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:

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

Example JSON Configuration

{
    "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"
                    }
                }
            }
        }
    }
}

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Installation

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

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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• Details: This version is no longer actively maintained and will not receive updates or bug fixes.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:

  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:

  pip install git+https://github.com/cloudmrhub/mroptimum-tools.git

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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

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Migration

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

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Contributors

Dr. Eros Montin, PhD

Prof. Riccardo Lattanzi, PhD