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atlasBREX.sh
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#!/usr/bin/env bash
#atlasBREX: Automated template-derived brain extraction for animal MRI
#https://github.com/jlohmeier/atlasBREX
#LIC: BSD-3-Clause
#Author: Johannes Lohmeier
#Email: johannes.lohmeier@charite.de
#Changed: 04.05.2022 (v1.5)
#Number of threads for ANTs
#set number of threads: ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=32
#NPROCESSORS_ONLN on FreeBSD/PC-BSD
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$(/bin/sh -c 'getconf _NPROCESSORS_ONLN')
# controls multi-threading
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS
export LC_NUMERIC=C
HELP() {
cat <<HELP
atlasBREX [ver: 1.5]
---
Documentation: https://github.com/jlohmeier/atlasBREX
Requirement: FSL ≥ 5 (optional usage of AFNI and ANTs)
---
Usage:
bash $0 -b <input> -nb <input> -h <input> -f <input>
Compulsory arguments:
-b brain-extracted atlas or template
-nb whole-head (non-brain) atlas or template
-h target 3D volume
-f fractional intensity threshold [1 > n > 0] for provisional (BET) brain-extraction (e.g. -f 0.2).
interactive pilot: [-f n] proposes 3 default thresholds for user selection.
for multi-step registration, different values for high-res,
low-res and native volumes can be entered (e.g. -f 0.2,0.5,0.8)
Optional arguments:
-l low-resolution 3D volume (3-step registration)
-n (functional) 3D/4D volume (2-/3-step registration)
-t/-tmp disable removal [1] of temporary files (default: 0)
-w/-wrp define FNIRT (FSL) warp-resolution (e.g. -wrp 10,10,10),
for SyN (ANTs) enter warp [-wrp 1] flag (e.g. -wrp 1 -reg 2)
-r/-reg FNIRT w/ bending- [-reg 0] or membrane-energy regularization [-reg 1]
ANTs/SyN w/ [-reg 2] or w/o [-reg 3] additional N4BiasFieldCorrection (def: 1)
-nrm provisional intensity normalization w/ T1 [-nrm 1] or T2 [-nrm 2] (req: AFNI)
(recommended for low-resolution volumes)
-lr optimized parameter settings for low-resolution volumes:
[1] non-linear registration between whole-head template and target volume with mask
[2] non-linear registration based on skullstripped template and target volume (def: 0)
-msk mask binarization threshold (in %) for fslmaths
w/ optional erosion and dilation (e.g. -msk b,10,0,0) (def: b,0.5,0,0)
[-msk b,[100 < n > 0] for threshold, [0-9] for n-times erosion,
[0-9] for n-times dilation] or 3dAutomask (e.g. -msk a,0,0, req: AFNI)
[-msk a,[0-9] for n-times erosion,[0-9] for n-times dilation]
-vox provisional voxel-size adjustment [-vox 1] (def: 0)
-dil n-times dilation of the brain-extraction from linear registration
prior to non-linear registration (e.g. -dil 4)
HELP
}
#/********************/
#/********************/
if [[ $# -eq 0 ]]
then
HELP >&2
exit 1
fi
ARGS="$@"
SYN=">> Incorrect syntax. See -help"
while [ "$#" -gt 0 ]
do
case "$1" in
-b | -B )
if [[ -n "$2" ]]; then standard_BE_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-nb |-NB )
if [[ -n "$2" ]]; then standard_nonBE_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-h |-H )
if [[ -n "$2" ]]; then highres_nonBE_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-l |-L )
if [[ -n "$2" ]]; then lowres_nonBE_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-n |-N )
if [[ -n "$2" ]]; then func_nonBE_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-f |-F )
if [[ -n "$2" ]]; then THR_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-r |-R |-reg |-REG )
if [[ -n "$2" ]]; then METHOD_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-lr |-LR )
if [[ -n "$2" ]]; then LOWRES_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-w |-W |-wrp |-WRP )
