Visualization

This is a list of analysis and quantification software.

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 

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

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

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

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 

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