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. |
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 | |
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 | |
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 |