MRIRecipes.jl

Recipes for image reconstruction using the MRIReco.jl package.

Includes a working example for spiral reconstruction with GIRF correction and a Cartesian reconstruction example for sensitivity and off-resonance map calculation.

NEW DOCS:

Getting Started!

1. To get started, make sure you have Julia installed. At least v1.6 is preferable (v1.7 is optimal).
2. Clone the MRIRecipes.jl project via Github to a local directory
3. Download the data supplement from Zenodo (https://doi.org/10.5281/zenodo.6510020) and extract somwhere.
   • Note: This might take a few minutes. You can skip ahead and continue with step 5-10 in the meantime.
4. Move the extracted folder (data) into the MRIRecipes.jl directory
5. Clone the MRIGradients project via Github to your Julia dev folder (usually /home/.julia/dev/ on Linux or C:\Users\<username>\.julia\dev on Windows). MRIGradients can be found at: https://github.com/BRAIN-TO/MRIGradients.jl
   • or you can do this in one step by typing ]add https://github.com/BRAIN-TO/MRIGradients.jl.git
6. Open a Julia REPL in your editor of choice
7. In the REPL, type ] to enter package mode
8. type activate . to activate a new Julia environment for the MRIRecipes.jl project
9. type dev MRIGradients to tell Julia which MRIGradients to use (this will be fixed upon package registration)
10. type instantiate to download and install all of the necessary packages.
11. Proceed to run the demos found in the /recon/ directory.

OLD DOCS

2. Open the GIRFReco folder in the text editor of your choice (we use Atom with the Julia extension Juno) after configuring the text editor to use Julia.

3. Once your editor is prepared, and the GIRFReco folder is opened, open the package cmd line by typing

   ]
   

   • Your prompt should now say pkg> instead of julia>
   • All the following commands are within the pkg> prompt.
   • If you have to get back to the julia prompt later, press CTRL+C

4. Within the package cmd line, activate the project environment:

   activate .
   

   • This activates the Julia environment for the GIRFReco code.
   • After typing this, wait for a while until the command line finishes setting up the Julia environment.

5. If this is your first timing activating this environment, you have to instantiate it after activating it via

   instantiate
   

   • Some packages might fail to install, but they are usually not needed by our code.

6. Add MRIReco.jl to your environment's package list via

   add MRIReco
   

Examples

• To run the following examples, open the listed files in your editor.
• Make sure your current folder is GIRFReco and its environment is activated.
• For Atom/Juno:
  • right-click on the folder, then Juno -> Work in Folder and Juno -> Activate Environment in Folder (or activate via the pkg> prompt as above)
  • Juno shortcut for running an open file: CTRL+SHIFT+ENTER
  • Juno shortcut for running a block (separated by a line startin with ## in the file): ALT+ENTER

1. GIRF.jl in action: Predicting an actual gradient waveform from a nominal one using the GIRF

   girf/GIRFDemo.jl
   

2. Interplay of GIRF.jl and MRIReco.jl: Using the julia recon package to reconstruct a spiral image with a GIRF-predicted trajectory

   recon/SpiralRecon.jl