N4Process.sh

#!/bin/bash
exe_name=$0
exe_name=`readlink -f ${exe_name}`
exe_dir=`dirname "$exe_name"`

if [ $# -lt "3" ]; then
  echo "Usage:
  ./N4Process.sh INPUT N4field OUTPUTDIR
 
 INPUT         Directory containing original tiff images (e.g., 640 channel
               images), or a 3D tiff/nifti image
 N4FIELD       N4 bias field image, must have same number of slices as the INPUT,
               could be downsampled only in x-y direction. The downsampling 
               factor should be an integer so that,
               dim(INPUT) = dsfactor x dim(N4FIELD)
 OUTPUTDIR     Output directory where corrected images are written
 DSFACTOR      (Optional) A downsampling factor to downsample the field image
               to compute its mode. Default 5x5x5. It can be same as the
               downsampling factor used originally. It must be string separated
               by x, e.g. 6x6x5
 
  "
  exit 1
fi

export MCR_INHIBIT_CTF_LOCK=1
export MCR_CACHE_ROOT=/tmp/mcr_${USER}_${RANDOM}
mkdir -p ${MCR_CACHE_ROOT}

MCRROOT=/usr/local/matlab-compiler/v912
LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
export LD_LIBRARY_PATH;


args=
while [ $# -gt 0 ]; do
  token=$1
  args="${args} ${token}" 
  shift
done
echo ${exe_dir}/N4Process $args
${exe_dir}/N4Process $args

rm -rf ${MCR_CACHE_ROOT}