if [[ -n "$2" ]]; then WARP_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-t |-T |-tmp |-TMP )
if [[ -n "$2" ]]; then TEMP_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-rot |-ROT )
if [[ -n "$2" ]]; then REORIENT_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-msk |-MSK )
if [[ -n "$2" ]]; then MASK_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-nrm |-NRM )
if [[ -n "$2" ]]; then NORM_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-vox |-VOX )
if [[ -n "$2" ]]; then VOX_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-dil |-DIL )
if [[ -n "$2" ]]; then voxfac_="$2"; else echo $SYN; exit 1 ; fi
shift 2
;;
-help|--help)
HELP >&2
exit 1
shift
;;
*)
if [[ $arguments -eq 0 ]] && [[ "$1" != "" ]]
then
echo ">> Unknown argument '$1'. See -help." >&2;
exit 1
fi
shift 1
;;
esac
done
#error handling
set -o errexit
set -o pipefail
trap "trap - SIGTERM && kill -- -$$" SIGINT SIGTERM EXIT
removetemp() {
if [[ $TEMP -eq "0" ]]
then
rm -f *'mask'*
rm -f *'orig'*
rm -f *'tmp'*
rm -f *'temp'*
rm -f *'high2'*
#keep non-linear warp
find . -maxdepth 1 -name "*_.nii.gz*" ! -name "*std2high_warp*" -delete
find . -maxdepth 1 -name "*std2*" ! -name "*.nii.gz" ! -name "*std2high_warp*" -delete
rm -f *'low2'*
fi
}
trap removetemp SIGINT
trap removetemp 0
#/********************/
#/********************/
#/********************/
#/********************/
#prep region
#compulsory input
if [[ -z "${standard_BE_}" || -z "${standard_nonBE_}" || -z "${highres_nonBE_}" ]] || [[ -z "${THR_}" ]]
then
echo '>> Compulsory parameters were not specified! See -help'
exit 1
fi
#warning not in common folder
SDIR=$(dirname "$0")
if [[ ! $(dirname "${standard_BE_}") == $SDIR ]] || [[ ! $(dirname "${standard_nonBE_}") == $SDIR ]] || [[ ! $(dirname "${highres_nonBE_}") == $SDIR ]]
then
echo ">> All files need to be within a common folder."
exit 1
fi
#warning conflicting file/folder names
tfd=$(echo *temp*)
ofd=$(echo *orig*)
if [[ -f ${tfd[0]} ]] || [[ -d ${tfd[0]} ]] || [[ -f ${ofd[0]} ]] || [[ -d ${ofd[0]} ]]
then
echo ">> Rename files or folders with [temp] or [orig] within this directory."
exit 1
fi
#set temp flag
TEMP=0
if [[ -n "${TEMP_}" ]]
then
if [[ ${TEMP_} -eq "1" ]] || [[ ${TEMP_} -eq "0" ]]
then
#remove temp
TEMP=${TEMP_}
else
echo '>> Input needs to be either [1] or [0] (default: 0). See -help'
exit 1
fi
fi
#default
MASK="b,0.5,0,0"
#(\d?[1-9]|[1-9]0)
#set mask
if [[ -n "${MASK_}" ]]
then
if [[ ${MASK_} =~ ^a,[0-9]{1},[0-9]{1}$ ]] || [[ ${MASK_} =~ ^b,([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),[0-9]{1},[0-9]{1}$ ]]
then
MASK=${MASK_}
if [[ $(echo $MASK | cut -d"," -f1) == "a" ]]
then
if ! type 3dAutomask &>/dev/null
then
echo '>> 3dAutomask was not found. Check your .bashrc profile or reinstall AFNI.'
exit 1
fi
fi
else
echo '>> Specified mask input is not valid. See -help'
exit 1
fi
fi
#set method
#FSL default
METHOD=0
REGM='membrane_energy'
if [[ -n "${METHOD_}" ]]
then
if [[ $METHOD_ =~ ^[0-4]$ ]]
then
case $METHOD_ in
"0")
#FSL bending
METHOD=0
REGM='bending_energy'
;;
"1")
#FSL membrane
METHOD=0
REGM='membrane_energy'
;;
"2")
#ANTs w/ BF
METHOD=1
BIAS=1
;;
"3")
#ANTs w/o BF
METHOD=1
;;
esac
else
echo '>> Input needs to be a number from [1-4] (default: 0). See -help'
exit 1
fi
fi
if [[ $METHOD -eq "1" ]]
then
if ! type antsRegistration &>/dev/null || ! type antsApplyTransforms &>/dev/null || ! type antsRegistrationSyN.sh &>/dev/null || ! type N4BiasFieldCorrection &>/dev/null || ! type ImageMath &>/dev/null
then
echo '>> Define $ANTSPATH in your .bashrc profile. Assure that antsRegistration, antsApplyTransforms, N4BiasFieldCorrection, ImageMath and antsRegistrationSyN are available.'
