ITK-SNAP. ITK-SNAP is a software application used to segment structures in 3D medical images (GPL license, see http://www.itksnap.org).

Slicer. Slicer is a free, open source software package for visualization and image analysis (BSD-style open source license, see http://www.slicer.org).

MITK. The Medical Imaging Interaction Toolkit (MITK) is a free open source software platform aimed at providing support for an efficient software-development of methods and applications dealing with medical images (BSD-style license, see http://www.mitk.org).

SimpleITK. SimpleITK is a simplified layer built on top of ITK to facilitate its use in rapid prototyping of image analysis that can be used in interpreted languages, e.g. Python, (Apache 2.0 License license, see http://www.simpleitk.org/).

Convert3D. C3D is a command-line tool for converting 3D images between common file formats, which also includes a growing list of commands for image manipulation, such as thresholding and resampling (GPL license, see http://www.itksnap.org/pmwiki/pmwiki.php?n=Downloads.C3D).