How to install QMRITools

QMRITools installation

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Overview

The latest release of QMRITools can be found here. For optimal performance, it is recommended to install the toolbox via the Mathematica paclet system.

Automatic Installation

  1. Download the Latest Paclet:
  2. Download the latest QMRITools-x.x.x.paclet from the release page.

Install the Paclet Using PacletInstall:

Automatic installation

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

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

Alternatively, you can directly install it from the release page:

  1. Using PacletInstall with a link

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

  1. Using the resource function GithubInstall

ResourceFunction["GitHubInstall"]["mfroeling", "QMRITools"]

External dependencies

Some functions in QMRITools require external executables and software. These executables are included in the release but can be replaced if needed. However, functionality with alternate versions is not guaranteed. For the latest versions and user licenses, visit their respective websites:

All functionalities are tested on Windows and macOS with the latest Mathematica version. The Mathematica code is cross-platform compatible, except for external tools compiled for each OS. The included versions are:

  • Elastix: Version 5.2.0 with OpenCL support
  • dcm2niix: Latest version, and various versions for windows

Cross-platform compatibility is supported but not extensively tested. Please report any issues encountered.

Loading the toolbox

To load the toolbox, use the following command in Mathematica:

<<QMRITools`

For monitoring package loading, use:

QMRITools`$Verbose = True;
<<QMRITools`

Listing Available Packages and Functions

To generate a list of all QMRITools packages:

QMRIToolsPackages[]

To list all functions in DTITools or a specific toolbox:

QMRIToolsFunctions[]
QMRIToolsFunctions["toolbox name"]

Helpfull functions

After loading the toolbox to find the install location of the toolbox run

OpenQMRIToolsLocation[]

And to open the ‘Demonstrations.nb’ notebook run

OpenDemonstrationNotebook[]

Documentation

An online version of the documention can be found here.

To print documentation of all functions:

QMRIToolsFuncPrint[]
QMRIToolsFuncPrint["toolbox name"]

A comprehensive list of all functions and their help documentation is available in All-Functions.nb, which can also be downloaded as a pdf file.