NAME

       dcmstack - DICOM to NIfTI conversion - python3 package

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 ...]

       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 separated 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.

AUTHOR

       This  manpage  was written by Nilesh Patra for the Debian distribution and can be used for
       any other usage of the program.