Complete list of software packages
This is a list of analysis and quantification software.
2SPECIAL vGRAPPA
This algorithm decomposes simultaneously acquired multi-voxel data to their respective origin regions. Based on the split-slice GRAPPA code by Steen Moeller, University of Minnesota, USA.
| 2SPECIAL vGRAPPA | |
|---|---|
| Developer | Layla Tabea Riemann, M.Sc. (Physikalisch-Technische Bundesanstalt, PTB) |
| Language | MATLAB |
| License | CC BY-NC-SA 4.0 |
| Credit | Please cite the following publication if you use the vGRAPPA algorithm: L.T.Riemann, C.S.Aigner, R.Mekle, S.Schmitter, B.Ittermann, A.Fillmer; Fourier-based decomposition approach for simultaneous acquisition of 1H spectra from two voxels in vivo at short echo times, Proc. Int. Soc. Magn. Reson. Med. 2021:007 |
Assessment of measurement precision in single-voxel spectroscopy at 7 T
Code from the Paper: Assessment of Measurement Precision in Single Voxel Spectroscopy at 7 T: Towards Minimal Detectable Changes of Metabolite Concentrations in the Human Brain In-Vivo, Magn. Reson. Med. 87:1119-1135 (2022); DOI 10.1002/mrm.29034
| Assessment of measurement precision in single-voxel spectroscopy at 7 T | |
|---|---|
| Developer | Layla Tabea Riemann, M.Sc. (Physikalisch-Technische Bundesanstalt, PTB) |
| Language | Python, R |
| License | CC BY-NC-SA 4.0 |
| Credit | Please cite the following publication if you use this code: L.T.Riemann, C.S.Aigner, S.L.R.Ellison, R.Brühl, R.Mekle, S.Schmitter, O.Speck, G.Rose, B.Ittermann, A.Fillmer; Assessment of Measurement Precision in Single Voxel Spectroscopy at 7 T: Towards Minimal Detectable Changes of Metabolite Concentrations in the Human Brain In-Vivo, Magn. Reson. Med. 87:1119-1135 (2022) |
CloudBrain-MRS
CloudBrain-MRS is a cloud-based computational platform for MRS data. The platform deploys the mainstream quantification tool LCModel and advanced deep learning denoising and quantification algorithms. The platform has been developed with a module for the statistical analysis of biomarkers. Users can batch preprocess and quantitative analysis MRS data with only one browser. The platform has been developed with a range of visualization techniques to provide a user-friendly interface.
| CloudBrain-MRS | |
|---|---|
| Developer | Jiayu Li, Xiaodie Chen, Dicheng Chen, Yirong Zhou, Zhangren Tu, Meijin Lin, Xiaobo Qu |
| Language | Python, JavaScript |
| License | BSD3 |
| Credit | Please reference the following publication if you use CloudBrain-MRS: X. Chen et al., “CloudBrain-MRS: An intelligent cloud computing platform for in vivo magnetic resonance spectroscopy preprocessing, quantification, and analysis,” arXiv:2306.11021, 2023. D. Chen et al., “Magnetic resonance spectroscopy deep learning denoising using few in vivo data,” IEEE Trans. Comput. Imaging, vol. 9, pp. 448-458, 2023. D. Chen et al., “Magnetic resonance spectroscopy quantification aided by deep estimations of imperfection factors and overall macromolecular signal,” arXiv:2306.09681, 2023. |
MRSCloud
MRSCloud allows MRS users to simulate a vendor-specific and sequence-specific basis set online in a convenient and time-efficient manner. This tool can simulate basis sets for GE, Philips, and Siemens MR scanners.
| MRSCloud | |
|---|---|
| Developer | Steve C N Hui, Muhammad G Saleh, Helge J Zöllner, Georg Oeltzschner, Hongli Fan, Yue Li, Yulu Song, Hangyi Jiang, Jamie Near, Hanzhang Lu, Susumu Mori, Richard A E Edden |
| Language | MATLAB |
| License | BSD3 |
| Credit | Please reference the original publication if you use MRSCloud for basis set simulation. |
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
Read_JMRUIHTML
Python module for processing the HTML files created by AMARES in jMRUI when saving the fit results for a series of spectra with the ‘publish all’ command.
| Read_JMRUIHTML | |
|---|---|
| Developer | Ronald Ouwerkerk, NIDDK/NIH, Bethesda MD, USA |
| Language | Python |
| License | BSD-3-Clause |
| Credit | If you would be so kind to acknowledge me as the source of this software when you use it for a publication it will be much appreciated. |
SimnTG
Generates simulated spectra of triglycerides with unsaturated fatty acids as would be acquired with a TE series with PRESS localization. The fatty acid chain length can be specified.
