antsIntroduction.sh

#!/bin/bash

VERSION="0.0.8 dev"

# trap keyboard interrupt (control-c)
trap control_c SIGINT

if ! command -v ANTS &> /dev/null
then
  echo "ANTS program can't be found. Please (re)define \$PATH in your environment."
  exit
fi

function Usage {
    cat <<USAGE

Usage:

`basename $0` -d ImageDimension -r fixed.ext -i moving.ext

Compulsory arguments:

-d:  ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration)

-i:  Input image

-r:  Reference image

Optional arguments

-f:  Force script to proceed even if headers may be incompatible (0 = no, 1 = yes (default))

-l:  Labels-In-Fixed-Image-Space-To-Deform-To-Moving-Image (default is off)

-m:  Max-iterations

-n:  N4BiasFieldCorrection of moving image ( 0 = off (default); 1 = on )

-o:  OUTPREFIX; A prefix that is prepended to all output files.

-q:  Perform a Quality Check (QC) of the result ( 0 = off (default); 1 = on ).

-s:  Type of similarity metric used for registration.

-t:  Type of transformation model used for registration.

 You can change the values for each of these methods in this script.

 Use `basename $0` -h for extended help.
--------------------------------------------------------------------------------------
 ANTS was created by:
 Brian B. Avants, Nick Tustison and Gang Song
 Penn Image Computing And Science Laboratory
 University of Pennsylvania
--------------------------------------------------------------------------------------
 script written by N.M. van Strien, www.mri-tutorial.com | NTNU MR-Center
--------------------------------------------------------------------------------------

USAGE
    exit 1
}

function Help {
    cat <<Help

 `basename $0` will perform an elastic or diffeomorphic transformation of the moving image
 into the fixed image space.

 this script encodes some reasonable defaults for the parameters and is useful for testing and comparing methods

 ANTS will test for convergence after 10 iterations to prevent the program from running forever.
 Convergence is determined by occurrence of a flat or inflection point in the similarity term time series.

 Usage:

 `basename $0` -d ImageDimension -r fixed.ext -i moving.ext

 Compulsory arguments:

 -d:  ImageDimension: 2 or 3 (for 2 or 3 Dimensional registration)

 -i:  Input image

 -r:  Reference image

 Optional arguments

 -f:  Force script to proceed even if headers may be incompatible (0 = no, 1 = yes (default)). ANTS will perform
      a basic header sanity check. If you want to trust it, use -f 0.

 -l:  Labels-In-Fixed-Image-Space-To-Deform-To-Moving-Image (default is off)

      This maps a template labeled image to the target space --- for instance
      for template-based segmentation. Applies the inverse warp to the labels
      to estimate the label positions in target space.

 -m:  Max-iterations

      Max-Iterations in form: JxKxL where
	J = max iterations at coarsest resolution (here, reduce by power of 2^2)
	K = middle resolution iterations (here,reduce by power of 2)
	L = fine resolution iterations (here, full resolution) !!this level takes much
            more time per iteration!!

	Adding an extra value before JxKxL (i.e. resulting in IxJxKxL) would add another
	iteration level.

 -n:  N4BiasFieldCorrection of moving image ( 0 = off (default); 1 = on )

 -o:  OUTPREFIX; A prefix that is prepended to all output files.

 -q:  Perform a Quality Check (QC) of the result ( 0 = off (default); 1 = on ).

      calculates:
      - image similarity - 0 = intensity difference, 1 = correlation, 2 = mutual information

      - dice overlap

	Dice Overlap is a standard measure for segmentation accuracy that shows a
	percentage of agreement between two segmentations.  It is defined:

	D =  2  #(A U B) /  (  #A + #B )

	where the U indicates union and  # indicates the number of voxels in
	the labeled object.

     - min-dist-sum from the approximately segmentedbrain (3 tissues and background)

	Min-dist-sum is the minimum distance sum which is the total shortest distance
	between A and B evaluated over the object surfaces. This tells the overall
	euclidean disagreement between the boundaries of the labeled regions.

