MRI Studio (https://www.mristudio.org/ ) is a Windows-based software package, developed at Johns Hopkins University that includes support for 3D visualization, the processing of diffusion tensor data, and image registration. The package supports a number of different image data types from Philips PAR and REC files to DICOM.  MRI Studio can be obtained from the S. Mori group website here. The package is supported through several mailing lists (https://lists.mristudio.org/mailman/listinfo).

To access this tool: https://www.mristudio.org/

FreeSurfer is a set of software tools that can be used to process structural (T1-weighted) and functional MR images. The tools can construct models of the white matter, cortical gray matter, as well as the pial surface. Once these surfaces are known, an host of anatomical measures becomes available, such as cortical thickness, surface area, curvature, and surface normal at each point on the cortex. Tools also exist to inflate or flatten for further measurement or visualization. Much of the FreeSurfer pipeline is automated, thereby making it ideal for processing large data sets.

The FreeSurfer source code has been released under an open-source licensing agreement. Making the FreeSurfer source code available to the public has many advantages: users can gain a greater understanding of the underlying algorithms; users can build FreeSurfer on currently unsupported OS platforms; and users can inspect the code for possible bugs, or suggest improvements, thus improving the overall quality. Approximately 2500 FreeSurfer licenses have been distributed.

Now that FreeSurfer is open source, commercial-level support and quality assurance is being provided. Currently there are 407 unit tests, 64 system tests, nightly builds/tests on an array of platforms, and integration of the Doxygen documentation system for FreeSurfer documentation.

To access the tool: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki