x.PreProc_MEANTS-4D

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

# Outputs a mean time-series within a mask

if [ $# -ne 4 ]
then
    echo "********************************************************************************************************"
    echo "Insufficient arguments supplied"
    echo "Input 1 should be the full path to the input scan*"
    echo "Input 2 should be the full path to the mask*"
    echo "Input 3 should be the mask name e.g. WholeBrain, GM, V1"
    echo "Input 4 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}
mask_name=${3}
output_dir=${4}

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

if [ ! -f "${mask_file}.nii.gz" ]
then
  echo "***************************************************"
  echo "Cannot locate the NIFTI input file ${mask_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)"

#Save mean functional time series over the mask
if [ ! -f ${output_dir}/${input_prefix}_${mask_name}_MeanTS.txt ]
then
  echo "*********************************************************************"
  echo "Saving a mean time series from ${input_prefix} in ${mask_name} voxels"
  echo "*********************************************************************"
  fslmeants -i ${input_file}.nii.gz -o ${output_dir}/${input_prefix}_${mask_name}_MeanTS.txt -m ${mask_file}.nii.gz
else
 echo "*******************************************************************"
 echo "Mean time series from ${input_prefix} in ${mask_name} already made"
 echo "*******************************************************************"
fi