dcmstack - Online in the Cloud

PROGRAM:

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.

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