Convert tarfile of dicoms

convert_dcm2niix.sh

#!/bin/bash

# Written by Jonah Chaiken and Nate Vack
# Support: [email protected]

help=" Usage: convert_dcm2niix.sh <in_file> <out_file>

This program will individually convert a dicom archive file to a NIfTI file.

The input can be either a .tar file containing bzip2'd dicom slices, or a
compressed tarfile containing uncompressed slices.

Creates a temporary directory in the same directory as <out_file>, and should
clean it up afterwards.

<out_file> can be either a .nii or .nii.gz file. dcm2niix will create a .json
file suitable for BIDS along with the NIfTI data.

For help, contact [email protected]
"

if [[ "$1" == "-h" ]]; then
  echo "${help}"
  exit 1
fi

if [[ $# != 2 ]]; then
  echo "Usage: convert_dcm2niix <in_file> <out_file>"
  exit 1
fi

in_file=$1
in_extension=${in_file##*.}
out_path=$2  # Example: /study/foo/output.nii.gz
out_dir=$( dirname ${out_path} )  # /study/foo
out_filename=$( basename ${out_path} )  # output.nii.gz
out_base=${out_filename%%.*}  # output
out_extension=${out_filename##*.}  # gz

# Also get the gzip status into a variable, fill it with "-z" if we want a .nii.gz

gzip_cmd="-z n"
if [[ ${out_extension} == gz ]]; then
  gzip_cmd="-z i"
fi

temp_dicom_dir=$( mktemp -p "${out_dir}" -d )

if [[ $? != 0 ]]; then
  echo "Could not create temporary directory in ${out_dir}! Exiting."
  exit 2
fi

echo "Extracting ${in_file} to ${temp_dicom_dir}"
tar -xf $in_file -C $temp_dicom_dir

if [[ "${in_extension}" == "tar" ]]; then
  echo "Decompressing dicom slices"
  bunzip2 ${temp_dicom_dir}/*.bz2
fi

echo "Creating ${out_file}"
/apps/x86_64_sci7/current/bin/dcm2niix -b y -o ${out_dir} -f ${out_base} ${gzip_cmd} ${temp_dicom_dir}

echo "Cleaning up"
rm -rf $temp_dicom_dir
exit 0