DCMfx

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CLI Tool ​

The dcmfx CLI tool makes the capabilities of DCMfx available on the command line.

Installation ​

Select your platform below to see its installation instructions.

Windows

Download the latest version of dcmfx.exe for Windows here.

macOS

Install Homebrew, then install DCMfx using the provided tap:

sh
brew tap dcmfx/tap
brew install dcmfx
Linux

  • For Ubuntu, Debian, Linux Mint, and other Debian-based distributions, an APT repository is provided:

    sh
    echo "deb [trusted=yes] https://dcmfx.github.io/apt-repository stable main" | sudo tee /etc/apt/sources.list.d/dcmfx.list
sudo apt update
sudo apt install dcmfx

  • For Red Hat, Fedora, Amazon Linux, and other RPM-based distributions, a YUM repository is provided:

    sh
    echo -e "[dcmfx]\nname=DCMfx\nbaseurl=http://dcmfx.github.io/yum-repository\nenabled=1\ngpgcheck=0" | sudo tee /etc/yum.repos.d/dcmfx.repo
sudo yum makecache
sudo yum install dcmfx

  • For Arch Linux, a package is provided in the Arch User Repository (AUR). Install it with your preferred AUR helper (e.g. Yay):

    sh
    yay -S dcmfx
  • Alternatively, download the latest binary or package here and install it manually.

Usage ​

After installation, run dcmfx --help to see the available commands:

$ dcmfx --help

DCMfx is a CLI tool for working with DICOM and DICOM JSON

Usage: dcmfx [OPTIONS] <COMMAND>

Commands:
  get-pixel-data  Extracts pixel data from DICOM P10 files, writing it to image
                  and video files
  modify          Modifies the content of DICOM P10 files
  print           Prints the content of DICOM P10 files
  json-to-dcm     Converts DICOM JSON files to DICOM P10 files
  dcm-to-json     Converts DICOM P10 files to DICOM JSON files
  help            Print this message or the help of the given subcommand(s)

Options:
      --print-stats  Write timing and memory stats to stderr on exit
  -h, --help         Print help
  -V, --version      Print version

Examples ​

  1. Print a DICOM P10 file's data set to stdout:

    sh
    dcmfx print input.dcm

  2. Convert a DICOM P10 file to a DICOM JSON file:

    sh
    dcmfx dcm-to-json input.dcm

    To pretty-print the DICOM JSON directly to stdout:

    sh
    dcmfx dcm-to-json input.dcm --pretty --output-filename -

  3. Convert a DICOM JSON file to a DICOM P10 file:

    sh
    dcmfx json-to-dcm input.json

  4. Extract pixel data from a DICOM P10 file to one image file per frame:

    sh
    dcmfx get-pixel-data input.dcm

    Each frame of pixel data can be decoded and written to PNG, 16-bit PNG, JPEG, or WebP Lossless images:

    sh
    dcmfx get-pixel-data input.dcm --format png
dcmfx get-pixel-data input.dcm --format png16
dcmfx get-pixel-data input.dcm --format jpg --jpeg-quality 90
dcmfx get-pixel-data input.dcm --format webp

    Single channel data can also specify a VOI window center and width and/or a well-known color palette to use:

    sh
    dcmfx get-pixel-data input.dcm --format png --voi-window 500 2000 \
  --color-palette hot-iron

    The images can be rotated or flipped by specifying a transform:

    sh
    dcmfx get-pixel-data input.dcm --format jpg --transform rotate90
dcmfx get-pixel-data input.dcm --format jpg --transform flip-vertical

  5. Extract pixel data from a DICOM P10 file to an MP4 video:

    sh
    dcmfx get-pixel-data input.dcm --format mp4

    Additional options are available to specify the codec, video quality, encoder preset, pixel format, frame rate override, and so on.

  6. Rewrite a DICOM P10 file. This will convert the specific character set to UTF-8, change sequences and items to undefined length, and correct invalid files where possible:

    sh
    dcmfx modify input.dcm --output-filename output.dcm

  7. Modify a DICOM P10 file to use the 'Deflated Explicit VR Little Endian' transfer syntax with maximum compression:

    sh
    dcmfx modify input.dcm output.dcm \
  --transfer-syntax deflated-explicit-vr-little-endian \
  --zlib-compression-level 9

    The modify command can only convert between the following transfer syntaxes:

    • Implicit VR Little Endian
    • Explicit VR Little Endian
    • Deflated Explicit VR Little Endian
    • Explicit VR Big Endian

    Conversion between other transfer syntaxes is not supported.

  8. Anonymize a DICOM P10 file in-place by removing all identifying data elements and private data elements:

    sh
    dcmfx modify input.dcm --in-place --anonymize

    Note that this does not remove any identifying information baked into pixel data or other binary data elements.

  9. Remove the top-level '(7FE0,0010) Pixel Data' data element from a DICOM P10 file:

    sh
    dcmfx modify input.dcm --in-place --delete-tag 7FE00010

    Multiple data elements can be deleted by using a comma as a separator:

    sh
    dcmfx modify input.dcm --in-place --delete-tag 00100010 --delete-tag 00100030

Gleam CLI ​

The above examples assume the Rust version of the CLI tool is in use, however most functionality is also supported by the Gleam version of the CLI, which can be run with gleam run in /src/gleam/dcmfx_cli.

The Gleam CLI is primarily used when working on the Gleam implementation of DCMfx. The Rust CLI is recommended for regular use as it is faster, has more features, and is a single standalone binary.