exit 1
fi
fi
#set linear or non-linear
LIN=1
LINMSG='>> For SyN registration (ANTs), warp argument needs to be set to [1] (e.g. -wrp 1 -reg 2).\nFor FNIRT registration (FSL), warp resolution must be entered in the specified manner (e.g. -wrp 10,10,10). See -help'
if [[ -n "$WARP_" ]]
then
if [[ $WARP_ =~ ^[0-9]{1,3},[0-9]{1,3},[0-9]{1,3}$ ]] || [[ $WARP_ -eq "1" ]]
then
if [[ $METHOD -eq "0" ]] && [[ $WARP_ =~ ^[0-9]{1,3},[0-9]{1,3},[0-9]{1,3}$ ]]
then
LIN=0
WARP=${WARP_}
fi
if [[ $METHOD -eq "0" ]] && [[ ! $WARP_ =~ ^[0-9]{1,3},[0-9]{1,3},[0-9]{1,3}$ ]]
then
echo -e $LINMSG
exit 1
fi
if [[ $METHOD -eq "1" ]] && [[ $WARP_ =~ ^[1]$ ]]
then
LIN=0
fi
if [[ $METHOD -eq "1" ]] && [[ ! $WARP_ =~ ^[1]$ ]]
then
echo -e $LINMSG
exit 1
fi
else
echo -e $LINMSG
exit 1
fi
fi
#set flag for rotation to common orientation
REORIENT=0
if [[ -n "${REORIENT_}" ]]
then
if [[ ${REORIENT_} -eq "0" ]] || [[ ${REORIENT_} -eq "1" ]]
then
REORIENT=${REORIENT_}
else
echo '>> Input needs to be either [1] or [0] (default: 0). See -help'
exit 1
fi
fi
#set flag for normalization
if [[ -n "${NORM_}" ]]
then
if [[ ${NORM_} -eq "1" ]] || [[ ${NORM_} -eq "2" ]]
then
NORM=${NORM_}
if ! type 3dUnifize &>/dev/null
then
echo '3dUnifize was not found. Check .bashrc profile or reinstall AFNI.'
exit 1
fi
else
echo '>> Input needs to be either [1] for T1-weighted or [2] for T2-weighted volumes. See -help'
exit 1
fi
fi
#set flag for voxel scaling
VOX=0
if [[ -n "${VOX_}" ]]
then
if [[ ${VOX_} -eq "0" ]] || [[ ${VOX_} -eq "1" ]]
then
VOX=${VOX_}
else
echo '>> Input needs to be either [0] or [1] (default: 0). See -help'
exit 1
fi
fi
#set n-step registration
if [[ -n "${lowres_nonBE_}" ]] && [[ -n "${func_nonBE_}" ]]
then
#2 = 3-step/LR+N
STEP=2
fi
if [[ -n "${lowres_nonBE_}" ]] && [[ -z "${func_nonBE_}" ]]
then
echo '>> Either set the low-res volume as native volume or specify an additional native-volume.'
