---
name: "dcmstack"
section: "1"
platform: "linux"
package: "python3-dcmstack"
version: "0.9-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/dcmstack"
---

# dcmstack(1)

DICOM to NIfTI conversion - python3 package

## NAME

dcmstack - DICOM to NIfTI conversion - python3 package

## DESCRIPTION

usage: dcmstack \[-h\] \[--force-read\] \[--file-ext FILE\_EXT\] \[--allow-dummies\]

-

  \[--dest-dir DEST\_DIR\] \[-o OUTPUT\_NAME\] \[--output-ext OUTPUT\_EXT\] \[-d\] \[--embed-meta\] \[-g GROUP\_BY\] \[--voxel-order VOXEL\_ORDER\] \[-t TIME\_VAR\] \[--vector-var VECTOR\_VAR\] \[--time-order TIME\_ORDER\] \[--vector-order VECTOR\_ORDER\] \[-l\] \[--disable-translator DISABLE\_TRANSLATOR\] \[--extract-private\] \[-i INCLUDE\_REGEX\] \[-e EXCLUDE\_REGEX\] \[--default-regexes\] \[-v\] \[--strict\] \[--version\] \[src\_dirs ...\]

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 separated 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.

## AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.