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antsMultivariateTemplateConstruction2.sh
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#!/bin/bash
shopt -s extglob
VERSION="0.0.0"
# trap keyboard interrupt (control-c)
trap control_c SIGINT
function setPath {
cat <<SETPATH
--------------------------------------------------------------------------------------
Error locating ANTS
--------------------------------------------------------------------------------------
It seems that the ANTSPATH environment variable is not set. Please add the ANTSPATH
variable. This can be achieved by editing the .bash_profile in the home directory.
Add:
ANTSPATH=/home/yourname/bin/ants/
Or the correct location of the ANTS binaries.
Alternatively, edit this script ( `basename $0` ) to set up this parameter correctly.
SETPATH
exit 1
}
# Uncomment the line below in case you have not set the ANTSPATH variable in your environment.
# export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} # EDIT THIS
if [[ ${#ANTSPATH} -le 3 ]];
then
setPath >&2
fi
# Test availability of helper scripts.
# No need to test this more than once. Can reside outside of the main loop.
ANTS=${ANTSPATH}/antsRegistration
WARP=${ANTSPATH}/antsApplyTransforms
N4=${ANTSPATH}/N4BiasFieldCorrection
PEXEC=${ANTSPATH}/ANTSpexec.sh
SGE=${ANTSPATH}/waitForSGEQJobs.pl
PBS=${ANTSPATH}/waitForPBSQJobs.pl
XGRID=${ANTSPATH}/waitForXGridJobs.pl
SLURM=${ANTSPATH}/waitForSlurmJobs.pl
fle_error=0
for FLE in $ANTS $WARP $N4 $PEXEC $SGE $XGRID $PBS $SLURM
do
if [[ ! -x $FLE ]];
then
echo
echo "-----------------------------------------------------------------------------"
echo " FILE $FLE DOES NOT EXIST -- OR -- IS NOT EXECUTABLE !!! $0 will terminate."
echo "-----------------------------------------------------------------------------"
echo " if the file is not executable, please change its permissions. "
fle_error=1
fi
done
if [[ $fle_error = 1 ]];
then
echo "missing helper script"
exit 1
fi
function Usage {
cat <<USAGE
Usage:
`basename $0` -d ImageDimension -o OutputPrefix <other options> <images>
Compulsory arguments (minimal command line requires SGE/PBS cluster, otherwise use -c and
-j options):
-d: ImageDimension: 2 or 3 (for 2 or 3 dimensional registration of single volume)
ImageDimension: 4 (for template generation of time-series data)
<images> List of images in the current directory, eg *_t1.nii.gz. Should be at the end
of the command. Optionally, one can specify a .csv or .txt file where each
line is the location of the input image. One can also specify more than
one file for each image for multi-modal template construction (e.g. t1 and t2).
For the multi-modal case, the templates will be consecutively numbered (e.g.
${OutputPrefix}template0.nii.gz, ${OutputPrefix}template1.nii.gz, ...).
NB: All images to be added to the template should be in the same directory, and this
script should be invoked from that directory.
Optional arguments:
-a image statistic used to summarize images (default 1)
0 = mean
1 = mean of normalized intensities
2 = median
Normalization here means dividing each image by its mean intensity.
-A sharpening applied to template at each iteration (default 1)
0 = none
1 = Laplacian
2 = Unsharp mask
-b: Backup images and results from all iterations (default = 0): Boolean to save
the transform files, bias corrected inputs, templates, transforms, and warped images
for each iteration. By default, only the templates and the shape update warp field
are saved.
-c: Control for parallel computation (default 0):
0 = run serially
1 = SGE qsub
2 = use PEXEC (localhost)
3 = Apple XGrid
4 = PBS qsub
5 = SLURM
-e use single precision ( default 1 )
-g: Gradient step size (default 0.25): smaller in magnitude results in more
cautious steps. Use smaller steps to refine template details.
0.25 is an upper (aggressive) limit for this parameter.
-i: Iteration limit (default 4): iterations of the template construction
(Iteration limit)*NumImages registrations.
-j: Number of cpu cores to use locally for pexec option (default 2; requires "-c 2")
-k: Number of modalities used to construct the template (default 1): For example,
if one wanted to create a multimodal template consisting of T1,T2,and FA
components ("-k 3").
-w: Modality weights used in the similarity metric (default = 1): specified as
e.g. 1x0.5x0.75.
