Work

Monalisa: an open source, documented MATLAB toolbox for magnetic resonance imaging reconstruction

Year: 2025

Type: preprint

Abstract: Summary Purpose An open-source, user-friendly MATLAB framework for Magnetic Resonance Imaging (MRI) reconstruction was developed to simplify the reconstruction process, with a specific focus on non-Cartesian imaging and dynamic applications in the presence of motion. Methods Monalisa is decomposing the reconstruction pipeline into clear modular steps, including raw data reading with flexible file-type abstraction, trajectory computation, density compensation, advanced coil sensitivity mapping, and tailored binning strategies through its “mitosius” preprocessing stage. The framework supports a suite of reconstruction methods, including iterative-SENSE (also named CG-SENSE), GeneRalized Autocalibrating Partial Parallel Acquisition (GRAPPA) reconstructions, and regularized reconstructions supporting both spatial and temporal regularization using l 1 (Compressed Sensing (CS)) and l 2 techniques, accommodating both Cartesian and non-Cartesian acquisitions. We performed benchmark experiments comparing Monalisa with the Berkeley Advanced Reconstruction Toolbox (BART) toolbox on simulated 2D radial acquisitions. Results Results of the comparison demonstrate competitive performance, yielding higher Structural Similarity Index (SSIM) and lower l 2 error. Notably, Monalisa reconstructions exhibited fewer visible artifacts than BART. Conclusion By providing comprehensive documentation, Monalisa serves not only as a powerful tool for research and clinical imaging but also as an educational platform to facilitate innovation in MRI reconstruction.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.1101/2025.06.06.658299

Authors: Mauro Leidi, Yiwei Jia, Dominik Helbing, Jaime Barranco, Berk Can Açikgöz, Eva Peper, Jean-Baptiste Ledoux, Jessica A.M. Bastiaansen, Bastien Milani, Benedetta Franceschiello

Institutions: University of Bern, HES-SO University of Applied Sciences and Arts Western Switzerland, Ghent University, HES-SO Valais-Wallis, The Sense Innovation and Research Center, Centre Hospitalier Universitaire Vaudois, Centre d'Imagerie BioMedicale, University of Lausanne

Language: English

Topic: Advanced MRI Techniques and Applications

Subfield: Radiology, Nuclear Medicine and Imaging

Field: Medicine

Domain: Health Sciences

Open Access status: green

Funder: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

Awards: Quantitative magnetic resonance biopsies: Exploiting signal asymmetries for next-generation noninvasive biomarker mapping, A Multidimensional Free-Running Framework for Comprehensive and Quantitative High-Resolution Magnetic Resonance Imaging of the Human Heart and its Vessels, A high-resolution, sub-second and fast-sampled resting state fMRI protocol for a better disentangling of neural, hemodynamic, physiological and movement activity in BOLD signal, 2.0 MR-EYE Towards a consensual Magnetic resonance Imaging protocol of the Human Eye

OpenAlex ID: W4411180995

Cites: 56

Cited by: 1

Related to: 10