 -s:  Type of similarity metric used for registration.

	For intramodal image registration, use:
	CC = cross-correlation
	MI = mutual information
	PR = probability mapping (default)
	MSQ = mean square difference

	For intermodal image registration, use:
	MI = mutual information
	PR = probability mapping (default)

	You can change the values for each of these methods in this script.

 -t:  Type of transformation model used for registration.

	For rigid image registration, use:
	RI = Purely rigid
	RA = Affine rigid

	For elastic image registration, use:
	EL = Elastic transformation model (less deformation possible)

	For diffeomorphic image registration, use:
	SY = SyN with time (default) with arbitrary number of time points in time discretization
	S2 = SyN with time optimized specifically for 2 time points in the time discretization
	GR = Greedy SyN
	EX = Exponential
        DD = Diffeomorphic Demons style exponential mapping

 You can change the values for each of these methods in this script.

--------------------------------------------------------------------------------------

 Default number of iterations is $MAXITERATIONS. Most often this is sufficient.

 The other parameters in this script are updates to the defaults that were used in the
 Neuroimage 2009 paper; for more information read:

 - Klein A, et al. 2009. Evaluation of 14 nonlinear deformation algorithms applied to
 human brain MRI registration. NeuroImage, 46(3):786-802

 http://www.ncbi.nlm.nih.gov/pubmed/19195496

--------------------------------------------------------------------------------------
 I/O Data Formats In ANTS
--------------------------------------------------------------------------------------
 see: http://picsl.upenn.edu/ANTS/ioants.php

--------------------------------------------------------------------------------------
 Get the latest ANTS version at:
 http://sourceforge.net/projects/advants/

 Read the ANTS documentation at:
 http://picsl.upenn.edu/ANTS/
--------------------------------------------------------------------------------------
 ANTS was created by:
 Brian B. Avants, Nick Tustison and Gang Song
 Penn Image Computing And Science Laboratory
 University of Pennsylvania

 script adapted by N.M. van Strien, www.mri-tutorial.com | NTNU MR-Center
--------------------------------------------------------------------------------------

Help
    exit 0
}

function reportMappingParameters {
    cat <<reportMappingParameters
--------------------------------------------------------------------------------------
Mapping parameters
--------------------------------------------------------------------------------------
Dimensionality:				$DIM
Fixed image:				$FIXED
Moving image:				$MOVING
Use label image:			$LABELIMAGE
N4BiasFieldCorrection:			$N4CORRECT
DoANTS Quality Check: 			$DoANTSQC
Similarity Metric:			$METRICTYPE
Transformation:				$TRANSFORMATIONTYPE
Regularization:				$REGULARIZATION
MaxIterations:				$MAXITERATIONS
Number Of MultiResolution Levels:	$NUMLEVELS
OutputName prefix:			$OUTPUTNAME
--------------------------------------------------------------------------------------
reportMappingParameters
}

function dataCheck {
    cat <<dataCheck
--------------------------------------------------------------------------------------
Data integrity check failed
--------------------------------------------------------------------------------------
There seems to be a problem with the header definitions of the input files. This
script has tried to repair this issue automatically by invoking:

ImageMath $DIM ${OUTPUTNAME}repaired.nii.gz CompareHeadersAndImages $FIXED $MOVING

The repaired image is:

${OUTPUTNAME}repaired.nii.gz

and should be located in:

$currentdir

Try passing the original input image to antsaffine.sh. If the affine normalization succeeds,
you can safely ignore this warning. Otherwise, you may need to reorient your date to correct
the orientation incompatibility.
--------------------------------------------------------------------------------------

dataCheck

}


cleanup()
{
  echo "\n*** Performing cleanup, please wait ***\n"
  
  runningANTSpids=$( ps --ppid $$ -o pid= )
  
  for thePID in $runningANTSpids
  do
      echo "killing:  ${thePID}"
      kill ${thePID}
  done
  
  return $?
}

control_c()
# run if user hits control-c
{
  echo -en "\n*** User pressed CTRL + C ***\n"
  cleanup
  exit $?
  echo -en "\n*** Script cancelled by user ***\n"
}

time_start=`date +%s`
currentdir=`pwd`
nargs=$#

MAXITERATIONS=30x90x20
LABELIMAGE=0 # initialize optional parameter
DoANTSQC=0 # initialize optional parameter
METRICTYPE="PR" # initialize optional parameter
TRANSFORMATIONTYPE="GR" # initialize optional parameter
N4CORRECT=0 # initialize optional parameter
RIGID=0
IGNORE_HDR_WARNING=1

if [ "$1" == "-h" ]
then
Help >&2
elif [ $nargs -lt 6 ]
then
Usage >&2
fi

# reading command line arguments
while getopts "d:f:r:i:h:o:m:n:l:q:s:t:" OPT
do
    case $OPT in
    h) #help
        echo "$Help"
        exit 0
        ;;
    d) #dimensions
        DIM=$OPTARG
        ;;
    f) #ignore header warnings
        IGNORE_HDR_WARNING=$OPTARG
        ;;
    i) #input or moving image
        MOVING=$OPTARG
        OUTPUTNAME=` echo basename $MOVING | cut -d '.' -f 1 `
        ;;
    l) #use label image
        LABELIMAGE=$OPTARG
        ;;
    m) #max iterations other than default
        MAXITERATIONS=$OPTARG
        ;;
    n) #apply bias field correction
        N4CORRECT=$OPTARG
        ;;
    o) #output name prefix
        OUTPUTNAME=$OPTARG
        ;;
    q) #perform quality check after running ANTS
        DoANTSQC=$OPTARG
        ;;
    r) #ref image
        FIXED=$OPTARG
        ;;
    s) #similarity model
        METRICTYPE=$OPTARG
        ;;
    t) #transformation model
        TRANSFORMATIONTYPE=$OPTARG
        ;;
    \?) # getopts issues an error message
        echo "$USAGE" >&2
        exit 1
        ;;
    esac
done

tmpdir=${currentdir}/tmp_${RANDOM}_${RANDOM}_${RANDOM}_$$
(umask 077 && mkdir ${tmpdir}) || {
	echo "Could not create temporary directory! Exiting." 1>&2
	exit 1
}

cp ${FIXED} ${MOVING} ${tmpdir}/
cd ${tmpdir}/

FIXED=`basename ${FIXED}`
MOVING=`basename ${MOVING}`

# test input parameter before starting
if  [ ${#DIM} -gt 1 ]
then
echo "Problem with specified ImageDimension => User Specified Value = $DIM"
exit
fi

if  [ ${#FIXED} -lt 1 -o  ! -f $FIXED ]
then
echo "Problem with specified Fixed Image => User Specified Value = $FIXED"
exit
fi

if  [ ${#MOVING} -lt 1 -o  ! -f $MOVING ]
then
echo "Problem with specified Moving Image => User Specified Value = $MOVING"
exit
fi

# check the image headers
echo "input files: checking"
compareheaders=`ImageMath $DIM ${OUTPUTNAME}repaired.nii.gz CompareHeadersAndImages $FIXED $MOVING  | grep FailureState | cut -d ' ' -f 4 `

if [[ $compareheaders -ne 0 ]] ; then
  dataCheck
  if [[ $IGNORE_HDR_WARNING -eq 0 ]] ; then
      exit 1
  fi
else
  echo "input files: check passed"
fi

