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#!/bin/bash
if [[ ! -s ${ANTSPATH}/antsRegistration ]]
then
echo "Cannot find antsRegistration. Please \(re\)define \$ANTSPATH in your environment."
fi
if [[ ! -s ${ANTSPATH}/antsApplyTransforms ]]
then
echo "Cannot find antsApplyTransforms. Please \(re\)define \$ANTSPATH in your environment."
fi
if [[ ! -s ${ANTSPATH}/antsIntermodalityIntrasubject.sh ]]
then
echo "Cannot find antsIntermodalityIntrasubject.sh script. Please \(re\)define \$ANTSPATH in your environemnt."
fi
function Usage {
cat <<USAGE
`basename $0` performs ASL processing based on ANTs tools. Preprocessing of T1 images using antsCorticalThickness.sh is assumed. The following steps are performed:
1) Calculation of average pCASL image.
2) Skull stripping of average pCASL image.
3) Registration of average pCASL image to T1 image.
4) (Robust) calculation of mean CBF.
5) Warping tissue priors and labels to ASL space.
6) Warping mean CBF image to template space for VBM analysis.
Usage:
Required arguments:
`basename $0` -a anatomical image (skull stripped)
-p brain segmentation priors (C-style, e.g. priors%d.nii.gz)
-g hard brain segmentation
-x t1 brain mask
-s raw pCASL image
-e brain template
-l template labels
-t skull-stripped t1 to template transform prefix
-o output prefix
Optional arguments:
-b blood T1 value (defaults to 0.67 s^-1)
-r robustness parameter (defaults to 0.95)
-h print help and exit
-n number of bootstrap samples (defaults to 20)
-c percent to sample per bootstrap run (defaults to 70)
-k keep tmp files, including warps (defaults to false--takes lots of space to save)
-i use inverse warps. Warps are assumed to go in the direction of subject to template.
If you are instead using template to subject warps (e.g. the brain segmentation prior warps from
antsCorticalThickness.sh), use -i (binary switch--no arguments).
-f bootstrap with replacement? takes arguments "false" or "true"; defaults to false.
USAGE
exit 1
}
echoParameters() {
cat <<PARAMETERS
Using `basename $0` with the following parameters:
anatomical image: ${ANATOMICAL_IMAGE}
brain mask: $BRAINMASK
segmentation probs: $SEGMENTATION_PROB
hard segmentation: $SEGMENTATION
pCASL image: $PCASL
template: $TEMPLATE
template labels: $LABELS
transform prefix: $TRANSFORM_PREFIX
output prefix: $OUTNAME
blood relaxation: $BLOODT1 s^-1
robustness: $ROBUST
num bootstraps: $NBOOTSTRAP
pct per bootstrap: $PCTBOOTSTRAP
keep tmp files: $KEEP_TMP_FILES
use inverse warps: $USE_INVERSE_WARPS
sample w/ replacement: $SAMPLE_WITH_REPLACEMENT
PARAMETERS
}
function logCmd() {
cmd="$*"
echo "BEGIN >>>>>>>>>>>>>>>>>>>>"
echo $cmd
$cmd
echo "END <<<<<<<<<<<<<<<<<<<<"
echo
echo
}
KEEP_TMP_FILES=false
USE_INVERSE_WARPS=false
if [[ $# -lt 3 ]]
then
Usage >&2
exit 1
else
while getopts "a:s:e:p:t:o:x:l:b:r:g:n:c:f:k:i:h" OPT
do
case $OPT in
a) #anatomical t1 image
ANATOMICAL_IMAGE=$OPTARG
;;
s) # raw pCASL image
PCASL=$OPTARG
;;
e) # brain template
TEMPLATE=$OPTARG
;;
p) # segmentation probabilities
SEGMENTATION_PROB=$OPTARG
;;
g) # hard seg
SEGMENTATION=$OPTARG
;;
t) # transform prefix
TRANSFORM_PREFIX=$OPTARG
;;
o) # output prefix
OUTNAME=$OPTARG
;;
x) # mask
BRAINMASK=$OPTARG
;;
l) # labels
LABELS=$OPTARG
;;
b) # blood t1
BLOODT1=$OPTARG
;;
r) # robustness
ROBUST=$OPTARG
;;
n) # number of bootstrap runs
NBOOTSTRAP=$OPTARG
;;
c) # pct to sample per bootstrap
PCTBOOTSTRAP=$OPTARG
;;
f) # sample with replacement?
