MRtrix was developed with simplicity, performance, flexibility and consistency in mind, which has led to a number of fundamental design decisions. The main concepts are explained in the following pages:

The build process is based on a Python script rather than Makefiles, and all dependencies are resolved at build-time. This is explained in The build process.
The configure script allows you to create different co-existing configurations, for example to easily switch from a release build to a debug build. This is explained in The configure script.
You are encouraged to set up your own, separate module on top of the MRtrix codebase. This allows you to write your own code, stored on your own (potentially private) repository, without affecting the MRtrix core repository. This is explained in the section Writing separate modules.
The basic steps for writing applications based on MRtrix are explained in the section Creating a new MRtrix command.
The concepts behind accessing and processing Image data are outlined in Accessing image data.
There are a number of convenience classes to simplify development of multi-threaded applications, in particular the Image::ThreadedLoop and Thread::Queue classes. These are outlined in the section Writing multi-threaded applications.