mr_utils: magnetic resonance utilities¶
Contents:
This repo is a collection of my implementations of algorithms and tools for MR image reconstruction, mostly in python.
Orientation¶
There are few different things going on here. There are algorithms, like the geometric solution to the elliptical signal model, as well as simulations, like simulated bSSFP contrast.
There’s also some python functions and objects that interact with more polished tools such as Gadgetron and BART. You can use these python interfaces to easily write in Gadgetron, MATLAB, or BART functionality into your python scripts. These functions are written with the assumption of Gadgetron, MATLAB, etc. being run on some processing server (not necessarily on your local machine). If you use these, you’ll want to create a config file.
Documentation and Tests¶
Documentation is almost exclusively found in the docstrings of modules, functions, and classes.
Another great way to learn how things are used is by looking in the examples. Run examples from the root directory (same directory as setup.py) like this:
python3 examples/cs/reordering/cartesian_pe_fd_iht.py
If there’s not an example, there might be some tests. Individual tests can be run like this from the root directory (I recommend that you run tests from the home directory - imports will get messed up otherwise):
python3 -m unittest mr_utils/tests/recon/test_gs_recon.py
All tests can be run like so:
pyhon3 -m unittest discover