exit 1
fi
if [[ -z "${lowres_nonBE_}" ]]
then
#1 = 2-step/N
STEP=1
fi
if [[ -z "${lowres_nonBE_}" ]] && [[ -z "${func_nonBE_}" ]]
then
#0 = 1-step/HR
STEP=0
fi
#set flag for brain dilation
voxfac=0
if [[ -n "${voxfac_}" ]]
then
if [[ ${voxfac_} -gt "0" ]]
then
voxfac=${voxfac_}
else
echo '>> Input needs to be a number greater than [0]. See -help'
exit 1
fi
fi
#set fractional intensity value
thrmsg=">> Input needs to be a number (e.g. -f 0.8). Entering [n] will propose 3 default thresholds during the procedure. For multi-step registration either enter a single paramater or parameters matching the registration steps (e.g. -f 0.2,0.3,0.4 for 3-step). See -help"
if [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]] || [[ ${THR_} == "n" ]] || [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]] || [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
if [[ $STEP -eq "0" ]]
then
if [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]] || [[ ${THR_} == "n" ]]
then
THR=${THR_}
else
echo $thrmsg
exit 1
fi
fi
if [[ $STEP -eq "1" ]]
then
if [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]] || [[ ${THR_} == "n" ]] || [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
THR=${THR_}
else
echo $thrmsg
exit 1
fi
fi
if [[ $STEP -eq "2" ]]
then
if [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]] || [[ ${THR_} == "n" ]] || [[ ${THR_} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
THR=${THR_}
else
echo $thrmsg
exit 1
fi
fi
else
echo $thrmsg
exit 1
fi
#set flag for low-res mode
LOWRES=0
if [[ -n "${LOWRES_}" ]] && [[ $LIN -eq "0" ]]
then
if [[ ${LOWRES_} -eq "0" ]] || [[ ${LOWRES_} -eq "1" ]] || [[ ${LOWRES_} -eq "2" ]]
then
if [[ ${LOWRES_} -eq "1" ]]
then
LOWRES=1
fi
if [[ ${LOWRES_} -eq "2" ]]
then
LOWRES=2
fi
else
echo '>> Input needs to be either [1] or [2] (default: 0). See -help'
exit 1
fi
fi
#prep endregion
#/********************/
#/********************/
#/********************/
#/********************/
#functions region
declare -A output
ic=0
up_time() {
start=$1
end=$2
process="$3"
dt=$(echo "$end - $start" | bc)
dd=$(echo "$dt/86400" | bc)
dt2=$(echo "$dt-86400*$dd" | bc)
dh=$(echo "$dt2/3600" | bc)
dt3=$(echo "$dt2-3600*$dh" | bc)
dm=$(echo "$dt3/60" | bc)
ds=$(echo "$dt3-60*$dm" | bc)
result=$(printf ": %d:%02d:%02d:%02.4f\n" $dd $dh $dm $ds)
output+=([$ic+1]=$(echo "${process} ${result} \n"))
}
check_file() {
tmp=$1
fin=$2
if [[ -f "${tmp}" ]]
then
if [[ "${tmp}" == *'.nii.gz'* ]]
then
#check volume validity
if [[ `$FSLDIR/bin/imtest "${tmp}"` -ne 1 ]]
then
echo "${tmp} is not a valid input volume."
exit 1
fi
cp -f ${tmp} ${tmp%%.*}_.nii.gz
eval "${fin}"="${tmp%%.*}_.nii.gz"
else
echo ">> .nii.gz file extension expected."
exit 1
fi
else
echo ">>" ${tmp} "could not be found! Correct the entered filename and path."
exit 1
fi
}
report() {
for (( c=1; c<=3; c++ ))
do
echo ">>" | tee -a log.txt
done
echo -e ">> Summary:" | tee -a log.txt
echo ">" $0 $ARGS | tee -a log.txt
printf "${output[@]}" | tee -a log.txt
}
detvoxsize()
{
filename=$1
tar=$2
tar_=$3
xval=$(fslval $filename pixdim1)
yval=$(fslval $filename pixdim2)
zval=$(fslval $filename pixdim3)
FACx=$(printf %.0f $(echo "$tar/$xval" | bc -l))
