x.PreProc_Mask-4D

#!/bin/sh
# x.PreProc_Mask-4D

# Applies a mask to an image
# This is useful if you want to run BET on one image and apply the mask to other images in the same space.

if [ $# -ne 3 ]
then
  echo "*****************************************************************************************************"
  echo "Insufficient arguments supplied"
  echo "Input 1 should be the full path to the input scan to be masked*"
  echo "Input 2 should be the full path to the mask*"
  echo "Input 3 should be the full path to the output directory"
  echo "*Note: do not include file extension - assumes nii.gz"
  echo "*****************************************************************************************************"
  exit
fi

#define inputs
input_file=${1}
mask_file=${2}
output_dir=${3}

#Check the input file exists
echo "***************************"
echo "Input file is ${input_file}"
echo "***************************"
if [ ! -f "${input_file}.nii.gz" ]
then
  echo "************************************************"
  echo "Cannot locate the NIFTI input file ${input_file}"
  echo "...exiting!"
  echo "************************************************"
  exit
fi

#If output directory is not present, make it
if [ ! -d ${output_dir} ]
then
  mkdir ${output_dir}
fi
echo "********************************"
echo "Output directory is ${output_dir}"
echo "********************************"

#Get the input filename without the path
input_prefix="$(basename -- $input_file)"

# Apply mask

if [ ! -f "${output_dir}/${input_prefix}_brain.nii.gz" ]
then
  echo "*************************************"
  echo "Appling mask to ${input_prefix}.nii.gz"
  echo "*************************************"

  3dcalc -a ${input_file}.nii.gz -b ${mask_file}.nii.gz[0] \
  -expr "a*b" -prefix ${output_dir}/${input_prefix}_brain.nii.gz

else
  echo "****************************************"
  echo "${input_prefix}_brain.nii.gz already made"
  echo "****************************************"
fi