MRTwin is a tool to code sequences manually and simulate MR images using the included Bloch simulation. The Documentation/Script of the course is in /script. It covers A : basic echoes in 1D, B : gradient echo encoding and fast GRE MRI, C : spin echo and RARE, D : balanced SSFP, E : exporting and scanning at a real MRI system, F : non-cartesian trajectories, undersampling and reconstruction.
The course format is full time two weeks. We meet daily from 9:30 am to 5:30 pm (CET). The first week is very interactive, with small inputs, and interleaved exercises and discussion of them. The second week is more independent.
For virtual attendence read the README_VIRTUAL.md.
Check the readmes for your system:
- README_HOME.md for installation on your own Windows or Linux system, Mac is currently not supported.
- README_CIP.md for the installation in the FAU CIP pool.
- run script data/brainweb/generate_maps.py to generate brainweb phantoms
See if you can run the python files ex/ex_help_01 and ex/exB05. If errors occur check the versions of the required packages. Or get help from the admin.
We use python in here as it is open source and easy to debug and extend. Also with pytorch python provides a rather simple possibility of parallelization of code, auto-differentiation.
If you are not familiar with python, please make sure to understand the file ex_help01_python.py from the MRTwin code, as it covers most of the used functions in the whole code and course.
- Python: Programming language
- Pulseq: Open-source, vendor agnostic MRI sequence definition
- pyPulseq: Pulseq port to python
- pyTorch: Tensor computations with automatic differentiation and GPU acceleration
- Bloch Simulator: Visualization Tool (this repository contains an extension for Pulseq files)
- LaTeX: Used for the script of the course
- mrzero-core.readthedocs