-q: Max iterations for each pairwise registration (default = 100x100x70x20):
specified in the form ...xJxKxL where
J = max iterations at coarsest resolution (here, reduced by power of 2^2)
K = middle resolution iterations (here, reduced by power of 2)
L = fine resolution iteratioxns (here, full resolution).
Finer resolutions take much more time per iteration than coarser resolutions.
-f: Shrink factors (default = 6x4x2x1): Also in the same form as -q max iterations.
Needs to have the same number of components.
-s: Smoothing factors (default = 3x2x1x0): Also in the same form as -q max
iterations. Needs to have the same number of components.
-n: N4BiasFieldCorrection of moving image: 0 == off, 1 == on (default 1).
-o: OutputPrefix; A prefix that is prepended to all output files (default = "antsBTP").
-p: Commands to prepend to job scripts (e.g., change into appropriate directory, set
paths, etc)
-r: Do rigid-body registration of inputs to the initial template, before doing the main
pairwise registration. 0 == off 1 == on (default 0). If you are trying to refine or update
an existing template, you would use '-r 0'.
Rigid initialization is useful when you do not have an initial template, or you want to use
a single image as a reference for rigid alignment only. For example,
"-z tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz -y 0 -r 1"
will rigidly align the inputs to the MNI template, and then use their average to begin the
template building process.
-l: Use linear image registration stages during the pairwise (template/subject)
deformable registration. Otherwise, registration is limited to SyN or
B-spline SyN (see '-t' option). This is '1' by default.
-m: Type of similarity metric used for pairwise registration (default = CC). Options are case
sensitive.
CC = cross-correlation
MI = mutual information
MSQ = mean square difference
DEMONS = demon's metric
A similarity metric per modality can be specified. If the CC metric is chosen,
one can also specify the radius in brackets, e.g. "-m CC[ 4 ]". This option controls
the metric for the transformation specified with "-t", so "-m CC -t SyN" means the SyN
stage is run with the CC metric; preceding linear stages use MI.
-t: Type of transformation model used for registration (default = SyN): Options are case
sensitive.
SyN = Greedy SyN
BSplineSyN = Greedy B-spline SyN
TimeVaryingVelocityField = Time-varying velocity field
TimeVaryingBSplineVelocityField = Time-varying B-spline velocity field
The transformations above are used after Rigid + Affine linear registration, unless linear
registration is disabled with "-l". To use linear registration only, options are:
Affine = Affine (runs Rigid + Affine)
Rigid = Rigid (runs Rigid only).
-u: Walltime (default = 20:00:00): Option for PBS/SLURM qsub specifying requested time
per pairwise registration.
-v: Memory limit (default = 8gb): Option for PBS/SLURM qsub specifying requested memory
per pairwise registration.
-x: XGrid arguments (e.g., -x "-p password -h controlhost")
-y: Update the template with the full affine transform (default 1). If 0, the rigid
component of the affine transform will not be used to update the template. If your
template drifts in translation or orientation try "-y 0".
-z: Use this this volume as the target of all inputs. When not used, the script will create an unbiased
starting point by averaging all inputs, then aligning the center of mass of all inputs to that of
the initial average. If you do not use -z, it is recommended to use "-r 1". Use the full path.
For multiple modalities, specify -z modality1.nii.gz -z modality2.nii.gz ...
in the same modality order as the input images.
Example:
`basename $0` -d 3 -i 3 -k 1 -f 4x2x1 -s 2x1x0vox -q 30x20x4 -t SyN -m CC -c 0 -r 1 -o MY sub*avg.nii.gz
Multimodal example:
`basename $0` -d 3 -i 3 -k 2 -f 4x2x1 -s 2x1x0vox -q 30x20x4 -t SyN -z t1.nii.gz -z t2.nii.gz \\
-m CC -c 0 -o MY templateInput.csv
where templateInput.csv contains
subjectA_t1.nii.gz,subjectA_t2.nii.gz
subjectB_t1.nii.gz,subjectB_t2.nii.gz
...
