Osprey (Open-Source Processing, Reconstruction & Estimation of MRS data) Overview

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.

Features include:

  • 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!

Georg Oeltzschner

I am a French master’s student in biomedical imaging, I am working on a dissertation: SRM-in vivo quantification with Osprey, I have Matlab 2022 I have installed your osprey guide but the “FIT” module does not appear even in gray I do not understand not why?

I apologize for disturbing you