Analysis & Quantification Software

This is a list of analysis and quantification software.

Wat_Lip_Removal_L2

Water and lipid signal removal in MRSI by L2 regularization

Wat_Lip_Removal_L2
Developer Liangjie Lin
Language MATLAB
License BSD3
Credit Please cite the publication mentioned below if you use Wat_Lip_Removal_L2.

MRSHub Code 

Publication

FID-A

The FID Appliance (FID-A) is an open-source software package for simulation of MRS experiments, design and analysis of radiofrequency (RF) pulses, and processing of MRS data.

FID-A
Developer Jamie Near
Language MATLAB
License open-source
Credit

Author Website  Publication

FSL-MRS

FSL-MRS is a collection of python modules and wrapper scripts for pre-processing and model fitting of Magnetic Resonance Spectroscopy (MRS) and Spectroscopic Imaging (MRSI) data.

FSL-MRS
Developer William Clarke and Saad Jbabdi
Language Python
License FSL License https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
Credit If you use FSL-MRS in your research please cite the publication below.

Author Website  Publication

Gannet

Open-source, MATLAB-based software for automated data processing and quantification of edited magnetic resonance spectroscopy (MRS) data.

Gannet
Developer Richard Edden, Mark Mikkelsen, Georg Oeltzschner, Sofie Tapper, Muhammad Saleh, C. John Evans, Ashley Harris, Nicolaas Puts
Language MATLAB
License open-source
Credit Should you publish material that made use of Gannet, please cite the publications listed under https://github.com/richardedden/gannet3.1#license.

Author Website  Publication

INSPECTOR

Toolbox to process, analyse and visualize MRS data.

INSPECTOR
Developer Christoph Juchem
Language MATLAB
License Closed-source, limited-term academic license
Credit

Author Website 

jMRUI

jMRUI is a software package for advanced time-domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.

jMRUI
Developer MRUI consortium (http://www.jmrui.eu/about/coordinator-developers/)
Language Java
License Closed-source proprietary free for non-commercial use (http://www.jmrui.eu/license-and-download/jmrui-license/)
Credit

Author Website  Publication

LCModel

Automatic quantification of in vivo proton MR spectra.

LCModel
Developer Stephen Provencher
Language Fortran (compiled)
License Commercial product (http://lcmodel.ca/lcm-license.shtml)
Credit

Author Website  Publication

MRSpa

Magnetic Resonance spectral processing and analysis (MRspa) is a spectral post-processing and analysis package that runs under MATLAB.

MRSpa
Developer Dinesh Deelchand
Language MATLAB
License closed-source
Credit

Author Website 

Osprey

Osprey is an all-in-one open-source software suite for state-of-the art processing, quantitative analysis, and visualization of in-vivo magnetic resonance spectroscopy (MRS) data.

Osprey
Developer Georg Oeltzschner, Helge J Zöllner, Richard AE Edden
Language MATLAB
License MIT
Credit Should you publish material that made use of Osprey, please cite the publication below.

Author Website  Publication

OXSA

Open-source library with functions for processing and fitting MRS data.

OXSA
Developer Lucian Purvis, Christopher Rodgers
Language MATLAB
License Non-commercial use, https://github.com/OXSAtoolbox/OXSA/blob/master/LICENSE.txt
Credit If you use this software in an academic publication, please reference the publications mentioned under https://github.com/OXSAtoolbox/OXSA#oxsa-oxford-spectroscopy-analysis-toolbox.

Author Website  Publication

QMRITools

QMRITools is written in Mathematica using Wolfram Workbench and Eclipse and contains a collection of tools and functions for processing quantitative MRI data. The software tools for spectroscopy are mostly focussed on 31P CSI analysis but do not exclude other nuclei and/or acquistion methods. The basic features include methods for manipulating and processing spectra (including PCA denoising and deconvolution), generation of basis spectra using j-coupling simulations and fitting of basis spectra to the spectra.

QMRITools
Developer Martijn Froeling, PhD
Language Mathematica
License BSD-3
Credit Please cite the publication mentioned below if you use QMRITools. A publication on the spectro specific tools is in preparation.

Author Website  Publication Publication 2 Publication 3

SIVIC

SIVIC is an open-source, standards-based software framework and application suite for processing and visualizing DICOM MR Spectroscopy data.

SIVIC
Developer Nelson Lab, UCSF
Language C++
License Open-source, https://github.com/SIVICLab/sivic/blob/master/LICENSE
Credit

Author Website  Publication

SMAL

The Stanford CNI MRS Library (SMAL) provides algorithms and methods to read and analyze data from Magnetic Resonance Spectroscopy (MRS) experiments. It provides an API for fitting models of the spectral line-widths of several different molecular species, and quantify their relative abundance in human brain tissue

SMAL
Developer Ariel Rokem, PhD
Language Python
License BSD3
Credit

Author Website 

spant

spant (Spectroscopy Analysis Tools) provides a full suite of tools to build automated analysis pipelines for Magnetic Resonance Spectroscopy (MRS) data.

spant
Developer Martin Wilson
Language R
License Open-source
Credit

Author Website 

Tarquin

Open-source GUI to process and fit MRS data.

Tarquin
Developer Martin Wilson
Language C++
License GPL
Credit

Author Website  Publication

Vespa

The free, open source Vespa suite contains four magnetic resonance (MR) spectroscopy software applications: RFPulse (for RF pulse design), Simulation (for spectral simulation), Priorset (for creating simulated MR spectroscopic data) and Analysis (for spectral data processing and analysis).

Vespa
Developer Brian J. Soher
Language Python
License BSD-3
Credit

Author Website