Example of first building an affine template, then refining it with SyN:
`basename $0` -d 3 -i 2 -A 2 -k 1 -f 6x4x2x1 -s 4x2x1x0vox -q 200x100x50x0 -t Affine -m MI -c 0 \\
-r 1 -o MY_Affine_ sub*avg.nii.gz
`basename $0` -d 3 -i 5 -k 1 -f 6x4x2x1 -s 4x2x1x0vox -q 50x100x70x20 -t SyN -m CC -c 0 \\
-r 0 -o MY_Deformable_ -z MY_Affine_template0.nii.gz sub*avg.nii.gz
Output
{OutputPrefix}template{m}.nii.gz
final template for each modality m.
{OutputPrefix}template{m}{inputFile}{n}WarpedToTemplate.nii.gz
{OutputPrefix}template{m}{inputFile}{n}0GenericAffine.mat
{OutputPrefix}template{m}{inputFile}{n}1Warp.nii.gz
{OutputPrefix}template{m}{inputFile}{n}1InverseWarp.nii.gz
each of n input images warped to the penultimate template m, with transforms. If the template has converged,
these should be well aligned to {OutputPrefix}template{m}.nii.gz.
intermediateTemplates/
initial_{OutputPrefix}template{m}.nii.gz :
initial template
initialRigid_{OutputPrefix}template{m}.nii.gz :
initial rigid template if requested with "-r 1"
{transform}_iteration{i}_{OutputPrefix}template{m}.nii.gz
Template computed with {transform} (-t) for each iteration (-i) and modality.
{transform}_iteration{i}_shapeUpdateWarp.nii.gz
Shape update warp applied to the template at iteration i. As the template converges,
the magnitude of the update warp will converge to a minimal value.
--------------------------------------------------------------------------------------
ANTS was created by:
--------------------------------------------------------------------------------------
Brian B. Avants, Nick Tustison and Gang Song
Penn Image Computing And Science Laboratory
University of Pennsylvania
Please reference http://www.ncbi.nlm.nih.gov/pubmed/20851191 when employing this script
in your studies. A reproducible evaluation of ANTs similarity metric performance in
brain image registration:
* Avants BB, Tustison NJ, Song G, Cook PA, Klein A, Gee JC. Neuroimage, 2011.
Also see http://www.ncbi.nlm.nih.gov/pubmed/19818860 for more details.
The script has been updated and improved since this publication.
--------------------------------------------------------------------------------------
Script by Nick Tustison
--------------------------------------------------------------------------------------
Apple XGrid support by Craig Stark
--------------------------------------------------------------------------------------
USAGE
exit 1
}
function reportMappingParameters {
cat <<REPORTMAPPINGPARAMETERS
--------------------------------------------------------------------------------------
Mapping parameters
--------------------------------------------------------------------------------------
ANTSPATH is $ANTSPATH
Dimensionality: $DIM
Do N4 bias correction: $N4CORRECT
Back up each iteration: $BACKUPEACHITERATION
Similarity metric: ${METRICTYPE[@]}
Gradient step: $GRADIENTSTEP
Transformation: $TRANSFORMATIONTYPE
Max iterations: $MAXITERATIONS
Smoothing factors: $SMOOTHINGFACTORS
Shrink factors: $SHRINKFACTORS
Output prefix: $OUTPUTNAME
Template: $TEMPLATENAME
Template update steps: $ITERATIONLIMIT
Template population: $IMAGESETVARIABLE
Number of modalities: $NUMBEROFMODALITIES
Modality weights: $MODALITYWEIGHTSTRING
Image statistic: $STATSMETHOD
Sharpening method: $SHARPENMETHOD
Shape update full affine: $AFFINE_UPDATE_FULL
--------------------------------------------------------------------------------------
REPORTMAPPINGPARAMETERS
}
function summarizeimageset() {
local dim=$1
shift
local output=$1
shift
local summarizemethod=$1
shift
local sharpenmethod=$1
shift
local images=( "${@}" )
if [[ ${#images[@]} -ne ${IMAGESPERMODALITY} ]]
then
echo "ERROR summarizeimageset - imagelist length is ${#images[@]}, expected ${IMAGESPERMODALITY}"
exit 1
fi
rm -f "$output"
case $summarizemethod in
0) #mean
${ANTSPATH}/AverageImages $dim $output 0 ${images[@]}
;;
1) #mean of normalized images
${ANTSPATH}/AverageImages $dim $output 2 ${images[@]}
;;
2) #median
local image
for image in "${images[@]}";
do
echo $image >> ${output}_list.txt
done
${ANTSPATH}/ImageSetStatistics $dim ${output}_list.txt ${output} 0
rm ${output}_list.txt
;;
esac
if [[ ! -f "$output" ]];
then
echo "summarizeimageset: ERROR - output file $output could not be created"
exit 1
fi
case $sharpenmethod in
0)
echo "Sharpening method none"
;;
1)
echo "Laplacian sharpening"
${ANTSPATH}/ImageMath $dim $output Sharpen $output
;;
2)
echo "Unsharp mask sharpening"
${ANTSPATH}/ImageMath $dim $output UnsharpMask $output 0.5 1 0 0
;;
esac
local sharpenExit=$?
