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Commit bc151fff authored by Vaanathi Sundaresan's avatar Vaanathi Sundaresan
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Bashscript for data preprocessing using FSL

parent 910ef315
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truenet_tumseg/scripts/prepare_tumseg_data 0 → 100644
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#!/bin/sh
# Copyright (C) 2021 University of Oxford
# SHCOPYRIGHT
#set -e
#set -x
######
if [ $# -lt 3 ] ; then
echo "Usage: `basename $0` <Base_modality_type> <output_basename> <FLAIR_image_name> <T1_image_name> <T1ce_image_name> <T2_image_name>"
echo " "
echo "The script applies the preprocessing pipeline on FLAIR, T1, T1ce and T2 to be used in FSL truenet_tumseg with a specified output basename"
echo "Base_modality_name and output_basename are mandatory inputs"
echo "Remaining inputs are optional, image corresponding to Base_modality_name must be provided. Images to be provided in the given order."
echo "In case you do not have a modality, provide 'None' for that modality."
echo "Base_modality_name = name of the modality that the rest will be registered to (preferable ~1mm iso); valid options: flair, t1, t1ce, t2"
echo "output_basename = name to be used for the processed images (use absolute path); output_basename_FLAIR.nii.gz, output_basename_T1.nii.gz .... will be saved"
echo "FLAIR_image_name = name of the input unprocessed FLAIR image"
echo "T1_image_name = name of the input unprocessed T1 image"
echo "T1ce_image_name = name of the input unprocessed T1-contrast enhanced image"
echo "T2_image_name = name of the input unprocessed T2 image"
echo " "
echo "For example, if you have flair, t1 and t2 and want to register everything to t1, use the following command"
echo "prepare_tumseg_data t1 path/to/outputbasename path/to/input_flair.nii.gz path/to/input_t1.nii.gz None path/to/input_t2.nii.gz"
exit 0
fi
error_exit()
{
echo "Error: $1" 1>&2
exit 1
}
if [ $# -lt 6 ] ; then
error_exit "Inputs missing! Cannot proceed..."
fi
if [[ $1 == 'flair' || $1 == 't1' || $1 == 't1ce' || $1 == 't2' ]]; then
base_type=$1
else
error_exit "Invalid option provided for Base_modality_type! Cannot proceed..."
fi
outbasename=$2
outname=`basename ${outbasename}`
outdir=`dirname ${outbasename}`
pushd $outdir > /dev/null
outdir=`pwd`
popd > /dev/null
flairfile=$3
if [[ $flairfile == 'None' || $flairfile == 'none' ]]; then
flairflag=0
else
flairflag=1
flairimg=`basename ${flairfile} .nii.gz`
flairdir=`dirname ${flairfile} `
pushd $flairdir > /dev/null
flairdir=`pwd`
popd > /dev/null
fi
t1file=$4
if [[ $t1file == 'None' || $t1file == 'none' ]]; then
t1flag=0
else
t1flag=1
t1img=`basename ${t1file} .nii.gz`
t1dir=`dirname ${t1file} `
pushd $t1dir > /dev/null
t1dir=`pwd`
popd > /dev/null
fi
t1cefile=$5
if [[ $t1cefile == 'None' || $t1cefile == 'none' ]]; then
t1ceflag=0
else
t1ceflag=1
t1ceimg=`basename ${t1cefile} .nii.gz`
t1cedir=`dirname ${t1cefile} `
pushd $t1cedir > /dev/null
t1cedir=`pwd`
popd > /dev/null
fi
t2file=$6
if [[ $t2file == 'None' || $t2file == 'none' ]]; then
t2flag=0
else
t2flag=1
t2img=`basename ${t2file} .nii.gz`
t2dir=`dirname ${t2file} `
pushd $t1dir > /dev/null
t2dir=`pwd`
popd > /dev/null
fi
if [[ $base_type == 'flair' ]]; then
if [ $flairflag -eq 0 ] ; then
error_exit "FLAIR_image_name cannot be None if Base_modality_type is flair! Cannot proceed..."
else
inbasename=$flairfile
fi
elif [[ $base_type == 't1' ]]; then
if [ $t1flag -eq 0 ] ; then
error_exit "T1_image_name cannot be None if Base_modality_type is t1! Cannot proceed..."
else
inbasename=$t1file
fi
elif [[ $base_type == 't1ce' ]]; then
if [ $t1ceflag -eq 0 ] ; then
error_exit "T1ce_image_name cannot be None if Base_modality_type is t1ce! Cannot proceed..."
else
inbasename=$t1cefile
fi
elif [[ $base_type == 't2' ]]; then
if [ $t2flag -eq 0 ] ; then
error_exit "T2_image_name cannot be None if Base_modality_type is t2! Cannot proceed..."
