njvack · October 11, 2017 23:02
diff --git a/convert_dcm2niix.sh b/convert_dcm2niix.sh
 #!/bin/bash

 # Written by Jonah Chaiken and Nate Vack
 # Support: bit_help@lists.wisc.edu

 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 bit_help@lists.wisc.edu
 "

 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
	#!/bin/bash

	# Written by Jonah Chaiken and Nate Vack
	# Support: bit_help@lists.wisc.edu

	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 bit_help@lists.wisc.edu
	"

	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