x.PreProc_VolReg-4D

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

# Uses 3dvolreg to register a 4D image to a reference image and saves motion parameters

if [ $# -ne 5 ]
then
    echo "**************************************************************************************"
    echo "Insufficient arguments supplied"
    echo "Input 1 should be the full path to the 4D input scan*"
    echo "Input 2 should be the full path to reference scan* (this can be the same as input 1)"
    echo "Input 3 should be the volume number of reference scan"
    echo "Input 4 should be the full path to the output directory"
    echo "Input 5 should be 1 (yes) or 0 (no) to output motion derivatives and quadratic terms"
    echo "*Do not include file extension - assumes nii.gz"
    echo "**************************************************************************************"
    exit
fi

#define inputs
input_file=${1}
ref_file=${2}
ref_vol=${3}
output_dir=${4}
quad_deriv=${5}

#Check input 5 to output motion derivatives and quadratic terms
if [ ${quad_deriv} != 0 ] && [ ${quad_deriv} != 1 ]; then
  echo "*****************************"
  echo "Input 5 is unknown... exiting"
  echo "*****************************"
  exit
fi

#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)"

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

# Volume Registration

if [ ! -f ${output_dir}/${input_prefix}_mc.nii.gz ]
then
  echo "****************************************************"
  echo "Running volume registration on ${input_prefix}.nii.gz"
  echo "****************************************************"

  #Run volume registration (AFNI)
  3dvolreg -dfile ${output_dir}/${input_prefix}_mc.1D \
  -base ${ref_file}.nii.gz[${ref_vol}] \
  -maxdisp1D ${output_dir}/${input_prefix}_mc_maxdisp.1D \
  -prefix ${output_dir}/${input_prefix}_mc.nii.gz \
  ${input_file}.nii.gz

  #Demean the saved motion parameters
  # 0: roll; 1: pitch; 2: yaw; 3: dS (z); 4: dL (x); 5: dP (y)
  if [ ! -f ${output_dir}/${input_prefix}_mc_demean.1D ]
  then
    echo "*******************************************"
    echo "Demeaning and saving the motion parameters!"
    echo "*******************************************"
    1d_tool.py -infile ${output_dir}/${input_prefix}_mc.1D[1..6] \
    -demean -write ${output_dir}/${input_prefix}_mc_demean.1D
  fi

  #Calculate the motion derivatives and quadratic terms, if requested
  if [ "${quad_deriv}" -eq 1 ]; then
    echo "*************************************************"
    echo "Making derivative and quadratic motion regressors"
    echo "*************************************************"
    # Output temporal derivatives of motion regressor
    1d_tool.py -infile ${output_dir}/${input_prefix}_mc.1D[1..6] \
    -derivative -write ${output_dir}/${input_prefix}_mc_deriv.1D
    # Output quadratics (squared) of motion regressor
    1dcat `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[1] -expr 'a*a'` \
    `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[2] -expr 'a*a'` \
    `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[3] -expr 'a*a'` \
    `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[4] -expr 'a*a'` \
    `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[5] -expr 'a*a'` \
    `1deval -1D: -a ${output_dir}/${input_prefix}_mc.1D[6] -expr 'a*a'` > ${output_dir}/${input_prefix}_mc_quad.1D
    # Demean the derivative and quadratic motion regressor
    1d_tool.py -infile ${output_dir}/${input_prefix}_mc_deriv.1D \
    -demean -write ${output_dir}/${input_prefix}_mc_deriv_demean.1D
    1d_tool.py -infile ${output_dir}/${input_prefix}_mc_quad.1D \
    -demean -write ${output_dir}/${input_prefix}_mc_quad_demean.1D
  fi

else
  echo "**************************************************************"
  echo "Volume registration already complete for ${input_prefix}.nii.gz"
  echo "**************************************************************"
fi