| SimnTG | |
|---|---|
| Developer | Ronald Ouwerkerk, NIDDK/NIH, Bethesda MD, USA |
| Language | MATLAB |
| License | BSD-3-Clause |
| Credit | If you would be so kind to acknowledge me as the source of this software when you use it for a publication it will be much appreciated. |
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) |
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. |
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 |
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 | |
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. |
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. |
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. |
INSPECTOR
Toolbox to process, analyse and visualize MRS data.
| INSPECTOR | |
|---|---|
| Developer | Christoph Juchem |
| Language | MATLAB |
| License | Closed-source, limited-term academic license |
| Credit | |
IRIS-MRS-AI
IRIS-MRS-AI: Machine learning powered data analysis tool. IRIS-MRS-AI has 2 parts; i-Built-in models for classifying IDH and TERTp mutations in gliomas using 1H- MRS/MS data. ii- Users can create their own models using their own data (independent from the field).
| IRIS-MRS-AI | |
|---|---|
| Developer | Abdullah BAŞ |
| Language | MATLAB |
| License | MIT |
| Credit | Please cite the following publication if you use IRIS-MRS-AI: Bas A, Sacli-Bilmez B, Hatay GH, Ozcan A, Levi C, Danyeli AE, Can O, Yakicier C, Pamir MN, Ozduman K, Dincer A, Ozturk-Isik E. Glioma Genetic Diagnosis Software for Detection of IDH and TERTp Mutations based on 1H MR Spectroscopy and Mass Spectrometry. International Society for Magnetic Resonance in Medicine. Vancouver, Canada May 15-20, 2021 (Digital Poster) |
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 | |
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 | |
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 | |
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 | |
NMRScopeB (part of jMRUI)
As a plugin to jMRUI, NMRScopeB provides the functionality useful for assembling metabolite basis set for metabolite concentration estimation in jMRUI or other software packages. In the simulation, properties such as chemical shifts, spin-spin coupling, relaxation, spatial and/or spectral excitation selectivity, and customized pulse sequences are accounted for. The simulator can be also used for MR study and method development.
| NMRScopeB (part of jMRUI) | |
|---|---|
| Developer | Zenon Starcuk, Jana Starcukova |
| Language | Python, C++, Java |
| License | closed-source GUI, open-source calculation; distributed as a part of jMRUI software package (http://www.jmrui.eu/license-and-download/nmrscope-b-license/) under the same license |
| Credit | Please cite 'Starčuk Z Jr, Starčuková J. Quantum-mechanical simulations for in vivo MR spectroscopy: Principles and possibilities demonstrated with the program NMRScopeB. Anal Biochem. 2017 Jul 15;529:79-97. doi: 10.1016/j.ab.2016.10.007.', when NMRScopeB simulations are used in papers. |
Oryx-MRSI
ORYX-MRSI: A data analysis software for multi-slice 1H-MRSI
| Oryx-MRSI | |
|---|---|
| Developer | Sevim Cengiz |
| Language | MATLAB |
| License | MIT |
| Credit | Please cite the following publication if you use Oryx-MRSI: Cengiz S, Yildirim M, Bas A, Ozturk-Isik E. ORYX-MRSI: A data analysis software for multi-slice 1H-MRSI. International Society for Magnetic Resonance in Medicine. Virtual Meeting, May 15-20, 2021 (Digital Poster) |
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. |
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. |
PASTIS
PASTIS can be used to process and quantify single-voxel MRS data. It can also simulate data using various sequences, B0 fields and nuclei. It was originally developed to reconstruct, process and quantify spinal cord MRS data at 7T. PASTIS relies a lot on the suspect package.
| PASTIS | |
|---|---|
| Developer | Tangi Roussel |
| Language | Python 3 |
| License | BSD-3 |
| Credit | Please cite the publication mentioned below if you use PASTIS. |
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. |
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 |
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 | |
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 | |
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 | |
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. |
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 |
Tarquin
Open-source GUI to process and fit MRS data.
| Tarquin | |
|---|---|
| Developer | Martin Wilson |
| Language | C++ |
| License | GPL |
| Credit | |
Vespa
The open source Vespa suite contains four magnetic resonance (MR) spectroscopy software applications: RFPulse (for RF pulse design), Simulation (for spectral simulation), DataSim (for creating synthetic MRS data) and Analysis (for spectral data processing and analysis).
| Vespa | |
|---|---|
| Developer | Brian J. Soher |
| Language | Python |
| License | BSD-3 |
| Credit | Please reference the following publication if you use this software: Soher BJ et.al. Vespa: Integrated applications for RF pulse design, spectral simulation and MRS data analysis. 19th Meeting ISMRM, Montreal 2011 |