x.PreProc_BET-3D

#!/bin/sh
# x.PreProc_BET-3D

# Performs brain extraction on a 3D dataset (e.g. anatomical T1-weighted 3D dataset or SBREF image of an fMRI dataset)
# READ ME! IMPORTANT: Check the output and adjust the BET flags in this script (line 62) to ensure good brain extraction before proceeding to later analysis steps 
# If the brain extraction is poor, re-run BET with different flags
# See the following for info on BET flags: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide
# You can find examples of previously successful BET flag combinations on line 65

if [ $# -ne 2 ]
then
    echo "**************************************************************************************"
    echo "Insufficient arguments supplied"
    echo "Input 1 should be the full path to the 3D input file (no 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
anat_prefix="$(basename -- $input_file)"

#Create a symbolic link of the original dataset in the output directory
if [ ! -f "${output_dir}/${anat_prefix}_ORIG.nii.gz" ]
then
  ln -s "${input_file}.nii.gz" "${output_dir}/${anat_prefix}_ORIG.nii.gz"
fi

#Run brain extraction on the T1 dataset
if [ ! -f ${output_dir}/${anat_prefix}_bet.nii.gz ]
then

  echo "*****************************************************************"
  echo "Running brain extraction on the ${anat_prefix}"
  echo "Always check the ouput! FSL-BET settings may need to be optimized"
  echo "*****************************************************************"
  bet "${input_file}.nii.gz" ${output_dir}/${anat_prefix}_bet -m  -R
  
  #########################################
  ### Past successful flag combinations ###
  # User-Dataset-Datatype: [flags]
  # MCW-NeilsenBrainBH-SBREF: -m -R -f 0.4 -g -0.2
  #########################################
  
  #Open up an FSLeyes window with the BET mask and original file for user inspection
  ORIG_path="${output_dir}/${anat_prefix}_ORIG.nii.gz"
  mask_path="${output_dir}/${anat_prefix}_bet_mask.nii.gz"

  fsleyes ${ORIG_path} ${mask_path} -cm red -a 40 &

else
  echo "***************************************************"
  echo "Brain extraction of ${anat_prefix} already complete"
  echo "***************************************************"
fi