x.PreProc_BET-4D

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

# Runs brain extraction on a 4D dataset (e.g. motion corrected functional image)

if [ $# -ne 2 ]
then
  echo "*****************************************************************************************************"
  echo "Insufficient arguments supplied"
  echo "Input 1 should be the full path to the 4D input scan (do not include file extension - assumes nii.gz)"
  echo "Input 2 should be the full path to the output directory"
  echo "*****************************************************************************************************"
  exit
fi

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

#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)"

# Run brain extraction

if [ ! -f "${output_dir}/${input_prefix}_bet.nii.gz" ]
then

  echo "*****************************************************************"
  echo "Running brain extraction on ${input_prefix}.nii.gz"
  echo "Always check the ouput! FSL-BET settings may need to be optimized"
  echo "*****************************************************************"
  bet "${input_file}.nii.gz" "${output_dir}/${input_prefix}_bet.nii.gz" -m -F

  #erode edges for a more conservative brain mask
  echo "**************************************************"
  echo "Eroding edges from ${input_prefix}_bet.nii.gz"
  echo "**************************************************"
  fslmaths "${output_dir}/${input_prefix}_bet_mask.nii.gz" -ero "${output_dir}/${input_prefix}_bet_mask_ero.nii.gz"
  3dcalc -a "${output_dir}/${input_prefix}_bet.nii.gz" -b "${output_dir}/${input_prefix}_bet_mask_ero.nii.gz" -expr "a*b" -prefix "${output_dir}/${input_prefix}_bet_ero.nii.gz"


else
  echo "**********************************************************"
  echo "Brain extraction on ${input_prefix}.nii.gz already complete"
  echo "**********************************************************"
fi