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.