The main sources of documentation of NiftyRec is the Wiki. (The Programming Manual describes the projection and back-projection algorithms but is outdated).
The Matlab Toolbox is documented in the Matlab Help. After installing NiftyRec and the NiftyRec Matlab Toolbox (see the Wiki for instructions), click on the Matlab Help button and select ‘NiftyRec Toolbox’ from the Contents list in order to visualize the (incomplete) documentation of the NiftyRec Toolbox for Matlab. All the functions of the NiftyRec Toolbox for Matlab have inline documentation: e.g. digit ‘help et_project’ at the Matlab prompt. Digit ‘et_’+'Tab’ (autocompletion) to see the list of the Matlab scripts for emission tomography and ‘tt_’+'Tab’ to see the list of the Matlab scripts for transmission tomography. Digit ‘et_demo’+'Tab’ and ‘tt_demo’+'Tab’ to see the list of demos. The most important demos are documented in the Wiki.
For help on how to use the Python interface use e.g. dir(NiftyRec) and help(NiftyRec.et_project). If you intend to use Python, check out occiput.io
Documentation of the C source code is generated with Doxygen.