MR Optimum

MR Optimum provides tools for advanced signal-to-noise ratio (SNR) estimation and image reconstruction methods for Magnetic Resonance Imaging (MRI). It is designed for researchers and developers to efficiently perform SNR calculations, reconstructions, and custom pipeline configurations.

Quickstart

Run an SNR calculation using a JSON configuration:

bash python -m mroptimum.snr -j /path/to/config.json -o /output/path/ -c True -g True -v True -m True

Example JSON Configuration

json { "version": "v0", "acquisition": 2, "type": "SNR", "id": 2, "name": "PMR", "options": { "NR": 20, "reconstructor": { "type": "recon", "name": "GRAPPA", "id": 4, "options": { "noise": { "type": "file", "options": { "filename": "/data/PROJECTS/mroptimum/_data/noise.dat", "vendor": "Siemens" } }, "signal": { "type": "file", "options": { "filename": "/data/PROJECTS/mroptimum/_data/signal.dat", "vendor": "Siemens" } } } } } }

Installation

```

create an environment

python3 -m venv MRO source MRO/bin/activate pip install git+https://github.com/cloudmrhub/mroptimum-tools.git ```

Live Example

https://colab.research.google.com/drive/1-8wcaS9IBZ5aCcLvwY6D3mhwcNxlJr4y?usp=sharing

Versioning

The MR Optimum package has two versions:

V1 (Deprecated)

• Name: mroptimum
• Status: Deprecated, but still functional for backward compatibility. (v1 branch)
• Details: This version is no longer actively maintained and will not receive updates or bug fixes.
• Installation: bash pip install git+https://github.com/cloudmrhub/mroptimum-tools.git@v1

Version 2 (Current)

• Name: mroptimum-tools
• Status: Actively maintained (main branch).
• Details: This is the recommended version for new projects. It includes updated functionality, GUI tools, and expanded features.
• Installation: bash pip install git+https://github.com/cloudmrhub/mroptimum-tools.git

Key Differences

| Feature | Version 1 (v1) | Version 2 (main) | |-------------------------|------------------------------|-----------------------------| | Maintenance | Deprecated | Actively maintained | | Compatibility | Legacy projects | New and legacy projects |

| Features | Limited | GUI tools, expanded options |

Migration

If you're currently using Version 1, consider migrating to Version 2 to take advantage of the latest features and updates.

Contributors

Dr. Eros Montin, PhD\ \ \

Prof. Riccardo Lattanzi, PhD\ \ \