dcmstack1

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.