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dcmstack - DICOM to NIfTI converter

DCMSTACK(1) User Commands DCMSTACK(1)

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.
September 2015 dcmstack 0.7.0dev