jammy (1) dcmstack.1.gz

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.

AUTHORThis manpage was written by Nilesh Patra for the Debian distribution andcan be used for any other usage of

       the program.