else
inbasename=$t2file
fi
fi
# SPECIFY ORIGINAL DIRECTORY
origdir=`pwd`
# CREATE TEMPORARY DIRECTORY
logID=`echo $(date | awk '{print $1 $2 $3}' | sed 's/://g')`
TMPVISDIR=`mktemp -d ${outdir}/tumseg_${logID}_${flairimg}_${t1img}_XXXXXX`
# REORIENTING THE AVAILABLE IMAGES TO STD SPACE AND BRAIN EXTRACTION
if [ $flairflag -eq 1 ] ; then
$FSLDIR/bin/fslreorient2std ${flairfile}.nii.gz ${TMPVISDIR}/FLAIR.nii.gz
$FSLDIR/bin/bet ${TMPVISDIR}/FLAIR.nii.gz ${TMPVISDIR}/FLAIR_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/FLAIR_brain.nii.gz -bin -fillh ${TMPVISDIR}/FLAIR_brain_mask.nii.gz
fi
if [ $t1flag -eq 1 ] ; then
$FSLDIR/bin/fslreorient2std ${t1file}.nii.gz ${TMPVISDIR}/T1.nii.gz
$FSLDIR/bin/bet ${TMPVISDIR}/T1.nii.gz ${TMPVISDIR}/T1_brain.nii.gz
fi
if [ $t1ceflag -eq 1 ] ; then
$FSLDIR/bin/fslreorient2std ${t1cefile}.nii.gz ${TMPVISDIR}/T1ce.nii.gz
$FSLDIR/bin/bet ${TMPVISDIR}/T1ce.nii.gz ${TMPVISDIR}/T1ce_brain.nii.gz
fi
if [ $t2flag -eq 1 ] ; then
$FSLDIR/bin/fslreorient2std ${t2file}.nii.gz ${TMPVISDIR}/T2.nii.gz
$FSLDIR/bin/bet ${TMPVISDIR}/T2.nii.gz ${TMPVISDIR}/T2_brain.nii.gz
fi
# CONSIDERING FLAIR AS BASE MODALITY; PROCESSING AVAILABLE MODALITIES WRT FLAIR
if [[ $base_type == 'flair' ]]; then
${FSLDIR}/bin/imcp ${TMPVISDIR}/FLAIR_brain.nii.gz ${outdir}/${outname}_FLAIR.nii.gz
if [ $t1flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1_brain.nii.gz -ref ${TMPVISDIR}/FLAIR_brain.nii.gz -out ${TMPVISDIR}/T1_2FLAIR.nii.gz -omat ${TMPVISDIR}/T1_2FLAIR.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1.nii.gz -ref ${TMPVISDIR}/FLAIR.nii.gz -out ${TMPVISDIR}/T1_2FLAIR.nii.gz -init ${TMPVISDIR}/T1_2FLAIR.mat -applyxfm
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2FLAIR.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1_2FLAIR_brain.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1_2FLAIR_brain.nii.gz ${outdir}/${outname}_T1.nii.gz
fi
if [ $t1ceflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1ce_brain.nii.gz -ref ${TMPVISDIR}/FLAIR_brain.nii.gz -out ${TMPVISDIR}/T1ce_2FLAIR.nii.gz -omat ${TMPVISDIR}/T1ce_2FLAIR.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1ce.nii.gz -ref ${TMPVISDIR}/FLAIR.nii.gz -out ${TMPVISDIR}/T1ce_2FLAIR.nii.gz -init ${TMPVISDIR}/T1ce_2FLAIR.mat -applyxfm
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2FLAIR.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2FLAIR_brain.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1ce_2FLAIR_brain.nii.gz ${outdir}/${outname}_T1ce.nii.gz
fi
if [ $t2flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T2_brain.nii.gz -ref ${TMPVISDIR}/FLAIR_brain.nii.gz -out ${TMPVISDIR}/T2_2FLAIR.nii.gz -omat ${TMPVISDIR}/T2_2FLAIR.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T2.nii.gz -ref ${TMPVISDIR}/FLAIR.nii.gz -out ${TMPVISDIR}/T2_2FLAIR.nii.gz -init ${TMPVISDIR}/T2_2FLAIR.mat -applyxfm
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_2FLAIR.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T2_2FLAIR_brain.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/T2_2FLAIR_brain.nii.gz ${outdir}/${outname}_T2.nii.gz
fi
# CONSIDERING T1 AS BASE MODALITY; PROCESSING AVAILABLE MODALITIES WRT T1 (IF FLAIR, TAKE BRAIN_MASK FROM FLAIR)
elif [[ $base_type == 't1' ]]; then
if [ $flairflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/FLAIR_brain.nii.gz -ref ${TMPVISDIR}/T1_brain.nii.gz -out ${TMPVISDIR}/FLAIR_2T1.nii.gz -omat ${TMPVISDIR}/FLAIR_2T1.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/FLAIR.nii.gz -ref ${TMPVISDIR}/T1.nii.gz -out ${TMPVISDIR}/FLAIR_2T1.nii.gz -init ${TMPVISDIR}/FLAIR_2T1.mat -applyxfm
$FSLDIR/bin/bet ${TMPVISDIR}/FLAIR_2T1.nii.gz ${TMPVISDIR}/FLAIR_2T1_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/FLAIR_2T1_brain.nii.gz -bin -fillh ${TMPVISDIR}/FLAIR_brain_mask.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/FLAIR_2T1_brain.nii.gz ${outdir}/${outname}_FLAIR.nii.gz
fi