if [[ $? -ne 0 ]]
then
echo "summarizeimageset: ERROR - template sharpening failed with status $?"
exit 1
fi
}
function shapeupdatetotemplate() {
echo "shapeupdatetotemplate()"
# local declaration of values
dim=$1
template=$2
templatename=$3
outputname=$4
gradientstep=-$5
whichtemplate=$6
statsmethod=$7
sharpenmethod=$8
# debug only
# echo $dim
# echo ${template}
# echo ${templatename}
# echo ${outputname}
# echo ${outputname}*WarpedToTemplate.nii*
# echo ${gradientstep}
# We find the average warp to the template and apply its inverse to the template image
# This keeps the template shape stable over multiple iterations of template building
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate---voxel-wise averaging of the warped images to the current template"
date
#echo " ${ANTSPATH}/AverageImages $dim ${template} 1 ${templatename}${whichtemplate}*WarpedToTemplate.nii.gz "
#echo " ${ANTSPATH}/ImageSetStatistics $dim ${whichtemplate}WarpedToTemplateList.txt ${template} 0"
echo "--------------------------------------------------------------------------------------"
imagelist=(`ls ${outputname}template${whichtemplate}*WarpedToTemplate.nii.gz`)
if [[ ${#imagelist[@]} -ne ${IMAGESPERMODALITY} ]]
then
echo "ERROR shapeupdatedtotemplate - imagelist length is ${#imagelist[@]}, expected ${IMAGESPERMODALITY}"
exit 1
fi
summarizeimageset $dim $template $statsmethod $sharpenmethod ${imagelist[@]}
WARPLIST=( `ls ${outputname}*[0-9]Warp.nii.gz 2> /dev/null` )
NWARPS=${#WARPLIST[*]}
echo "number of warps = $NWARPS"
echo "$WARPLIST"
if [[ $whichtemplate -eq 0 ]];
then
if [[ $NWARPS -ne 0 ]]; then
echo "$NWARPS does not equal 0"
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate---voxel-wise averaging of the inverse warp fields (from subject to template)"
echo " ${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`"
date
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/AverageImages $dim ${templatename}${whichtemplate}warp.nii.gz 0 `ls ${outputname}*Warp.nii.gz | grep -v "InverseWarp"`
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate---scale the averaged inverse warp field by the gradient step"
echo " ${ANTSPATH}/MultiplyImages $dim ${templatename}${whichtemplate}warp.nii.gz ${gradientstep} ${templatename}${whichtemplate}warp.nii.gz"
date
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/MultiplyImages $dim ${templatename}${whichtemplate}warp.nii.gz ${gradientstep} ${templatename}${whichtemplate}warp.nii.gz
fi
echo
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate---average the affine transforms (template <-> subject)"
echo " ---transform the inverse field by the resulting average affine transform"
echo " ${ANTSPATH}/${AVERAGE_AFFINE_PROGRAM} ${dim} ${templatename}0GenericAffine.mat ${outputname}*GenericAffine.mat"
echo " ${WARP} -d ${dim} -e vector -i ${templatename}0warp.nii.gz -o ${templatename}0warp.nii.gz -t [ ${templatename}0GenericAffine.mat,1 ] -r ${template} --verbose 1"
echo "--------------------------------------------------------------------------------------"
