Welcome to QRMITools

Content

• Introduction
• Installation
• Citing
• Documentation
• External dependencies
• Toolboxes
• License

Introduction

QMRITools is written in Mathematica and contains a collection of tools and functions for processing quantitative MRI data. The toolbox does not provide a GUI and its primary goal is to allow for fast and batch data processing, and facilitate development and prototyping of new functions. The core of the toolbox contains various functions for data manipulation and restructuring.

For more information visit our website

Installation

The latest release can be found here. The toolbox is best installed via the Mathematica paclet system. For more information visit the website.

Automatic installation:

1. Download the QMRITools-x.x.x.paclet.
2. Install the paclet using PacletInstall.

PacletInstall["xxx\\QMRITools-x.x.x.paclet"]

Or alternatively you can directly install it from the latest release page

PacletInstall["https://github.com/mfroeling/QMRITools/releases/download/x.x.x/QMRITools-x.x.x.paclet"]

Citing

When using the toolbox please cite one of the following references:

1. Froeling M: QMRTools: a Mathematica toolbox for quantitative MRI analysis. J Open Source Softw 2019; 4:1204. link
2. Froeling M, et al.: Reproducibility of diffusion tensor imaging in human forearm muscles at 3.0 T in a clinical setting. Magn Reson Med 2010; 64:1182-1190. link
3. Froeling M, et al.: Diffusion-tensor MRI reveals the complex muscle architecture of the human forearm. J Magn Reson Imaging 2012; 36:237-248. link
4. Schlaffke et al.: Multicenter evaluation of stability and reproducibility of quantitative MRI measures in healthy calf muscles; NMR Biomed. 2019;32:e4119 link

Media and awards

• During the 2023 ISMRM in Toronto QMRITools was awarded received the Best Open Source Tool Award from the Quantitative MRI study group.
• If you want to learn more about the workings of QMRITools you can watch a live discussion with the Wolfram academic outreach team about QMRITools and the role of computational Wolfram technology.
• A more in depth explanation of the paclet functionality was presented to the Wolfram R&D Team.
• QMRITools is build using Wolfram language for which it was awarded the Wolfram Innovator Award in 2023 during the Wolfram Technology conference.

Documentation

An online version of the full documentation can be found here.

External dependencies

Some functions of QMRITools call on external executables and software. These executables need to be present in QMRITools and are included in the release. If for any reason you want to use other (older/newer) versions you can replace them but functionality is not guaranteed. For the latest version of these tools and their user license please visit their website.

• dcm2niix
• Elastix

Toolboxes

QMRITools contains the following toolboxes:

• CardiacTools
• CoilTools
• DenoiseTools
• DixonTools
• ElastixTools
• FasciculationTools
• GeneralTools
• GradientTools
• IVIMTools
• JcouplingTools
• LoggingTools
• MaskingTools
• MuscleBidsTools
• NiftiTools
• PlottingTools
• ProcessingTools
• ReconstructionTools
• RelaxometryTools
• SegmentationTools
• SimulationTools
• SpectroTools
• TaggingTools
• TensorTools
• TractographyTools

License

https://opensource.org/licenses/BSD-3-Clause

Note that restrictions imposed by these patents (and possibly others) exist independently of and may be in conflict with the freedoms granted in BSD-3-Clause license, which refers to copyright of the program, not patents for any methods that it implements. Both copyright and patent law must be obeyed to legally use and redistribute this program and it is not the purpose of this license to induce you to infringe any patents or other property right claims or to contest validity of any such claims. If you redistribute or use the program, then this license merely protects you from committing copyright infringement. It does not protect you from committing patent infringement. So, before you do anything with this program, make sure that you have permission to do so not merely in terms of copyright, but also in terms of patent law.

Some code in the NiiTools packages was based on https://github.com/tomdelahaije/nifti-converter