ITERATLEVEL=(`echo $MAXITERATIONS | tr 'x' ' '`)
NUMLEVELS=${#ITERATLEVEL[@]}

# Transformation model
if [ "${TRANSFORMATIONTYPE}" == "RI" ]
then
RIGID=1
RIGIDTRANSF=" --do-rigid true "

elif [ "${TRANSFORMATIONTYPE}" == "RA" ]
then
RIGID=1
RIGIDTRANSF=" --rigid-affine true "

elif [ "${TRANSFORMATIONTYPE}" == "EL" ]
then
# Mapping Parameters
TRANSFORMATION="Elast[ 1 ]"
REGULARIZATION="Gauss[ 3,0.5 ]"
# Gauss[3,x ] is usually the best option.    x is usually 0 for SyN --- if you want to reduce flexibility/increase mapping smoothness, the set x > 0.
# We did a large scale evaluation of SyN gradient parameters in normal brains and found 0.25 => 0.5 to perform best when
# combined with default Gauss[3,0 ] regularization.    You would increase the gradient step in some cases, though, to make
# the registration converge faster --- though oscillations occur if the step is too high and other instability might happen too.

elif [ "${TRANSFORMATIONTYPE}" == "S2" ]
then
# Mapping Parameters for the LDDMM style SyN --- the params are SyN[ GradientStepLength,NTimeDiscretizationPoints,IntegrationTimeStep]
# increasing IntegrationTimeStep increases accuracy in the diffeomorphism integration and takes more computation time.
# NTimeDiscretizationPoints is set to 2 here
TRANSFORMATION="SyN[ 1,2,0.05 ]"
REGULARIZATION="Gauss[ 3,0. ]"

elif [ "${TRANSFORMATIONTYPE}" == "SY" ]
then
# Mapping Parameters for the LDDMM style SyN --- the params are SyN[ GradientStepLength,NTimeDiscretizationPoints,IntegrationTimeStep]
# increasing IntegrationTimeStep increases accuracy in the diffeomorphism integration and takes more computation time.
# NTimeDiscretizationPoints is the number of spatial indices in the time dimension (the 4th dim when doing 3D registration)
# increasing NTimeDiscretizationPoints increases flexibility and takes more computation time.
# the --geodesic option enables either 1 asymmetric gradient estimation or 2 symmetric gradient estimation (the default here )
TRANSFORMATION=" SyN[ 1,2,0.05 ] --geodesic 2 "
REGULARIZATION="Gauss[ 3,0. ]"

elif [ "${TRANSFORMATIONTYPE}" == "LDDMM" ]
then
# Mapping Parameters for the LDDMM style SyN --- the params are SyN[ GradientStepLength,NTimeDiscretizationPoints,IntegrationTimeStep]
# increasing IntegrationTimeStep increases accuracy in the diffeomorphism integration and takes more computation time.
# NTimeDiscretizationPoints is the number of spatial indices in the time dimension (the 4th dim when doing 3D registration)
# increasing NTimeDiscretizationPoints increases flexibility and takes more computation time.
# the --geodesic option enables either 1 asymmetric gradient estimation or 2 symmetric gradient estimation (the default here )
TRANSFORMATION=" SyN[ 1,2,0.05 ] --geodesic 1 "
REGULARIZATION="Gauss[ 3,0. ]"

elif [ "${TRANSFORMATIONTYPE}" == "GR" ]
then
# Mapping Parameters for the greedy gradient descent (fast) version of SyN -- only needs GradientStepLength
TRANSFORMATION="SyN[ 0.25 ]"
REGULARIZATION="Gauss[ 3,0 ]"

elif [ "${TRANSFORMATIONTYPE}" == "GR_Constrained" ]
then
# Mapping Parameters for the greedy gradient descent (fast) version of SyN -- only needs GradientStepLength
TRANSFORMATION="SyN[ 0.25 ]"
REGULARIZATION="Gauss[ 3,0.5 ]"

elif [ "${TRANSFORMATIONTYPE}" == "EX" ]
then
# Mapping Parameters
TRANSFORMATION="Exp[ 0.5,10 ]"
REGULARIZATION="Gauss[ 3,0.5 ]"

elif [ "${TRANSFORMATIONTYPE}" == "DD" ]
then
# Mapping Parameters for diffemorphic demons style optimization Exp[GradientStepLength,NTimePointsInIntegration]
#  NTimePointsInIntegration controls the number of compositions in the transformation update , see the DD paper
TRANSFORMATION="GreedyExp[ 0.5,10 ]"
REGULARIZATION="Gauss[ 3,0.5 ]"

else
echo "Invalid transformation metric. Use RI, RA, EL, SY, S2, GR , DD or EX or type bash `basename $0` -h."
exit 1
fi