if [ $t2flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T2_brain.nii.gz -ref ${TMPVISDIR}/T1_brain.nii.gz -out ${TMPVISDIR}/T2_2T1.nii.gz -omat ${TMPVISDIR}/T2_2T1.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T2.nii.gz -ref ${TMPVISDIR}/T1.nii.gz -out ${TMPVISDIR}/T2_2T1.nii.gz -init ${TMPVISDIR}/T2_2T1.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_2T1.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T2_2T1_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T2_2T1.nii.gz ${TMPVISDIR}/T2_2T1_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_2T1_brain.nii.gz -bin -fillh ${TMPVISDIR}/T2_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T2_2T1_brain.nii.gz ${outdir}/${outname}_T2.nii.gz
fi
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1_brain.nii.gz
else
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_brain.nii.gz -bin -fillh ${TMPVISDIR}/T1_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1_brain.nii.gz ${outdir}/${outname}_T1.nii.gz
if [ $t1ceflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1ce_brain.nii.gz -ref ${TMPVISDIR}/T1_brain.nii.gz -out ${TMPVISDIR}/T1ce_2T1.nii.gz -omat ${TMPVISDIR}/T1ce_2T1.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1ce.nii.gz -ref ${TMPVISDIR}/T1.nii.gz -out ${TMPVISDIR}/T1ce_2T1.nii.gz -init ${TMPVISDIR}/T1ce_2T1.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T1.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T1_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T1.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T1_brain.nii.gz
elif [ -f "${TMPVISDIR}/T1_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T1.nii.gz -mul ${TMPVISDIR}/T1_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T1_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T1ce_2T1.nii.gz ${TMPVISDIR}/T1ce_2T1_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T1_brain.nii.gz -bin -fillh ${TMPVISDIR}/T1ce_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1ce_2T1_brain.nii.gz ${outdir}/${outname}_T1ce.nii.gz
fi
# CONSIDERING T1CE AS BASE MODALITY; PROCESSING AVAILABLE MODALITIES WRT T1CE (IF FLAIR, TAKE BRAIN_MASK FROM FLAIR)
elif [[ $base_type == 't1ce' ]]; then
if [ $flairflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/FLAIR_brain.nii.gz -ref ${TMPVISDIR}/T1ce_brain.nii.gz -out ${TMPVISDIR}/FLAIR_2T1ce.nii.gz -omat ${TMPVISDIR}/FLAIR_2T1ce.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/FLAIR.nii.gz -ref ${TMPVISDIR}/T1ce.nii.gz -out ${TMPVISDIR}/FLAIR_2T1ce.nii.gz -init ${TMPVISDIR}/FLAIR_2T1ce.mat -applyxfm
$FSLDIR/bin/bet ${TMPVISDIR}/FLAIR_2T1ce.nii.gz ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz -bin -fillh ${TMPVISDIR}/FLAIR_brain_mask.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz ${outdir}/${outname}_FLAIR.nii.gz
fi
if [ $t2flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T2_brain.nii.gz -ref ${TMPVISDIR}/T1ce_brain.nii.gz -out ${TMPVISDIR}/T2_2T1ce.nii.gz -omat ${TMPVISDIR}/T2_2T1ce.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T2.nii.gz -ref ${TMPVISDIR}/T1ce.nii.gz -out ${TMPVISDIR}/T2_2T1ce.nii.gz -init ${TMPVISDIR}/T2_2T1ce.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_2T1ce.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T2_2T1ce_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T2_2T1ce.nii.gz ${TMPVISDIR}/T2_2T1ce_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_2T1ce_brain.nii.gz -bin -fillh ${TMPVISDIR}/T2_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T2_2T1ce_brain.nii.gz ${outdir}/${outname}_T2.nii.gz
fi
if [ $t1flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1_brain.nii.gz -ref ${TMPVISDIR}/T1ce_brain.nii.gz -out ${TMPVISDIR}/T1_2T1ce.nii.gz -omat ${TMPVISDIR}/T1_2T1ce.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1.nii.gz -ref ${TMPVISDIR}/T1ce.nii.gz -out ${TMPVISDIR}/T1_2T1ce.nii.gz -init ${TMPVISDIR}/T1_2T1ce.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T1ce.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1_2T1ce_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T1ce.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1_2T1ce_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T1_2T1ce.nii.gz ${TMPVISDIR}/T1_2T1ce_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T1ce_brain.nii.gz -bin -fillh ${TMPVISDIR}/T1_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1_2T1ce_brain.nii.gz ${outdir}/${outname}_T1.nii.gz
