ORYX‐MRSI: A fully‐automated open‐source software for proton magnetic resonance spectroscopic imaging data analysis

• Published in: International journal of imaging systems and technology Vol. 32; no. 4; pp. 1068 - 1083
• Main Authors: Cengiz, Sevim, Yildirim, Muhammed, Bas, Abdullah, Ozturk‐Isik, Esin
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01-07-2022; Wiley Subscription Services, Inc
• Subjects: Brain; Chemical equilibrium; Data analysis; magnetic resonance spectroscopic imaging; Magnetic resonance spectroscopy; Medical imaging; Metabolites; MR spectral data analysis; Open source software; open‐source; Proton magnetic resonance; Quality control; software
• ISSN: 0899-9457; 1098-1098
• DOI: 10.1002/ima.22748

Proton magnetic resonance spectroscopic imaging (1H‐MRSI) provides a noninvasive, spatially resolved evaluation of brain metabolism. However, there are some limitations of 1H‐MRSI preventing its wider use in the clinics, including the spectral quality issues, partial volume effect and chemical shift artifact. Additionally, it is necessary to create metabolite maps for analyzing spectral data along with other MRI modalities. In this study, a MATLAB‐based open‐source data analysis software for three‐dimensional 1H‐MRSI, called Oryx‐MRSI, which includes modules for visualization of raw 1H‐MRSI data and LCModel outputs, chemical shift correction, tissue fraction calculation, metabolite map production, and registration onto standard MNI152 brain atlas while providing automatic spectral quality control, is presented. Oryx‐MRSI implements region of interest analysis at brain parcellations defined on MNI152 brain atlas. All generated metabolite maps are stored in NIfTI format. Oryx‐MRSI is publicly available at https://github.com/Computational-Imaging-LAB/Oryx-MRSI along with six example datasets.