Data Simulation & Basis Set Generation
This is a list of simulation software.
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. |
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) |
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 | |
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. |
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 | |
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. |
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 |
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 |