dicom_to_nifti_anonymize.sh

#!/bin/bash
# Usage dicom_to_nifti_anonymize [source dir] [dest dir] [participant ID]

if [[ $# -lt 2 ]]; then
	DEST=$1
else
  # make the directory if it doesn't exist
  if [ ! -d $2 ]; then
	  mkdir $2
  fi

	DEST=$2
fi

TEMPDIR=/tmp/dicom_to_nifti_anonymize/$3
mkdir -p $TEMPDIR
cp -r $1 $TEMPDIR

echo "===============================================" >> "$DEST/conversion_log.txt"
date >> "$DEST/conversion_log.txt"
echo "===============================================" >> "$DEST/conversion_log.txt"

dcm2niix -b y -o "$DEST" -x n -z y -t n "$TEMPDIR" | tee -a "$DEST/conversion_log.txt"

rm -rf $TEMPDIR

Requires: https://github.com/rordenlab/dcm2niix