Note that restrictions imposed by these patents (and possibly others) exist independently of and may be in conflict with the freedoms granted in BSD-3-Clause license, which refers to copyright of the program, not patents for any methods that it implements. Both copyright and patent law must be obeyed to legally use and redistribute this program and it is not the purpose of this license to induce you to infringe any patents or other property right claims or to contest validity of any such claims. If you redistribute or use the program, then this license merely protects you from committing copyright infringement. It does not protect you from committing patent infringement. So, before you do anything with this program, make sure that you have permission to do so not merely in terms of copyright, but also in terms of patent law.
Some code in the NiiTools packages was based on nifti-converter