sourCEntral - mobile manpages

pdf

DCMSTACK

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.

pdf