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#!/bin/bash
NUMPARAMS=$#
MAXITERATIONS=30x90x20
if [ ${#ANTSPATH} -le 3 ] ; then
echo we guess at your ants path
export ANTSPATH=${ANTSPATH:="/ipldev/scratch/aghayoor/ANTS/release/bin"} # EDIT THIS
fi
if [ ! -s ${ANTSPATH}/ANTS ] ; then
echo we cant find the ANTS program -- does not seem to exist. please \(re\)define \$ANTSPATH in your environment.
exit
fi
if [ $NUMPARAMS -lt 3 ]
then
echo " USAGE :: "
echo " sh ants.sh ImageDimension fixed.ext moving.ext OPTIONAL-OUTPREFIX OPTIONAL-max-iterations OPTIONAL-Labels-In-Fixed-Image-Space-To-Deform-To-Moving-Image Option-DoANTSQC "
echo " be sure to set ANTSPATH environment variable "
echo " Max-Iterations in form : JxKxL where "
echo " J = max iterations at coarsest resolution (here, reduce by power of 2^2) "
echo " K = middle resolution iterations ( here, reduce by power of 2 ) "
echo " L = fine resolution iterations ( here, full resolution ) -- this level takes much more time per iteration "
echo " an extra Ix before JxKxL would add another level "
echo " Default ierations is $MAXITERATIONS -- you can often get away with fewer for many apps "
echo " Other parameters are updates of the defaults used in the A. Klein evaluation paper in Neuroimage, 2009 "
exit
fi
#ANTSPATH=YOURANTSPATH
if [ ${#ANTSPATH} -le 0 ]
then
echo " Please set ANTSPATH=LocationOfYourAntsBinaries "
echo " Either set this in your profile or directly, here in the script. "
echo " For example : "
echo " ANTSPATH=/home/yourname/bin/ants/ "
exit
else
echo " ANTSPATH is $ANTSPATH "
fi
#initialization, here, is unbiased
DIM=$1
if [ ${#DIM} -gt 1 ]
then
echo " Problem with specified ImageDimension => User Specified Value = $DIM "
exit
fi
FIXED=$2
if [ ${#FIXED} -lt 1 -o ! -f $FIXED ]
then
echo " Problem with specified Fixed Image => User Specified Value = $FIXED "
exit
fi
MOVING=$3
if [ ${#MOVING} -lt 1 -o ! -f $MOVING ]
then
echo " Problem with specified Moving Image => User Specified Value = $MOVING "
exit
fi
OUTPUTNAME=` echo $MOVING | cut -d '.' -f 1 `
if [ $NUMPARAMS -gt 4 ]
then
MAXITERATIONS=$5
fi
LABELIMAGE=0
if [ $NUMPARAMS -gt 5 ]
then
LABELIMAGE=$6
fi
DoANTSQC=0
if [ $NUMPARAMS -gt 6 ]
then
DoANTSQC=$7
fi
if [ $NUMPARAMS -gt 3 ]
then
OUTPUTNAME=${4}
fi
# Mapping Parameters
TRANSFORMATION=SyN[0.25]
ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
NUMLEVELS=${#ITERATLEVEL[@]}
echo $NUMLEVELS
REGULARIZATION=Gauss[3,0]
METRIC=CC[
METRICPARAMS=1,4]
# echo " $METRICPARAMS & $METRIC "
# exit
echo " ANTSPATH is $ANTSPATH "
echo " Mapping Parameters :: "
echo " Transformation is: $TRANSFORMATION "
echo " MaxIterations : $MAXITERATIONS "
echo " Number Of MultiResolution Levels $NUMLEVELS "
echo " Regularization : $REGULARIZATION "
echo " Metric : ${METRIC} "
echo " OutputName : $OUTPUTNAME "
echo " "
echo " if the files and parameters are all ok then uncomment the exit call below this line "
echo " "
#exit
if [[ ! -s ${OUTPUTNAME}repaired.nii.gz ]] ; then
${ANTSPATH}/N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}repaired.nii.gz -s 2 -c [50x50x50x50,0.000001] -b [200]
# ${ANTSPATH}/N3BiasFieldCorrection $DIM $MOVING ${OUTPUTNAME}repaired.nii.gz 4
fi
exe=" ${ANTSPATH}/ANTS $DIM -m ${METRIC}${FIXED},${OUTPUTNAME}repaired.nii.gz,${METRICPARAMS} -t $TRANSFORMATION -r $REGULARIZATION -o ${OUTPUTNAME} -i $MAXITERATIONS --use-Histogram-Matching --number-of-affine-iterations 10000x10000x10000x10000x10000 --MI-option 32x16000 "
echo " $exe "
$exe
#below, some affine options
#--MI-option 16x8000 #-a InitAffine.txt --continue-affine 0
${ANTSPATH}/WarpImageMultiTransform $DIM ${OUTPUTNAME}repaired.nii.gz ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}
if [ ${#LABELIMAGE} -gt 3 ]
then
${ANTSPATH}/WarpImageMultiTransform $DIM $LABELIMAGE ${OUTPUTNAME}labeled.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${MOVING} --use-NN
fi
exit
if [ $DoANTSQC -eq 1 ] ; then
# measure image similarity
for SIM in 0 1 2 ; do
${ANTSPATH}/MeasureImageSimilarity $DIM $SIM $FIXED ${OUTPUTNAME}deformed.nii.gz
done
# measure dice overlap and mds
${ANTSPATH}/ThresholdImage $DIM $FIXED ${OUTPUTNAME}fixthresh.nii.gz Otsu 4
${ANTSPATH}/ThresholdImage $DIM $MOVING ${OUTPUTNAME}movthresh.nii.gz Otsu 4
${ANTSPATH}/WarpImageMultiTransform $DIM ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED} --use-NN
${ANTSPATH}/ImageMath $DIM ${OUTPUTNAME}dicestats.txt DiceAndMinDistSum ${OUTPUTNAME}fixthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}mindistsum.nii.gz
# labelstats for jacobian wrt segmenation
# below, to compose
# ${ANTSPATH}ComposeMultiTransform $DIM ${OUTPUTNAME}CompWarp.nii.gz -R $FIXED ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt
# ${ANTSPATH}CreateJacobianDeterminantImage $DIM ${OUTPUTNAME}CompWarp.nii.gz ${OUTPUTNAME}jacobian.nii.gz 0
# ${ANTSPATH}ImageMath $DIM ${OUTPUTNAME}movlabstat.txt LabelStats ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz
# ${ANTSPATH}ImageMath $DIM ${OUTPUTNAME}jaclabstat.txt LabelStats ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}jacobian.nii.gz
# we compare the output of these last two lines:
# the Volume of the movlabstat computation vs. the mass of the jaclabstat
fi
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