FACy=$(printf %.0f $(echo "$tar/$yval" | bc -l))
FACz=$(printf %.0f $(echo "$tar/$zval" | bc -l))
FAC=($FACx $FACy $FACz)
maxFAC=${FAC[0]}
for n in "${FAC[@]}"
do
[[ $n > $maxFAC ]] && maxFAC=$n
done
if [[ $(echo "$maxFAC > 1" | bc -l) ]]
then
#printf %.2f $(echo "$float/1.18" | bc -l)
nxval=$( printf "%.1f\n" $(echo "scale=1; ($xval * $maxFAC)" | bc -l) )
nyval=$( printf "%.1f\n" $(echo "scale=1; ($yval * $maxFAC)" | bc -l) )
nzval=$( printf "%.1f\n" $(echo "scale=1; ($zval * $maxFAC)" | bc -l) )
echo "> Upscale factor estimation: $maxFAC" | tee -a log.txt
fi
if [[ ! $(echo "$nxval >= 1" | bc -l) ]] || [[ ! $(echo "$nyval >= 1" | bc -l) ]] || [[ ! $(echo "$nzval >= 1" | bc -l) ]]
then
FACx=$(printf %.0f $(echo "$tar_/$xval" | bc -l))
FACy=$(printf %.0f $(echo "$tar_/$yval" | bc -l))
FACz=$(printf %.0f $(echo "$tar_/$zval" | bc -l))
FAC=($FACx $FACy $FACz)
maxFAC=${FAC[0]}
for n in "${FAC[@]}"
do
[[ $n > $maxFAC ]] && maxFAC=$n
done
if [[ $(echo "$maxFAC > 1" | bc -l) ]]
then
nxval=$( printf "%.1f\n" $(echo "scale=1; ($xval * $maxFAC)" | bc -l) )
nyval=$( printf "%.1f\n" $(echo "scale=1; ($yval * $maxFAC)" | bc -l) )
nzval=$( printf "%.1f\n" $(echo "scale=1; ($zval * $maxFAC)" | bc -l) )
echo "> Upscale factor estimation: $maxFAC" | tee -a log.txt
fi
fi
#fallback solution
if [[ ! $(echo "$nxval >= 1" | bc -l) ]] || [[ ! $(echo "$nyval >= 1" | bc -l) ]] || [[ ! $(echo "$nzval >= 1" | bc -l) ]]
then
maxFAC=10
fi
}
chvoxsize()
{
filename=$1
factor=$2
xval=$(fslval $filename pixdim1)
yval=$(fslval $filename pixdim2)
zval=$(fslval $filename pixdim3)
nxval=$( printf "%.1f\n" $(echo "($xval * $factor)" | bc -l) )
nyval=$( printf "%.1f\n" $(echo "($yval * $factor)" | bc -l) )
nzval=$( printf "%.1f\n" $(echo "($zval * $factor)" | bc -l) )
echo "> (Temp.) voxel dimension scaling $filename to $nxval $nyval $nzval using factor $factor" | tee -a log.txt
cp -f $filename ${filename%%.*}orig_.nii.gz
$FSLDIR/bin/fslchpixdim $filename $nxval $nyval $nzval
$FSLDIR/bin/fslorient -setqformcode 1 $filename
}
normalize()
{
filename=$1
case $NORM in
"1")
MSG=$(echo -e "> Intensity normalization: $filename \n")
echo -e "$MSG" | tee -a log.txt
output+=([$ic+1]=$(echo ""${MSG}" \n"))
3dUnifize -overwrite -GM -prefix $filename -input $filename | tee -a log.txt
;;
"2")
MSG=$(echo -e "> Intensity normalization: $filename \n")
echo -e "$MSG" | tee -a log.txt
output+=([$ic+1]=$(echo ""${MSG}" \n"))
3dUnifize -overwrite -GM -T2 -prefix $filename -input $filename | tee -a log.txt
;;
esac
}
pre_extraction() {
#provisional brain-extraction
filename=$1
out=$2
frct=$3
cp -f $filename ${filename%%.*}orig.nii.gz
#normalization
normalize $filename
#check for time dimension and extract 3D for ANTs
TAXIS=$(fslval $filename dim4)
if [[ $METHOD -eq "1" ]] && [[ $TAXIS -gt "1" ]]
then
DIM=$(echo "-d 4")
ImageMath 4 $filename ExtractSlice $filename 1
wait
cp $filename ${filename%%.*}temp_header.nii.gz
else
cp $filename ${filename%%.*}temp_header.nii.gz
fi
#temporarily change voxel size for prelim segmentation
if [[ $METHOD -eq "0" ]] && [[ $LIN -eq "0" ]] && [[ $VOX -eq "1" ]]
then
echo "> Skipping another upscaling step."
