dcmstack − DICOM to NIfTI converter
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.