SAMPLE_WITH_REPLACEMENT=$OPTARG
;;
k) # keep tmp files
KEEP_TMP_FILES=true
;;
i) # use inverse warps
USE_INVERSE_WARPS=true
;;
h) # help
Usage >&2
exit 0
;;
*)
echo "ERROR: unrecognized option -$OPT $OPTARG"
exit 1
;;
esac
done
fi
if [[ -z $BLOODT1 ]]
then
BLOODT1=0.67
fi
if [[ -z $ROBUST ]]
then
ROBUST=0.95
fi
if [[ -z $NBOOTSTRAP ]]
then
NBOOTSTRAP=20
fi
if [[ -z $PCTBOOTSTRAP ]]
then
PCTBOOTSTRAP=0.70
fi
if [[ -z $SAMPLE_WITH_REPLACEMENT ]]
then
SAMPLE_WITH_REPLACEMENT=false
fi
echoParameters >&2
# parse prior syntax
FORMAT=${SEGMENTATION_PROB}
PREFORMAT=${FORMAT%%\%*}
POSTFORMAT=${FORMAT##*d}
FORMAT=${FORMAT#*\%}
FORMAT=${FORMAT%%d*}
REPCHARACTER=''
TOTAL_LENGTH=0
if [ ${#FORMAT} -eq 2 ]
then
REPCHARACTER=${FORMAT:0:1}
TOTAL_LENGTH=${FORMAT:1:1}
fi
MAXNUMBER=1000
PRIOR_IMAGE_FILENAMES=()
for (( i = 1; i < $MAXNUMBER; i++ ))
do
NUMBER_OF_REPS=$(( $TOTAL_LENGTH - ${#i} ))
ROOT='';
for(( j=0; j < $NUMBER_OF_REPS; j++ ))
do
ROOT=${ROOT}${REPCHARACTER}
done
FILENAME=${PREFORMAT}${ROOT}${i}${POSTFORMAT}
if [[ -f $FILENAME ]];
then
PRIOR_IMAGE_FILENAMES=( ${PRIOR_IMAGE_FILENAMES[@]} $FILENAME )
else
break 1
fi
done
echo "Warning: antsASLProcessing.sh is being deprecated. Use antsASLProcessing.R instead."
# check for existence of all images
if [[ ! -f ${ANATOMICAL_IMAGE} ]]
then
echo "ERROR: Anatomical image ${ANATOMICAL_IMAGE} does not exist."
exit 1
fi
if [[ ! -f $BRAINMASK ]]
then
echo "ERROR: Brain mask $BRAINMASK does not exist."
exit 1
fi
if [[ ! -f $PCASL ]]
then
echo "ERROR: pCASL image $PCASL does not exist."
exit 1
fi
if [[ ! -f $TEMPLATE ]]
then
echo "ERROR: template image $TEMPLATE does not exist."
exit 1
fi
if [[ ! -f $LABELS ]]
then
echo "ERROR: Template label image $LABELS does not exist."
fi
if [[ ! -f $SEGMENTATION ]]
then
echo "ERROR: Segmentation image $SEGMENTATION does not exist."
exit 1
fi
if [[ ! -f ${TRANSFORM_PREFIX}SubjectToTemplate1Warp.nii.gz ]]
then
echo "ERROR: Warp ${TRANSFORM_PREFIX}SubjectToTemplate1Warp.nii.gz does not exist."
exit 1
fi
if [[ ${#PRIOR_IMAGE_FILENAMES[@]} -lt 3 ]]
then
echo "ERROR: Fewer than 3 prior images specified."
echo " Check that you defined prior file names correctly."
