is there any place I can read how to create a 5tt algorithm?
No; I’ve intended to do this for some time. I did recently have @rmito document the process of contributing a new Python script to MRtrix3 for the sake of a presentation, and I’d like to generate some more public documentation based on that experience. The software engineering side of things (i.e. not the novel content but the mechanisms of contributing such) is described here.
Contributing to scripts that use the algorithm module (currently 5ttgen, dwi2response, dwibiascorrect, dwinormalise) is slightly different to adding a new standalone script.
If you:
- Generate a copy of an existing functioning script in e.g.
lib/mrtrix3/_5ttgen/and give it an appropriate name; - Edit this line so that the name of the parser matches the name of the new file from step 1
, then 5ttgen should present this “new” entry as an algorithm that can be selected and executed from the command-line. From there it’s a matter of modifying the code relating to the command-line interface and the internal execution of commands in order to make the script manifest the behaviour you want. But starting from something that already works, and making small changes and seeing their influence, is always a good entry point.
Rob