bionic (1) dcmstack.1.gz

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.