Monalisa : a reconstruction tool-box for non-cartesian and cartesian MRI data

This repository contains code for performing MRI reconstruction with non-cartesian or cartesian data. Several iterative reconstruction are implemented. They all consist in minimizing a regularized or non-regularized least-square objective function.

Make sure to visit our documentation.

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Usage and installation

To get started with the MRI reconstruction code, follow these steps:

1. Clone the repository

   git clone https://github.com/MattechLab/monalisa.git
   cd monalisa

2. Make sure you have a compiler that is recognized by MATLAB. To check that you can run

mex -setup C++

Depending on your configuration, you should install a C++ compiler. (If you see a message like "No supported compiler or SDK was found. For options, visit https://www.mathworks.com/support/compilers".)

If you have to install a compiler, we recommend:

• g++ for Linux,
• Xcode Clang++ for macOS,
• Visual studio c++ or MinGW for windows. Normally, the compiler from Visual studio c++ will work. If it fails, you can also install MinGW alternatively following these instructions. After downloading the MinGW, such as mingw81, run the command % configuremingw('\path\to\mingw81'),then you are ready to compile Monalisa!

3. Compile the cpp code using the helper compiling function . On macOS you should change the libomp_dirs directory here:

   monalisa/src/mex/m/compile_mex_for_monalisa.m

   Line 62 in eed863d

   libomp_dirs = dir('/opt/homebrew/opt/libomp'); % Example path where Homebrew installs packages

   . If you are using brew for the installations, you can find the libomp_dirs path by running: brew --prefix libomp. (you need libomp as explained here)

4. Great, installation is done! You are now ready to run the first tutorial

Getting started

For better installation guidelines and much more check Monalisa's documentation here!

Navigating This Repository

This repository is organized into 5 main subfolders, each with a specific purpose:

• demo/ – Example scripts and tutorials demonstrating how to use the toolbox.

• docs/ – Documentation sources and build tools for generating the project’s documentation.

• src/ – Core source code of the Monalisa toolbox. This is where the main functionality is implemented.

• third_part/ – Third-party software dependencies (some with local modifications). These are distributed under licenses different from Monalisa’s.

• tests/ – Unit tests and validation scripts to ensure code reliability.

Help us improve

Monalisa is still very young. If you encounter an issue, please consider opening a GitHub issue in the repository. If you know how to fix the problem, feel free to submit a pull request!