${ANTSPATH}/${AVERAGE_AFFINE_PROGRAM} ${dim} ${templatename}0GenericAffine.mat ${outputname}*GenericAffine.mat
if [[ $NWARPS -ne 0 ]];
then
${WARP} -d ${dim} -e vector -i ${templatename}0warp.nii.gz -o ${templatename}0warp.nii.gz -t [ ${templatename}0GenericAffine.mat,1 ] -r ${template} --verbose 1
${ANTSPATH}/MeasureMinMaxMean ${dim} ${templatename}0warp.nii.gz ${templatename}warplog.txt 1
fi
fi
echo "--------------------------------------------------------------------------------------"
echo " shapeupdatetotemplate---warp each template by the resulting transforms"
echo " ${WARP} -d ${dim} --float $USEFLOAT --verbose 1 -i ${template} -o ${template} -t [ ${templatename}0GenericAffine.mat,1 ] -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -r ${template}"
echo "--------------------------------------------------------------------------------------"
if [[ -f "${templatename}0warp.nii.gz" ]];
then
${WARP} -d ${dim} --float $USEFLOAT --verbose 1 -i ${template} -o ${template} -t [ ${templatename}0GenericAffine.mat,1 ] -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -t ${templatename}0warp.nii.gz -r ${template}
else
${WARP} -d ${dim} --float $USEFLOAT --verbose 1 -i ${template} -o ${template} -t [ ${templatename}0GenericAffine.mat,1 ] -r ${template}
fi
}
function jobfnamepadding {
outdir=`dirname ${TEMPLATES[0]}`
if [[ ${#outdir} -eq 0 ]]
then
outdir=`pwd`
fi
files=`ls ${outdir}/job*.sh`
BASENAME1=`echo $files[1] | cut -d 'b' -f 1`
for file in ${files}
do
if [[ "${#file}" -eq "9" ]];
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_000${BASENAME2}"
elif [[ "${#file}" -eq "10" ]];
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_00${BASENAME2}"
elif [[ "${#file}" -eq "11" ]];
then
BASENAME2=`echo $file | cut -d 'b' -f 2 `
mv "$file" "${BASENAME1}b_0${BASENAME2}"
fi
done
}
function setCurrentImageSet() {
WHICHMODALITY=$1
CURRENTIMAGESET=()
COUNT=0
for (( g = $WHICHMODALITY; g < ${#IMAGESETARRAY[@]}; g+=$NUMBEROFMODALITIES ))
do
CURRENTIMAGESET[$COUNT]=${IMAGESETARRAY[$g]}
(( COUNT++ ))
done
}
cleanup()
{
echo "\n*** Performing cleanup, please wait ***\n"
runningANTSpids=$( 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"
}
#initializing variables with global scope
time_start=`date +%s`
currentdir=`pwd`
nargs=$#
STATSMETHOD=1
SHARPENMETHOD=1
USEFLOAT=1
BACKUPEACHITERATION=0
MAXITERATIONS=100x100x70x20
SMOOTHINGFACTORS=3x2x1x0
SHRINKFACTORS=6x4x2x1
METRICTYPE=()
TRANSFORMATIONTYPE="SyN"
NUMBEROFMODALITIES=1
MODALITYWEIGHTSTRING=""
N4CORRECT=1
DOLINEAR=1
NOWARP=0
DOQSUB=0
GRADIENTSTEP=0.25
ITERATIONLIMIT=4
CORES=2
TDIM=0
RIGID=0
range=0
REGTEMPLATES=()
TEMPLATES=()
CURRENTIMAGESET=()
XGRIDOPTS=""
SCRIPTPREPEND=""
WALLTIME="20:00:00"
MEMORY="8gb"
# System specific queue options, eg "-q name" to submit to a specific queue
# It can be set to an empty string if you do not need any special cluster options
QSUBOPTS="" # EDIT THIS
OUTPUTNAME=antsBTP
TEMPLATENAME=${OUTPUTNAME}template
AFFINE_UPDATE_FULL=1
##Getting system info from linux can be done with these variables.