# Similarity Measures
if [ "${METRICTYPE}" == "PR" ]
then
# Mapping Parameters
METRIC="PR[ "
METRICPARAMS="1,4 ]"

elif [ "${METRICTYPE}" == "CC" ]
then
# Mapping Parameters
METRIC="CC[ "
METRICPARAMS="1,5 ]"

elif [ "${METRICTYPE}" == "MI" ]
then
# Mapping Parameters
METRIC="MI[ "
METRICPARAMS="1,32 ]"

elif [ "${METRICTYPE}" == "MSQ" ]
then
# Mapping Parameters
METRIC="MSQ[ "
METRICPARAMS="1,0 ]"

else
echo "Invalid similarity metric. Use CC, MI, MSQ or PR or type bash`basename $0` -h."
exit 1
fi

# main script
reportMappingParameters
# write config file

MOVINGBASE=` echo ${MOVING} | cut -d '.' -f 1 `

if [ -f ${MOVINGBASE}.cfg ] ;
then
rm -f ${MOVINGBASE}.cfg
fi

echo "REGDIR=${currentdir}" >> ${MOVINGBASE}.cfg
echo "DIM=$DIM" >> ${MOVINGBASE}.cfg
echo "FIXED=$FIXED" >> ${MOVINGBASE}.cfg
echo "MOVING=$MOVING" >> ${MOVINGBASE}.cfg
echo "LABELIMAGE=$LABELIMAGE" >> ${MOVINGBASE}.cfg
echo "N4CORRECT=$N4CORRECT" >> ${MOVINGBASE}.cfg
echo "DoANTSQC=$DoANTSQC" >> ${MOVINGBASE}.cfg
echo "METRICTYPE=$METRICTYPE" >> ${MOVINGBASE}.cfg
echo "TRANSFORMATIONTYPE=$TRANSFORMATIONTYPE" >> ${MOVINGBASE}.cfg
echo "REGULARIZATION=$REGULARIZATION" >> ${MOVINGBASE}.cfg
echo "MAXITERATIONS=$MAXITERATIONS" >> ${MOVINGBASE}.cfg
echo "NUMLEVELS=$NUMLEVELS" >> ${MOVINGBASE}.cfg
echo "OUTPUTNAME=$OUTPUTNAME" >> ${MOVINGBASE}.cfg

# Default of 10000x10000x10000x10000x10000 retained for backwards compatibility, can cause
# memory problems (allocates too much RAM for five levels) and bad affine initialization (images downsampled too far)
#
# A value of 1000x1000x1000 should suffice for most purposes
AFFINEITERATIONS=10000x10000x10000x10000x10000

if  [ ${N4CORRECT} -eq 0 ] && [ ${RIGID} -eq 0 ]
then
# Apply ANTS mapping command without N4BiasFieldCorrection
exe="ANTS $DIM -m  ${METRIC}${FIXED},${MOVING},${METRICPARAMS} -t $TRANSFORMATION -r $REGULARIZATION -o ${OUTPUTNAME} -i $MAXITERATIONS --use-Histogram-Matching  --number-of-affine-iterations $AFFINEITERATIONS --MI-option 32x16000 "
echo
echo "--------------------------------------------------------------------------------------"
echo "ANTS command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execants=$exe" >> ${MOVINGBASE}.cfg

# Apply forward transformation to MOVING
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying forward transformation to ${MOVING}"
echo "--------------------------------------------------------------------------------------"
WarpImageMultiTransform $DIM ${MOVING} ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}
echo "warpfw=WarpImageMultiTransform $DIM ${MOVING} ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}" >> ${MOVINGBASE}.cfg