else
detvoxsize "$filename" "1.5" "2"
chvoxsize "$filename" "$maxFAC"
fi
preBE_start=$(date +%s.%N)
echo "> Provisional (BET) segmentation ($frct): $filename" | tee -a log.txt
#BET binary mask
if [[ $frct == "n" ]]
then
$FSLDIR/bin/bet $filename ${filename%%.*}temp_option_1 -f 0.3 -R -g 0 -m | tee -a log.txt
wait
$FSLDIR/bin/bet $filename ${filename%%.*}temp_option_2 -f 0.5 -R -g 0 -m | tee -a log.txt
wait
$FSLDIR/bin/bet $filename ${filename%%.*}temp_option_3 -f 0.8 -R -g 0 -m | tee -a log.txt
wait
fsleyes ${filename%%.*}temp_option_1.nii.gz &
fsleyes ${filename%%.*}temp_option_2.nii.gz &
fsleyes ${filename%%.*}temp_option_3.nii.gz &
for (( c=1; c<=3; c++ ))
do
echo ">>" | tee -a log.txt
done
echo -e "> Shall we proceed with option 1 (-f 0.3), option 2 (-f 0.5) or option 3 (-f 0.8)?\n> In addition, an arbitrary fractional intensity threshold can be entered with option 4.\n> Enter a number from [1]-[4] and close fsleyes." | tee -a log.txt
read -p "Option: " option
if [[ $option =~ ^[1-4]$ ]]
then
case $option in
"1")
mask=${filename%%.*}temp_option_1_mask.nii.gz
;;
"2")
mask=${filename%%.*}temp_option_2_mask.nii.gz
;;
"3")
mask=${filename%%.*}temp_option_3_mask.nii.gz
;;
"4")
echo -e "> Enter parameter:" | tee -a log.txt
read -p "Value: " option_
if [[ $option_ =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
$FSLDIR/bin/bet $filename ${filename%%.*}temp_1 -f $option_ -R -g 0 -m | tee -a log.txt
wait
mask=${filename%%.*}temp_1_mask.nii.gz
else
echo ">> Invalid input." | tee -a log.txt
exit 1
fi
;;
esac
MSG="> Proceeding with option $option"
echo $MSG | tee -a log.txt
output+=([$ic+1]=$(echo "$MSG\n"))
else
echo ">> Input needs to be a number from [1-4]." | tee -a log.txt
exit 1
fi
else
$FSLDIR/bin/bet $filename ${filename%%.*}temp_1 -f $frct -R -g 0 -m | tee -a log.txt
wait
mask=${filename%%.*}temp_1_mask.nii.gz
fi
#create filtered volume
#3dcalc -overwrite -prefix ${out}.nii.gz -a $filename -b $mask -expr 'a*b' | tee -a log.txt
${FSLDIR}/bin/fslmaths $filename -nan -mul $mask ${out}.nii.gz | tee -a log.txt
wait
MSG=$(printf "> Provisional BET : ${filename%%.*}")
preBE_end=$(date +%s.%N)
up_time $preBE_start $preBE_end "${MSG}"
#biasfieldcorr
if [[ $METHOD -eq "1" ]] && [[ $BIAS -eq "1" ]]
then
N4BiasFieldCorrection -i ${out}.nii.gz -o ${out}.nii.gz -x $mask | tee -a log.txt
MSG=$(echo -e "> N4BiasFieldCorrection (ANTs) : ${out}.nii.gz\n")
echo -e "$MSG" | tee -a log.txt
N4BiasFieldCorrection -i $filename -o $filename -x $mask | tee -a log.txt
MSG_=$(echo -e "> N4BiasFieldCorrection (ANTs) : $filename\n")
echo -e "$MSG_" | tee -a log.txt
output+=([$ic+1]=$(echo ""${MSG}" \n"))
output+=([$ic+1]=$(echo ""${MSG_}" \n"))
fi
#restore original header
${FSLDIR}/bin/fslcpgeom ${filename%%.*}temp_header.nii.gz ${out}.nii.gz
${FSLDIR}/bin/fslcpgeom ${filename%%.*}temp_header.nii.gz $filename
$FSLDIR/bin/fslorient -setqformcode 0 ${out}.nii.gz
$FSLDIR/bin/fslorient -setqformcode 0 $filename
}
binary_mask() {
filename=$1
ftype=$2
