Convert3D

Convert3D (c3d) is a command-line image processing tool that complements ITK-SNAP. It was originally developed to convert 3D medical images between file formats. It has since become a Swiss army knife for medical image processing, with commands for resampling, smoothing, thresholding, computing features and image statistics, and more. It also has commands for multi-label images, such as ITK-SNAP segmentations, and for multi-component images, such as RGB images.

c3d works like a Reverse Polish notation calculator. Images are placed on a stack, and each command acts on the images at the top of the stack. This lets you chain several operations into a single command without saving intermediate files. For example, this command smooths an image, resamples it to half its resolution and saves the result:

c3d input.nii.gz -smooth 2mm -resample 50% -o output.nii.gz

The companion tools c2d and c4d provide the same commands for 2D and 4D images.

Getting Convert3D

• ITK-SNAP: c3d comes with ITK-SNAP. Choose Help → Install Command-Line Tools from the ITK-SNAP menu.
• Binaries: download them from SourceForge.
• Source: build with CMake against ITK.
• Python: pip install picsl_c3d installs the Python wrapper (c3d_python). It runs c3d commands from Python and exposes the images on the c3d stack as SimpleITK images.

Documentation

• Reference manual, covering every command and option.
• Convert3D page on itksnap.org.
• README.txt explains how to add a new command.

The logo is made from real c3d outputs; see utilities/logo.

Convert3D is developed at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.