# Apply inverse transformation to FIXED
if [ "${TRANSFORMATIONTYPE}" == "EL" ]
then
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying inverse transformation to ${FIXED} is not possible for elastic registration."
echo "--------------------------------------------------------------------------------------"
else
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying inverse transformation to ${FIXED}"
echo "--------------------------------------------------------------------------------------"
FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -R ${MOVING} -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz
echo "warpinv=WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -R ${MOVING} -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz" >> ${MOVINGBASE}.cfg
fi

elif [ ${N4CORRECT} -eq 1 ] && [ ${RIGID} -eq 0 ]
then
# Apply N4BiasFieldCorrection
#Uncomment/comment below to switch between N3 and N4 bias field correction binaries
#exe="N3BiasFieldCorrection $DIM $MOVING ${OUTPUTNAME}.nii.gz 4"
exe="N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}.nii.gz -b [ 200 ] -s 3 -c [ 50x50x30x20,1e-6 ]"
echo
echo "--------------------------------------------------------------------------------------"
echo "N4BiasFieldCorrection command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execN4=$exe" >> ${MOVINGBASE}.cfg

# Apply ANTS mapping command on N3 corrected image
exe="ANTS $DIM -m  ${METRIC}${FIXED},${OUTPUTNAME}.nii.gz,${METRICPARAMS} -t $TRANSFORMATION -r $REGULARIZATION -o ${OUTPUTNAME} -i $MAXITERATIONS --use-Histogram-Matching  --number-of-affine-iterations $AFFINEITERATIONS --MI-option 32x16000  "
echo
echo "--------------------------------------------------------------------------------------"
echo "ANTS command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execants=$exe" >> ${MOVINGBASE}.cfg

# Apply forward transformation to MOVING
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying forward transformation to ${MOVING}"
echo "--------------------------------------------------------------------------------------"
WarpImageMultiTransform $DIM ${OUTPUTNAME}.nii.gz ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}
echo "warpfw=WarpImageMultiTransform $DIM ${OUTPUTNAME}.nii.gz ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}" >> ${MOVINGBASE}.cfg

# Apply inverse transformation to FIXED
if [ "${TRANSFORMATIONTYPE}" == "EL" ]
then
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying inverse transformation to ${FIXED} is not possible for elastic registration."
echo "--------------------------------------------------------------------------------------"
else
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying inverse transformation to ${FIXED}"
echo "--------------------------------------------------------------------------------------"
FIXEDBASE=` echo ${FIXED} | cut -d '.' -f 1 `
WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz -R ${OUTPUTNAME}.nii.gz
echo "warpinv=WarpImageMultiTransform $DIM ${FIXED} ${FIXEDBASE}_InverseWarp.nii.gz -R ${OUTPUTNAME}.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz" >> ${MOVINGBASE}.cfg
fi

elif  [ ${N4CORRECT} -eq 0 ] && [ ${RIGID} -eq 1 ]
then
exe=" ANTS $DIM -m ${METRIC}${FIXED},${MOVING},${METRICPARAMS} -o ${OUTPUTNAME}.nii.gz -i 0 --use-Histogram-Matching --number-of-affine-iterations $AFFINEITERATIONS --MI-option 32x16000 ${RIGIDTRANSF} "
echo
echo "--------------------------------------------------------------------------------------"
echo "ANTS command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execants=$exe" >> ${MOVINGBASE}.cfg