#rethreshold binary mask to prevent weighted average
${FSLDIR}/bin/fslmaths ${standard_BE%%.*}${ftype}_msk.nii.gz -thr 0.001 -bin ${standard_BE%%.*}${ftype}_msk_.nii.gz | tee -a log.txt
wait
#3dcalc -overwrite -prefix ${filename%%.*}brain.nii.gz -a ${filename%%.*}orig.nii.gz -b ${standard_BE%%.*}${ftype}_msk.nii.gz -expr 'a*b'
${FSLDIR}/bin/fslmaths ${filename%%.*}orig.nii.gz -nan -mul ${standard_BE%%.*}${ftype}_msk.nii.gz ${filename%%.*}brain_.nii.gz | tee -a log.txt
cp -f ${filename%%.*}brain_.nii.gz ${filename%%.*}brain.nii.gz
rm *'msk'*
if [[ $METHOD -eq "0" ]] && [[ $LIN -eq "0" ]] && [[ $VOX -eq "1" ]]
then
${FSLDIR}/bin/fslcpgeom ${filename%%.*}orig_.nii.gz ${filename%%.*}brain.nii.gz
fi
}
applytransform() {
BE=$1
nonBE=$2
ftype=$3
MTXPASS=$4
case $METHOD in
"0")
#FSL
if [[ $LIN -eq "1" ]]
then
${FSLDIR}/bin/flirt -in ${standard_BE%%.*}std_mask.nii.gz -ref ${BE} -applyxfm -init std2${ftype}.mat -out ${standard_BE%%.*}${ftype}_msk.nii.gz | tee -a log.txt
else
${FSLDIR}/bin/applywarp --ref=${nonBE} --in=${standard_BE%%.*}std_mask.nii.gz --warp=std2high_warp_${highres_BE%%.*} --postmat=high2${ftype}.mat --out=${standard_BE%%.*}${ftype}_msk.nii.gz | tee -a log.txt
fi
;;
"1")
#ANTs
if [[ $LIN -eq "1" ]]
then
antsApplyTransforms -d 3 -i ${standard_BE%%.*}std_mask.nii.gz -r ${BE} -o ${standard_BE%%.*}${ftype}_msk.nii.gz $MTXPASS | tee -a log.txt
else
antsApplyTransforms -d 3 -i ${standard_BE%%.*}std_mask.nii.gz -r ${BE} -o ${standard_BE%%.*}${ftype}_msk.nii.gz $MTXPASS -t std2high_warp_${highres_BE%%.*}.nii.gz -t std2high_warp_${highres_BE%%.*}.mat | tee -a log.txt
fi
;;
esac
}
showmet()
{
if [[ $METHOD -eq "0" ]]
then
if [[ $LIN -eq "1" ]]
then
local MET="FLIRT"
else
local MET="FNIRT"
fi
fi
if [[ $METHOD -eq "1" ]]
then
if [[ $LIN -eq "1" ]]
then
local MET="ANTs"
else
local MET="SyN"
fi
fi
echo "$MET"
}
#functions endregion
#/********************/
#/********************/
#/********************/
#/********************/
#check existence and set variables
check_file $standard_BE_ 'standard_BE'
check_file $standard_nonBE_ 'standard_nonBE'
check_file $highres_nonBE_ 'highres_nonBE'
if [[ -n "$lowres_nonBE_" ]]
then
check_file $lowres_nonBE_ 'lowres_nonBE'
fi
if [[ -n "$func_nonBE_" ]]
then
check_file $func_nonBE_ 'func_nonBE'
fi
#start log
echo -e "\n============" | tee -a log.txt
echo "> atlasBREX [1.5]" | tee -a log.txt
echo -e "============\n" | tee -a log.txt
echo ">> $(date)" | tee -a log.txt
echo ">> PID: $$" | tee -a log.txt
echo ">> Processing:" | tee -a log.txt
output+=([$ic+1]=$(echo "> $(date) \n"))
#timepoint start
total_start=$(date +%s.%N)
#/********************/
#/********************/
#reorient to MNI152
if [[ $REORIENT -eq "0" ]]
then
${FSLDIR}/bin/fslreorient2std $standard_BE $standard_BE | tee -a log.txt
${FSLDIR}/bin/fslreorient2std $standard_nonBE $standard_nonBE | tee -a log.txt
MSG=$(echo -e "> (Temp.) rotating template to match MNI152 orientation \n")
echo -e "$MSG" | tee -a log.txt
output+=([$ic+1]=$(echo ""${MSG}" \n"))
fi
if [[ $REORIENT -eq "0" ]]
then