fi
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1ce_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1ce_brain.nii.gz
elif [ -f "${TMPVISDIR}/T1_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce.nii.gz -mul ${TMPVISDIR}/T1_brain_mask.nii.gz ${TMPVISDIR}/T1ce_brain.nii.gz
else
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce.nii.gz -mul ${TMPVISDIR}/T1_brain_mask.nii.gz ${TMPVISDIR}/T1ce_brain.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1ce_brain.nii.gz ${outdir}/${outname}_T1ce.nii.gz
elif [[ $base_type == 't2' ]]; then
if [ $flairflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/FLAIR_brain.nii.gz -ref ${TMPVISDIR}/T1ce_brain.nii.gz -out ${TMPVISDIR}/FLAIR_2T1ce.nii.gz -omat ${TMPVISDIR}/FLAIR_2T1ce.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/FLAIR.nii.gz -ref ${TMPVISDIR}/T1ce.nii.gz -out ${TMPVISDIR}/FLAIR_2T1ce.nii.gz -init ${TMPVISDIR}/FLAIR_2T1ce.mat -applyxfm
$FSLDIR/bin/bet ${TMPVISDIR}/FLAIR_2T1ce.nii.gz ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz -bin -fillh ${TMPVISDIR}/FLAIR_brain_mask.nii.gz
${FSLDIR}/bin/imcp ${TMPVISDIR}/FLAIR_2T1ce_brain.nii.gz ${outdir}/${outname}_FLAIR.nii.gz
fi
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T2_brain.nii.gz
else
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T2_brain.nii.gz -bin -fillh ${TMPVISDIR}/T2_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T2_brain.nii.gz ${outdir}/${outname}_T2.nii.gz
if [ $t1flag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1_brain.nii.gz -ref ${TMPVISDIR}/T2_brain.nii.gz -out ${TMPVISDIR}/T1_2T2.nii.gz -omat ${TMPVISDIR}/T1_2T2.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1.nii.gz -ref ${TMPVISDIR}/T2.nii.gz -out ${TMPVISDIR}/T1_2T2.nii.gz -init ${TMPVISDIR}/T1_2T2.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T2.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1_2T2_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T2.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1_2T2_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T1_2T2.nii.gz ${TMPVISDIR}/T1_2T2_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1_2T2_brain.nii.gz -bin -fillh ${TMPVISDIR}/T1_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1_2T2_brain.nii.gz ${outdir}/${outname}_T1.nii.gz
fi
if [ $t1ceflag -eq 1 ] ; then
$FSLDIR/bin/flirt -dof 6 -in ${TMPVISDIR}/T1ce_brain.nii.gz -ref ${TMPVISDIR}/T2_brain.nii.gz -out ${TMPVISDIR}/T1ce_2T2.nii.gz -omat ${TMPVISDIR}/T1ce_2T2.mat
$FSLDIR/bin/flirt -in ${TMPVISDIR}/T1ce.nii.gz -ref ${TMPVISDIR}/T2.nii.gz -out ${TMPVISDIR}/T1ce_2T2.nii.gz -init ${TMPVISDIR}/T1ce_2T2.mat -applyxfm
if [ -f "${TMPVISDIR}/FLAIR_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T2.nii.gz -mul ${TMPVISDIR}/FLAIR_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T2_brain.nii.gz
elif [ -f "${TMPVISDIR}/T2_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T2.nii.gz -mul ${TMPVISDIR}/T2_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T2_brain.nii.gz
elif [ -f "${TMPVISDIR}/T1_brain_mask.nii.gz" ]; then
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T2.nii.gz -mul ${TMPVISDIR}/T1_brain_mask.nii.gz ${TMPVISDIR}/T1ce_2T2_brain.nii.gz
else
$FSLDIR/bin/bet ${TMPVISDIR}/T1ce_2T2.nii.gz ${TMPVISDIR}/T1ce_2T2_brain.nii.gz
$FSLDIR/bin/fslmaths ${TMPVISDIR}/T1ce_2T2_brain.nii.gz -bin -fillh ${TMPVISDIR}/T1ce_brain_mask.nii.gz
fi
${FSLDIR}/bin/imcp ${TMPVISDIR}/T1ce_2T2_brain.nii.gz ${outdir}/${outname}_T1ce.nii.gz
fi
fi
# REMOVES TEMPORARY DIRECTORY
rm -r ${TMPVISDIR}
exit 0
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