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dcmstack - Online in the Cloud

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This is the command dcmstack that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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