${FSLDIR}/bin/fslreorient2std $highres_nonBE $highres_nonBE | tee -a log.txt
if [[ -n "$lowres_nonBE" ]] ; then
${FSLDIR}/bin/fslreorient2std $lowres_nonBE $lowres_nonBE | tee -a log.txt
fi
if [[ -n "$func_nonBE" ]] ; then
${FSLDIR}/bin/fslreorient2std $func_nonBE $func_nonBE | tee -a log.txt
fi
MSG=$(echo -e "> (Temp.) rotating target volumes to match MNI152 orientation \n")
echo -e "$MSG" | tee -a log.txt
output+=([$ic+1]=$(echo ""${MSG}" \n"))
fi
#/********************/
#/********************/
#change voxel size for FNIRT
if [[ $METHOD -eq "0" ]] && [[ $LIN -eq "0" ]] && [[ $VOX -eq "1" ]]
then
detvoxsize "$highres_nonBE" "1.5" "2"
chvoxsize "$standard_BE" "$maxFAC"
chvoxsize "$standard_nonBE" "$maxFAC"
fi
#create_atlas_mask
msk_opt=$(echo $MASK | cut -d"," -f1)
mask_start=$(date +%s.%N)
case $msk_opt in
"a")
ERO_=$(echo $MASK | cut -d"," -f2)
DIL_=$(echo $MASK | cut -d"," -f3)
if [[ $ERO_ -gt "0" ]] ; then ERO=$(echo "-erode $ERO_" ) ; fi
if [[ $DIL_ -gt "0" ]] ; then DIL=$(echo "-dilate $DIL_" ) ; fi
3dAutomask $DIL $ERO -overwrite -prefix ${standard_BE%%.*}std_mask.nii.gz $standard_BE | tee -a log.txt
MSG="> Atlas mask created using 3dAutomask ($MASK): ${standard_BE%%.*}std_mask.nii.gz"
echo $MSG | tee -a log.txt
output+=([$ic+1]=$(echo $MSG '\n'))
;;
"b")
BTHR_=$(echo $MASK | cut -d"," -f2)
ERO_=$(echo $MASK | cut -d"," -f3)
DIL_=$(echo $MASK | cut -d"," -f4)
if [[ $BTHR_ > "0" ]] ; then BTHR=$(echo "-thrp $BTHR_" ) ; fi
if [[ $ERO_ -gt "0" ]]
then
for (( c=1; c<=$ERO_; c++ ))
do
ERO+="-ero "
done
fi
if [[ $DIL_ -gt "0" ]]
then
for (( c=1; c<=$DIL_; c++ ))
do
DIL+="-dilD "
done
fi
${FSLDIR}/bin/fslmaths $standard_BE $BTHR $DIL $ERO -bin ${standard_BE%%.*}std_mask.nii.gz | tee -a log.txt
MSG="> Atlas mask created using fslmaths ($MASK): ${standard_BE%%.*}std_mask.nii.gz"
echo $MSG | tee -a log.txt
output+=([$ic+1]=$(echo $MSG '\n'))
;;
esac
mask_end=$(date +%s.%N)
up_time $mask_start $mask_end "> Atlas binary mask"
#normalization
normalize $standard_BE
normalize $standard_nonBE
#change voxel size for FNIRT
if [[ $METHOD -eq "0" ]] && [[ $LIN -eq "0" ]] && [[ $VOX -eq "1" ]]
then
chvoxsize "$highres_nonBE" "$maxFAC"
if [[ -n "$lowres_nonBE" ]] ; then
chvoxsize "$lowres_nonBE" "$maxFAC"
fi
if [[ -n "$func_nonBE" ]] ; then
chvoxsize "$func_nonBE" "$maxFAC"
fi
fi
#provisional brain-extraction
if [[ ${THR} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
f1=$(echo $THR | cut -d"," -f1)
f2=$(echo $THR | cut -d"," -f2)
f3=$(echo $THR | cut -d"," -f3)
fi
if [[ ${THR} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*),([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
f1=$(echo $THR | cut -d"," -f1)
f2=$(echo $THR | cut -d"," -f2)
fi
if [[ ${THR} == "n" ]] || [[ ${THR} =~ ^([0-9]*[1-9][0-9]*(\.[0-9]+)?|[0]*\.[0-9]*[1-9][0-9]*)$ ]]
then
f1=$THR
fi
if [[ ! -f ${highres_nonBE%%.*}tmpbrain.nii.gz && -e $highres_nonBE ]] ; then
pre_extraction $highres_nonBE ${highres_nonBE%%.*}tmpbrain "$f1"
wait
highres_BE=${highres_nonBE%%.*}tmpbrain.nii.gz
fi