fi
time_start=`date +%s`
# Do processing.
if [[ ! -d `dirname $OUTNAME` ]]
then
mkdir -p `dirname $OUTNAME`
fi
if [[ ! -s ${OUTNAME}/AveragePCASL.nii.gz ]] ; then
logCmd ${ANTSPATH}/antsMotionCorr -d 3 -a $PCASL -o ${OUTNAME}AveragePCASL.nii.gz
fi
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz 600 999999
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz ME ${OUTNAME}tmp.nii.gz 2
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz GetLargestComponent ${OUTNAME}tmp.nii.gz
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}tmp.nii.gz MD ${OUTNAME}tmp.nii.gz 3
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}pCASLBrain.nii.gz m ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}tmp.nii.gz
INTERSUBJECT_PARAMS=" -d 3 -i ${OUTNAME}pCASLBrain.nii.gz -r $ANATOMICAL_IMAGE -x $BRAINMASK -w ${TRANSFORM_PREFIX}SubjectToTemplate -t 2 -o $OUTNAME "
if [[ -n $LABELS ]]
then
INTERSUBJECT_PARAMS=" ${INTERSUBJECT_PARAMS} -l $LABELS "
fi
logCmd ${ANTSPATH}/antsIntermodalityIntrasubject.sh $INTERSUBJECT_PARAMS
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 4
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 2
logCmd ${ANTSPATH}/N4BiasFieldCorrection -d 3 -i ${OUTNAME}AveragePCASL.nii.gz -o ${OUTNAME}AveragePCASL.nii.gz -r 1 -s 1
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}AveragePCASL.nii.gz ${OUTNAME}OtsuMask.nii.gz Otsu 4
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}OtsuMask.nii.gz 2 4
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}OtsuMask.nii.gz ME ${OUTNAME}OtsuMask.nii.gz 1
logCmd ${ANTSPATH}/ImageMath 3 ${OUTNAME}OtsuMask.nii.gz MD ${OUTNAME}OtsuMask.nii.gz 1
logCmd ${ANTSPATH}/ThresholdImage 3 ${OUTNAME}brainmask.nii.gz ${OUTNAME}BrainThresh.nii.gz 1 999
logCmd ${ANTSPATH}/MultiplyImages 3 ${OUTNAME}OtsuMask.nii.gz ${OUTNAME}BrainThresh.nii.gz ${OUTNAME}OtsuMask.nii.gz
if [ ! -f ${OUTNAME}_kcbf.nii.gz ]; then
logCmd ${ANTSPATH}/antsNetworkAnalysis.R \
-o $OUTNAME \
--freq 0.01x0.1 \
--mask ${OUTNAME}OtsuMask.nii.gz \
--labels ${OUTNAME}labels.nii.gz \
--fmri $PCASL \
--modality ASLCBF \
--bloodt1 $BLOODT1 \
--robust $ROBUST \
--nboot $NBOOTSTRAP \
--pctboot $PCTBOOTSTRAP \
--replace $SAMPLE_WITH_REPLACEMENT
fi
logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-i ${OUTNAME}_kcbf.nii.gz \
-r $TEMPLATE \
-o ${OUTNAME}MeanCBFWarpedToTemplate.nii.gz \
-n Linear \
-t ${TRANSFORM_PREFIX}SubjectToTemplate0GenericAffine.mat \
-t ${TRANSFORM_PREFIX}SubjectToTemplate1Warp.nii.gz \
-t ${OUTNAME}1Warp.nii.gz \
-t ${OUTNAME}0GenericAffine.mat
logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-i $LABELS \
-r ${OUTNAME}AveragePCASL.nii.gz \
-o ${OUTNAME}LabelsWarpedToPCASL.nii.gz \
-n MultiLabel \
-t ${TRANSFORM_PREFIX}TemplateToSubject0Warp.nii.gz \
-t ${TRANSFORM_PREFIX}TemplateToSubject1GenericAffine.mat \
-t [${OUTNAME}0GenericAffine.mat,1] \
-t ${OUTNAME}1InverseWarp.nii.gz
logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-i ${OUTNAME}_kcbf.nii.gz \
-r $ANATOMICAL_IMAGE \
-o ${OUTNAME}MeanCBFWarpedToT1.nii.gz \
-n Linear \
-t ${OUTNAME}1Warp.nii.gz \
-t ${OUTNAME}0GenericAffine.mat \
logCmd ${ANTSPATH}/antsApplyTransforms -d 3 \
-i $SEGMENTATION \
-r ${OUTNAME}AveragePCASL.nii.gz \
-o ${OUTNAME}SegmentationWarpedToPCASL.nii.gz \
-n MultiLabel \
-t [${OUTNAME}0GenericAffine.mat,1] \
-t ${OUTNAME}1InverseWarp.nii.gz \
if ! $KEEP_TMP_FILES
then
for FILE in 0GenericAffine.mat 1Warp.nii.gz 1InverseWarp.nii.gz anatomical.nii.gz template.nii.gz tmp.nii.gz
do
logCmd rm ${OUTNAME}${FILE}
done
fi
time_end=`date +%s`
time_elapsed=$((time_end - time_start))
echo
echo "--------------------------------------------------------------------------------------"
echo " Done with ANTs ASL processing pipeline."
echo " Script executed in $time_elapsed seconds."
echo " $(( time_elapsed / 3600 ))h $(( time_elapsed %3600 / 60 ))m $(( time_elapsed % 60 ))s"
echo "--------------------------------------------------------------------------------------"
exit 0