# Apply forward transformation to MOVING
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying rigid transformation to ${MOVING}"
echo "--------------------------------------------------------------------------------------"
WarpImageMultiTransform $DIM ${MOVING} ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}

elif  [ ${N4CORRECT} -eq 1 ] && [ ${RIGID} -eq 1 ]
then
# Apply N4BiasFieldCorrection
#Uncomment/comment below to switch between N3 and N4 bias field correction binaries
#exe="N3BiasFieldCorrection $DIM $MOVING ${OUTPUTNAME}.nii.gz 4"
exe="N4BiasFieldCorrection -d $DIM -i $MOVING -o ${OUTPUTNAME}.nii.gz -b [ 200 ] -s 3 -c [ 50x50x30x20,1e-6 ]"
echo
echo "--------------------------------------------------------------------------------------"
echo "N4BiasFieldCorrection command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execN4=$exe" >> ${MOVINGBASE}.cfg

exe=" ANTS $DIM -m MI[ ${FIXED},${MOVING},1,32 ] -o ${OUTPUTNAME}.nii.gz -i 0 --use-Histogram-Matching --number-of-affine-iterations $AFFINEITERATIONS --MI-option 32x16000 ${RIGIDTRANSF} "
echo
echo "--------------------------------------------------------------------------------------"
echo "ANTS command:"
echo "$exe "
echo "--------------------------------------------------------------------------------------"
$exe
echo "execants=$exe" >> ${MOVINGBASE}.cfg

# Apply forward transformation to MOVING
echo
echo "--------------------------------------------------------------------------------------"
echo "Applying rigid transformation to ${MOVING}"
echo "--------------------------------------------------------------------------------------"
WarpImageMultiTransform $DIM ${MOVING} ${OUTPUTNAME}deformed.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED}


fi

# Apply transformation on labeled image?
if  [ ${#LABELIMAGE} -gt 3 ]
then
WarpImageMultiTransform $DIM  $LABELIMAGE ${OUTPUTNAME}labeled.nii.gz -i ${OUTPUTNAME}Affine.txt ${OUTPUTNAME}InverseWarp.nii.gz  -R ${MOVING}   --use-NN
fi

if [ $DoANTSQC -eq 1 ]
then
#  measure image similarity - 0 = intensity difference, 1 = correlation , 2 = mutual information
for SIM in 0 1 2 ; do
MeasureImageSimilarity $DIM $SIM $FIXED ${OUTPUTNAME}deformed.nii.gz
done

# the lines below  measure dice overlap and min-dist-sum from the approximately segmented brain (3 tissues and background)
ThresholdImage $DIM $FIXED ${OUTPUTNAME}fixthresh.nii.gz Otsu 4
ThresholdImage $DIM $MOVING ${OUTPUTNAME}movthresh.nii.gz Otsu 4

WarpImageMultiTransform $DIM ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}defthresh.nii.gz ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt -R ${FIXED} --use-NN

ImageMath $DIM ${OUTPUTNAME}dicestats.txt DiceAndMinDistSum  ${OUTPUTNAME}fixthresh.nii.gz   ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}mindistsum.nii.gz

# below not used unless you want to compare segmentation volumes to those estimated by the jacobian
# labelstats for jacobian wrt segmenation below, to compose
# ComposeMultiTransform $DIM   ${OUTPUTNAME}CompWarp.nii.gz  -R $FIXED ${OUTPUTNAME}Warp.nii.gz ${OUTPUTNAME}Affine.txt
# CreateJacobianDeterminantImage $DIM ${OUTPUTNAME}CompWarp.nii.gz ${OUTPUTNAME}jacobian.nii.gz  0
# ImageMath $DIM ${OUTPUTNAME}movlabstat.txt LabelStats ${OUTPUTNAME}movthresh.nii.gz ${OUTPUTNAME}movthresh.nii.gz
# 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

# save output in starting dir - remove inputs, then remove tempdir
rm `basename ${FIXED}`
rm `basename ${MOVING}`
cp * ../
cd ${currentdir}
rm -rf ${tmpdir}/

time_end=`date +%s`
time_elapsed=$((time_end - time_start))

echo " ">> ${MOVINGBASE}.cfg
echo " Script executed in $time_elapsed seconds" >> ${MOVINGBASE}.cfg
echo " $(( time_elapsed / 3600 ))h $(( time_elapsed %3600 / 60 ))m $(( time_elapsed % 60 ))s" >> ${MOVINGBASE}.cfg

exit