Complete list of software packages

This is a list of analysis and quantification software.

MRS DeIdentification Tools

MATLAB tools to remove protected health information (PHI) from magnetic resonance spectroscopy data.

MRS DeIdentification Tools
Developer Georg Oeltzschner, Mark Mikkelsen
Language MATLAB
License BSD
Credit Please credit the use of MRS DeIdentification Tools by citing https://www.biorxiv.org/content/10.1101/2020.02.12.944207v1

MRSHub Code  Author Website  Publication

VDI

VDI (Visual Display Interface) is a collection of MATLAB libraries created to visualize and process multiresolution data, such as MRS, MRSI, fMRI and anatomical MRI. An additional sub-library called SpinTool (independently available for download) can be used to easily and quickly write Bloch simulations and simulations of J-coupled spins.

VDI
Developer Assaf Tal
Language MATLAB
License BSD3
Credit Please cite the software package using the APS style or equivalent (Tal, A (2020). Visual Display Interface (VDI) [Computer Software]. Retrieved from http://www.vdisoftware.net)

Author Website 

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

ABfit_paper

All code and data to reproduce the ABfit paper

ABfit_paper
Developer Martin Wilson
Language R
License BSD-3
Credit Please cite the publication mentioned below if you use ABfit

Author Website  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

GAMMA/PyGamma

Classic NMR simulation library.

GAMMA/PyGamma
Developer Brian J. Soher
Language C++, Python
License open-source
Credit Proper reference should be given, using the citation below, when GAMMA simulations are used in papers and/or presentations: 'Computer Simulations in Magnetic Resonance. An Object Oriented Programming Approach', S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst, J. Magn. Reson., 106a.

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

MARSS

A novel software package for fast and computationally efficient basis set simulation.

MARSS
Developer Christoph Juchem, Karl Landheer
Language MATLAB
License Closed-source, limited-term academic license
Credit

Author Website  Publication

MRS-voxel-plot

Simple scripts to produce informative MRS voxel and spectral plots for a group or groups of participants.

MRS-voxel-plot
Developer Niall Duncan, Vuong Truong
Language Python
License MIT
Credit Please cite the publication mentioned below if you use this code.

MRSHub Code  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

pymapVBVD

A python port of the Matlab mapVBVD tool for reading Siemens Twix files.

pymapVBVD
Developer William Clarke
Language Python
License MIT
Credit No credit is required for the use of this code.

MRSHub Code  Author Website 

pysoher

A collection of algorithms and general code tools (GUI, I/O etc.) for use with MRS research.

pysoher
Developer Brian J. Soher
Language Python
License BSD
Credit BSD license, byproducts of the Vespa Versatile Simulation Pulses and Analysis project for MRS research at https://scion.duhs.duke.edu/vespa/project

MRSHub Code  Author Website 

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 

spec2nii

A command-line tool for converting MRS and MRSI data from a variety of formats to NIfTI + JSON format.

spec2nii
Developer William Clarke
Language Python
License BSD-3-Clause
Credit Please acknowledge the use of the tool and any creators of the tool.

Author Website 

SpecVis

SpecVis is a repository of R functions to visualize quantitative MRS results from different linear-combination algorithms.

SpecVis
Developer Helge J. Zöllner, PhD
Language R, MATLAB
License MIT
Credit Please cite the publication mentioned below if you use SpecVis (Zöllner et al, Comparison of algorithms for linear-combination modelling of short-echo-time magnetic resonance spectra, bioRxiv (2020)).

MRSHub Code  Author Website  Publication

Spinach

Spinach is a fast (polynomial complexity scaling for liquid state NMR) open-source spin dynamics simulation library that supports NMR, EPR, MRI, DNP, MAS, Optimal Control, PHIP, singlet state NMR, and other forms of Magnetic Resonance spectroscopy.

Spinach
Developer Ilya Kuprov
Language MATLAB
License Open-source
Credit If you are using Spinach, cite appropriate papers from http://spindynamics.org/wiki/index.php?title=Appendix_C:_literature_citations

Author Website  Publication

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