# RAM=`cat /proc/meminfo | sed -n -e '/MemTotal/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# RAMfree=`cat /proc/meminfo | sed -n -e '/MemFree/p' | awk '{ printf "%s %s\n", $2, $3 ; }' | cut -d " " -f 1`
# cpu_free_ram=$((${RAMfree}/${cpu_count}))
if [[ ${OSTYPE:0:6} == 'darwin' ]];
then
cpu_count=`sysctl -n hw.physicalcpu`
else
cpu_count=`cat /proc/cpuinfo | grep processor | wc -l`
fi
# Provide output for Help
if [[ "$1" == "-h" ]];
then
Usage >&2
fi
# reading command line arguments
while getopts "A:a:b:c:d:e:f:g:h:i:j:k:l:m:n:o:p:q:s:r:t:u:v:w:x:y:z:" OPT
do
case $OPT in
h) #help
Usage >&2
exit 0
;;
A) # Sharpening method
SHARPENMETHOD=$OPTARG
;;
a) # summarizing statistic
STATSMETHOD=$OPTARG
;;
b) #backup each iteration
BACKUPEACHITERATION=$OPTARG
;;
e) #float boolean
USEFLOAT=$OPTARG
;;
c) #use SGE cluster
DOQSUB=$OPTARG
if [[ $DOQSUB -gt 5 ]];
then
echo " DOQSUB must be an integer value (0=serial, 1=SGE qsub, 2=try pexec, 3=XGrid, 4=PBS qsub, 5=SLURM) you passed -c $DOQSUB "
exit 1
fi
;;
d) #dimensions
DIM=$OPTARG
if [[ ${DIM} -eq 4 ]];
then
DIM=3
TDIM=4
fi
;;
g) #gradient stepsize (default = 0.25)
GRADIENTSTEP=$OPTARG
;;
i) #iteration limit (default = 3)
ITERATIONLIMIT=$OPTARG
;;
j) #number of cpu cores to use (default = 2)
CORES=$OPTARG
;;
k) #number of modalities used to construct the template (default = 1)
NUMBEROFMODALITIES=$OPTARG
;;
l) #do linear (rigid + affine) for deformable registration
DOLINEAR=$OPTARG
;;
w) #modality weights (default = 1)
MODALITYWEIGHTSTRING=$OPTARG
;;
q) #max iterations other than default
MAXITERATIONS=$OPTARG
;;
f) #shrink factors
SHRINKFACTORS=$OPTARG
;;
s) #smoothing factors
SMOOTHINGFACTORS=$OPTARG
;;
n) #apply bias field correction
N4CORRECT=$OPTARG
;;
o) #output name prefix
OUTPUTNAME=$OPTARG
TEMPLATENAME=${OUTPUTNAME}template
;;
p) #Script prepend
SCRIPTPREPEND=$OPTARG
;;
m) #similarity model
METRICTYPE[${#METRICTYPE[@]}]=$OPTARG
;;
r) #start with rigid-body registration
RIGID=$OPTARG
;;
t) #transformation model
TRANSFORMATIONTYPE=$OPTARG
;;
u)
WALLTIME=$OPTARG
;;
v)
MEMORY=$OPTARG
;;
x) #initialization template
XGRIDOPTS=$OPTARG
;;
y) # update with full affine, 0 for no rigid (default = 1)
AFFINE_UPDATE_FULL=$OPTARG
;;
z) #initialization template
REGTEMPLATES[${#REGTEMPLATES[@]}]=$OPTARG
;;
\?) # getopts issues an error message
echo "$USAGE" >&2
exit 1
;;
esac
done
# Provide different output for Usage and Help
if [[ ${TDIM} -eq 4 && $nargs -lt 5 ]];
then
Usage >&2
elif [[ ${TDIM} -eq 4 && $nargs -eq 5 ]];
then
echo ""
# This option is required to run 4D template creation on SGE with a minimal command line
elif [[ $nargs -lt 6 ]]
then
Usage >&2
fi
OUTPUT_DIR=`dirname ${OUTPUTNAME}`
if [[ ! -d $OUTPUT_DIR ]];
then
echo "The output directory \"$OUTPUT_DIR\" does not exist. Making it."
mkdir -p $OUTPUT_DIR
fi
# Intermediate template output. Keep the template for each iteration and also the average warp if defined.
# Useful for debugging and monitoring convergence
intermediateTemplateDir=${OUTPUT_DIR}/intermediateTemplates
mkdir -p $intermediateTemplateDir
if [[ $DOQSUB -eq 1 || $DOQSUB -eq 4 ]];
then
qq=`which qsub`
if [[ ${#qq} -lt 1 ]];
then
echo "do you have qsub? if not, then choose another c option ... if so, then check where the qsub alias points ..."
exit
fi
fi
if [[ $DOQSUB -eq 5 ]];
then
qq=`which sbatch`
if [[ ${#qq} -lt 1 ]];
then
echo "do you have sbatch? if not, then choose another c option ... if so, then check where the sbatch alias points ..."
