NAME

       dcmstack - DICOM to NIfTI converter

DESCRIPTION

       usage: dcmstack [-h] [--force-read] [--file-ext FILE_EXT] [--allow-dummies]

              [--dest-dir    DEST_DIR]    [-o   OUTPUT_NAME]   [--output-ext   OUTPUT_EXT]   [-d]
              [--embed-meta]   [-g   GROUP_BY]   [--voxel-order   VOXEL_ORDER]   [-t    TIME_VAR]
              [--vector-var  VECTOR_VAR]  [--time-order TIME_ORDER] [--vector-order VECTOR_ORDER]
              [-l]    [--disable-translator    DISABLE_TRANSLATOR]    [--extract-private]     [-i
              INCLUDE_REGEX]  [-e  EXCLUDE_REGEX] [--default-regexes] [-v] [--strict] [--version]
              [src_dirs [src_dirs ...]]

       Stack DICOM files from each source directory into 2D to 5D volumes, optionally  extracting
       meta data.

   positional arguments:
       src_dirs
              The source directories containing DICOM files.

   optional arguments:
       -h, --help
              show this help message and exit

   Input options:
       --force-read
              Try reading all files as DICOM, even if they are missing the preamble.

       --file-ext FILE_EXT
              Only try reading files with the given extension.  Default: .dcm

       --allow-dummies
              Allow  DICOM  files  that  are missing pixel data, filling that slice of the output
              nifti with the maximum representable value.

   Output options:
       --dest-dir DEST_DIR
              Destination directory, defaults to the source directory.

       -o OUTPUT_NAME, --output-name OUTPUT_NAME
              Python format string determining the output filenames based on DICOM tags.

       --output-ext OUTPUT_EXT
              The extension for the output file type. Default: .nii.gz

       -d, --dump-meta
              Dump the extracted meta data into a JSON file  with  the  same  base  name  as  the
              generated Nifti

       --embed-meta
              Embed the extracted meta data into a Nifti header extension (in JSON format).

   Stacking Options:
       -g GROUP_BY, --group-by GROUP_BY
              Comma seperated list of meta data keys to group input files into stacks with.

       --voxel-order VOXEL_ORDER
              Order  the  voxels  so  the  spatial indices start from these directions in patient
              space. The directions in patient space should be given as a three  character  code:
              (l)eft,  (r)ight, (a)nterior, (p)osterior, (s)uperior, (i)nferior. Passing an empty
              string will disable reorientation. Default: LAS

       -t TIME_VAR, --time-var TIME_VAR
              The DICOM element keyword to use for ordering the stack along the time dimension.

       --vector-var VECTOR_VAR
              The DICOM element keyword to use for ordering the stack along the vector dimension.

       --time-order TIME_ORDER
              Provide a text file with the desired order for the values (one  per  line)  of  the
              attribute used as the time variable. This option is rarely needed.

       --vector-order VECTOR_ORDER
              Provide  a  text  file  with the desired order for the values (one per line) of the
              attribute used as the vector variable. This option is rarely needed.

   Meta Extraction and Filtering Options:
       -l, --list-translators
              List enabled translators and exit

       --disable-translator DISABLE_TRANSLATOR
              Disable the translators for the provided tags. Tags should be given in  the  format
              "0x0_0x0".  More than one can be given in a comma separated list. If the word "all"
              is provided, all translators will be disabled.

       --extract-private
              Extract meta data from private elements, even if there is  no  translator.  If  the
              value  for  the  element  contains  non-ascii  bytes  it will still be ignored. The
              extracted meta data may still be filtered out by the regular expressions.

       -i INCLUDE_REGEX, --include-regex INCLUDE_REGEX
              Include any meta data where the key matches the provided regular  expression.  This
              will override any exclude expressions. Applies to all meta data.

       -e EXCLUDE_REGEX, --exclude-regex EXCLUDE_REGEX
              Exclude  any  meta data where the key matches the provided regular expression. This
              will supplement the default exclude expressions. Applies to all meta data.

       --default-regexes
              Print the list of default include and exclude regular expressions and exit.

   General Options:
       -v, --verbose
              Print additional information.

       --strict
              Fail on the first exception instead of showing a warning.

       --version
              Show the version and exit.

       IT IS YOUR RESPONSIBILITY TO KNOW IF THERE IS PRIVATE HEALTH INFORMATION IN  THE  METADATA
       EXTRACTED BY THIS PROGRAM.