resample

#!/bin/bash
# Resample image isotropically to new voxel size
#
# AUTHOR : Mike Tyszka
# PLACE  : Caltech
# DATES  : 2016-11-16 JMT From scratch

if [ $# -lt 3 ]; then
  echo "USAGE : resample <original image> <resampled image> <isotropic resolution in mm>"
  exit
fi

echo "Original image       : $1"
echo "Resampled image      : $2"
echo "Isotropic resolution : $3 mm"

# FLIRT options
flirt_opts="-init ${FSLDIR}/etc/flirtsch/ident.mat -applyisoxfm ${3} -interp sinc -sincwindow hanning"

# Get image dimensions
ndim=`fslinfo $1 | awk '{ if ($1 == "dim4") { if ($2 > 1) {print "4"} else {print "3"} } }'`

echo "Original image has ${ndim} dimensions"

if [ ${ndim} -eq "3" ]
then

    ${FSLDIR}/bin/flirt -in $1 -out $2 -ref $1 ${flirt_opts}

elif [ ${ndim} -eq "4" ]
then

    tmp_dir="./tmp"
    mkdir -p ${tmp_dir}

    echo "Splitting 4D volume into $tmp_dir"
    fslsplit $1 ${tmp_dir}/vol -t

    for vol in ${tmp_dir}/vol*
    do

        echo "  Resampling ${vol}"

        out_vol=${vol/.nii.gz/_resamp.nii.gz}

        ${FSLDIR}/bin/flirt -in ${vol} -out ${out_vol} -ref ${vol} ${flirt_opts}

    done

    fslmerge -t $2 ${tmp_dir}/*_resamp.nii.gz

    rm -rf ${tmp_dir}

else

    echo "Unsupported image dimensions : ${ndim}"
    exit

fi