exit
fi
fi
for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
do
TEMPLATES[$i]=${TEMPLATENAME}${i}.nii.gz
done
if [[ ${#METRICTYPE[@]} -eq 0 ]];
then
METRICTYPE[0]=CC
fi
if [[ ${#METRICTYPE[@]} -eq 1 ]];
then
for (( i = 1; i < $NUMBEROFMODALITIES; i++ ))
do
METRICTYPE[${#METRICTYPE[@]}]=${METRICTYPE[0]}
done
fi
if [[ ${#METRICTYPE[@]} -ne $NUMBEROFMODALITIES ]];
then
echo "The number of similarity metrics does not match the number of specified modalities (see -s option)"
exit
fi
if [[ ! -n "$MODALITYWEIGHTSTRING" ]];
then
for (( i = 0; i < $NUMBEROFMODALITIES; i++ ))
do
MODALITYWEIGHTS[$i]=1
done
else
MODALITYWEIGHTS=(`echo $MODALITYWEIGHTSTRING | tr 'x' "\n"`)
if [[ ${#MODALITYWEIGHTS[@]} -ne $NUMBEROFMODALITIES ]];
then
echo "The number of weights (specified e.g. -w 1x1x1) does not match the number of specified modalities (see -k option)";
exit 1
fi
fi
TRANSFORMATION=''
# Allow SyN[step] or SyN[ step ]
# Users should use the latter to avoid glob problems, but but don't want force that
#
if [[ $TRANSFORMATIONTYPE == "BSplineSyN"* ]];
then
if [[ $TRANSFORMATIONTYPE == "BSplineSyN["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="BSplineSyN[ 0.1,26,0,3 ]"
fi
elif [[ $TRANSFORMATIONTYPE == "SyN"* ]];
then
if [[ $TRANSFORMATIONTYPE == "SyN["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="SyN[ 0.1,3,0 ]"
fi
elif [[ $TRANSFORMATIONTYPE == "TimeVaryingVelocityField"* ]];
then
if [[ $TRANSFORMATIONTYPE == "TimeVaryingVelocityField["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="TimeVaryingVelocityField[ 0.5,4,3,0,0,0 ]"
fi
elif [[ $TRANSFORMATIONTYPE == "TimeVaryingBSplineVelocityField"* ]];
then
if [[ $TRANSFORMATIONTYPE == "TimeVaryingBSplineVelocityField["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="TimeVaryingVelocityField[ 0.5,12x12x12x2,4,3 ]"
fi
elif [[ $TRANSFORMATIONTYPE == "Affine"* ]];
then
echo "Linear transforms only!!!!"
NOWARP=1
if [[ $TRANSFORMATIONTYPE == "Affine["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="Affine[ 0.1 ]"
fi
elif [[ $TRANSFORMATIONTYPE == "Rigid"* ]];
then
echo "Rigid transforms only!!!!"
NOWARP=1
if [[ $TRANSFORMATIONTYPE == "Rigid["*"]" ]]
then
TRANSFORMATION=${TRANSFORMATIONTYPE}
else
TRANSFORMATION="Rigid[ 0.1 ]"
fi
else
echo "Invalid transformation. See `basename $0` -h for help menu."
exit 1
fi
if [[ $STATSMETHOD -lt 0 ]] || [[ $STATSMETHOD -gt 2 ]];
then
echo "Invalid stats type: using normalized mean (1)"
STATSMETHOD=1
fi
if [[ $SHARPENMETHOD -lt 0 ]] || [[ $SHARPENMETHOD -gt 2 ]];
then
echo "Invalid sharpening method: using Laplacian (1)"
SHARPENMETHOD=1
fi
AVERAGE_AFFINE_PROGRAM="AverageAffineTransform"
if [[ $AFFINE_UPDATE_FULL -eq 0 ]];
then
AVERAGE_AFFINE_PROGRAM="AverageAffineTransformNoRigid"
fi
# Creating the file list of images to make a template from.
# Shiftsize is calculated because a variable amount of arguments can be used on the command line.
# The shiftsize variable will give the correct number of arguments to skip. Issuing shift $shiftsize will
# result in skipping that number of arguments on the command line, so that only the input images remain.
shiftsize=$(($OPTIND - 1))
shift $shiftsize
# The invocation of $* will now read all remaining arguments into the variable IMAGESETVARIABLE
IMAGESETVARIABLE=$*
NINFILES=$(($nargs - $shiftsize))
IMAGESETARRAY=()
if [[ ${NINFILES} -eq 0 ]];
then
echo "Please provide at least 2 filenames for the template inputs."
