ${NameScript}
echo "cp ${PathScratch}/T1FLAIR* ${PathResults}/. " >> ${NameScript}
echo "cp ${PathScratch}/Data*T1FLAIR* ${PathResults}/. " >> ${NameScript}

echo "echo "Lesion segmentation"" >> ${NameScript}
echo "${PathSeg}/Seg_Analysis  -inTxt2 ${PathScratch}/${ModalitiesTot}_BiASM_${ID}_${Opt}.txt ${PathScratch}/${ModalitiesTot}_BiASM_${ID}_${Opt}.nii.gz -mask ${PathScratch}/GIF_${ID}_B1.nii.gz -Package 1 -SegType 1 -WeightedSeg 3 3 1 -connect -correct -inModa 2 1 3 -inRuleTxt ${RuleFileName} -WMCard 1 -inPriorsICSF ${PathScratch}/ICBM_ICSF_${ID}.nii.gz -inPriorsDGM ${PathScratch}/ICBM_DGM_${ID}.nii.gz -inPriorsCGM ${PathScratch}/ICBM_CGM_${ID}.nii.gz -inPriorsECSF ${PathScratch}/ICBM_ECSF_${ID}.nii.gz -TO 1 -ParcellationIn ${PathScratch}/GIF_Parcellation_${ID}.nii.gz -typeVentrSeg ${TVS} -Simple -Secondary 60 -juxtaCorr ${JC}  -SP ${OptSP} -LevelCorrection ${OptCL} ${ChangePathString} -LesWMI ${OptWMI} -Neigh 18" >> ${NameScript}



function finish {
     rm -rf ${PathScratch}
}
echo "trap finish EXIT ERR " >> ${NameScript}
echo "rm -rf ${PathScratch}" >> ${NameScript}



qsub -l h_rt=1:0:0 -l tmem=${Mem}G -l h_vmem=${Mem}G -N BaMoSLes${ID} ${NameScript}	

function finish {
    rm -rf ${PathScratch}
}

echo "trap finish EXIT ERR" >> ${NameScript}


#${PathSeg}/Seg_Analysis -inToAnalyse ${PathScratch}/CorrectMergedLesion_${ID}_corr.nii.gz -minSize 3 -Neigh 6