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MRIRecoTutorial

Tutorial on the Julia Package MRIReco.jl

Warning This tutorial is outdated and uses an old version of Julia and MRIReco.jl. We have transfered all content to the MRIReco.jl documentation.

Getting Started

This tutorial can be used and run in two ways:

  • You can directly use Pluto notebook you are reading right now. This needs some preparation discussed next.
  • You can also copy/past into a Julia REPL. This is in particular a good way if you are reading an HTML or PDF version of this tutorial.
  • Keep in mind that this notebook will run all cells, which needs some time since we also showcase some more computationally intensive methods.

Preparation

  • Go to https://julialang.org/downloads/ and download the most recent stable release (version 1.6 when this notebook was prepared).
  • Checkout https://github.com/MagneticResonanceImaging/MRIRecoTutorial.
  • Start Julia from within a terminal within the folder you checked out the repository.
  • We need to install some packages. With ] we can enter the Pkg mode and enter 
    (@v1.6) pkg> activate .
    which will install all necessary packages.
  • To run this notebook use the command import Pluto; Pluto.run() and open the notebook in the appearing file browser.
  • In the box Open from file: enter the filename of the notebook (MRIRecoTutorial.jl) and press enter.
  • We are using Pluto.jl, which is similar to Jupyter but has some advantages, in particular the notebook is stored as plain Julia code that you can access with a simple text editor.
  • Instead of running the notebook in the browser you can also run it in the REPL 
    julia> include("MRIRecoTutorial.jl")
    Note that this, however will only show the plot of the last reconstruction since this notebook is tailored for usage in Pluto.