echo "Use `basename $0` -h for help"
exit 1
elif [[ ${NINFILES} -eq 1 ]];
then
extension=`echo ${IMAGESETVARIABLE#*.}`
if [[ $extension = 'csv' || $extension = 'txt' ]];
then
IMAGESFILE=$IMAGESETVARIABLE
IMAGECOUNT=0
while read line
do
files=(`echo $line | tr ',' ' '`)
if [[ ${#files[@]} -ne $NUMBEROFMODALITIES ]];
then
echo "The number of files in the csv file does not match the specified number of modalities."
echo "See the -k option."
exit 1
fi
for (( i = 0; i < ${#files[@]}; i++ ));
do
IMAGESETARRAY[$IMAGECOUNT]=${files[$i]}
((IMAGECOUNT++))
done
done < $IMAGESFILE
else
range=`${ANTSPATH}/ImageMath $TDIM abs nvols ${IMAGESETVARIABLE} | tail -1 | cut -d "," -f 4 | cut -d " " -f 2 | cut -d " ]" -f 1 `
if [[ ${range} -eq 1 && ${TDIM} -ne 4 ]];
then
echo "Please provide at least 2 filenames for the template."
echo "Use `basename $0` -h for help"
exit 1
elif [[ ${range} -gt 1 && ${TDIM} -ne 4 ]]
then
echo "This is a multivolume file. Use -d 4"
echo "Use `basename $0` -h for help"
exit 1
elif [[ ${range} -gt 1 && ${TDIM} -eq 4 ]];
then
echo
echo "--------------------------------------------------------------------------------------"
echo " Creating template of 4D input. "
echo "--------------------------------------------------------------------------------------"
#splitting volume
#setting up working dirs
tmpdir=${currentdir}/tmp_${RANDOM}_${RANDOM}_${RANDOM}_$$
(umask 077 && mkdir ${tmpdir}) || {
echo "Could not create temporary directory! Exiting." 1>&2
exit 1
}
mkdir ${tmpdir}/selection
#split the 4D file into 3D elements
cp ${IMAGESETVARIABLE} ${tmpdir}/
cd ${tmpdir}/
# ${ANTSPATH}/ImageMath $TDIM vol0.nii.gz TimeSeriesSubset ${IMAGESETVARIABLE} ${range}
# rm -f ${IMAGESETVARIABLE}
# selecting 16 volumes randomly from the timeseries for averaging, placing them in tmp/selection folder.
# the script will automatically divide timeseries into $total_volumes/16 bins from wich to take the random volumes;
# if there are more than 32 volumes in the time-series (in case they are smaller
nfmribins=16
if [[ ${range} -gt 31 ]];
then
BINSIZE=$((${range} / ${nfmribins}))
j=1 # initialize counter j
for ((i = 0; i < ${nfmribins}; i++))
do
FLOOR=$((${i} * ${BINSIZE}))
BINrange=$((${j} * ${BINSIZE}))
# Retrieve random number between two limits.
number=0 #initialize
while [[ "$number" -le $FLOOR ]];
do
number=$RANDOM
if [[ $i -lt 15 ]];
then
let "number %= $BINrange" # Scales $number down within $range.
elif [[ $i -eq 15 ]];
then
let "number %= $range" # Scales $number down within $range.
fi
done
#debug only
echo
echo "Random number between $FLOOR and $BINrange --- $number"
# echo "Random number between $FLOOR and $range --- $number"
if [[ ${number} -lt 10 ]];
then
${ANTSPATH}/ImageMath $TDIM selection/vol000${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol000${number}.nii.gz selection/
elif [[ ${number} -ge 10 && ${number} -lt 100 ]];
then
${ANTSPATH}/ImageMath $TDIM selection/vol00${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol00${number}.nii.gz selection/
elif [[ ${number} -ge 100 && ${number} -lt 1000 ]];
then
${ANTSPATH}/ImageMath $TDIM selection/vol0${number}.nii.gz ExtractSlice ${IMAGESETVARIABLE} ${number}
# cp vol0${number}.nii.gz selection/
fi
let j++
done