Osprey (Open-Source Processing, Reconstruction & Estimation of MRS data) is an all-in-one software suite written in MATLAB for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data.
Osprey is completely free and entirely open-source, available on GitHub. It is designed to provide a modular analysis workflow, and to enable community development.
- 1-file job definition system for reproducible data analysis
- Automated recognition of input file format and sequence origin
- Fully-automated loading and pre-processing pipeline for optimal SNR, linewidth, phasing, and alignment
- Integrated linear-combination modeling module
- Full density-matrix simulated basis sets (using real pulses and sequence timings; including effects of localization and spectral editing) for many metabolites and common sequence implementations
- Functions to create custom basis sets and import basis sets from LCModel or Tarquin
- Integrated voxel co-registration and segmentation module (requires SPM12)
- Quantification based on tissue fractions and (customizable) metabolite/tissue water relaxation times
- GUI to display data, quality assessment, and quantitative results at each step of the analysis
- Rich ‘Overview’ GUI panel for batched datasets to visualize distributions of metabolite estimates and mean +/- SD spectra
If you encounter errors or bugs, have questions about Osprey, or would like to contribute a module of your own - this is the community space to do it. We’re looking forward to your messages!