QMRITools installation

The latest release can be found here.

Installation up

Manual installation:

  1. Download the QMRITools.zip.
  2. Extract the QMRITools folder and place it in the Mathematica UserBaseDirectory > Applications.

If you want to know your UserBaseDirectory run the following code in mathematica

SystemOpen[FileNameJoin[{$UserBaseDirectory, "Applications"}]]

Alternatively you can also use the $BaseDirectory if you want the tools to be availible to all users.

Automatic installation:

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

PackletInstall["download folder\\QMRIToolsx-x.x.x.paclet"]

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

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

External dependencies up

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.

All functionality is tested under Windows 10 with the latest Mathematica version. The Mathematica code is cross platform compatible with the exception of the external tools which are compiled for each OS. The toolbox provides compiled versions for each OS but their functionality is not guaranteed.

The Elastix version used is 4.9 with OpenCL support. Additionally Elastix needs to be compiles with the PCA metrics, all DTI related parameters and all affine related parameters.

Although cross platform compatibility is provided I have only limited options for testing so if any issues arise please let me know.

Loading the toolbox up

The toolbox can be loaded by using

<<QMRITools`

If you want to monitor the package loading you can use:

QMRITools`$Verbose = True;
<<QMRITools`

A list of all QMRITools packages is generated by

QMRIToolsPackages[]

A list of all DTITools functions or functions per toolbox is generated by

QMRIToolsFunctions[]
QMRIToolsFunctions["toolboxname"]

To print the documentation of all functions use

QMRIToolsFuncPrint[]
QMRIToolsFuncPrint["toolboxname"]

A list off all functions and their help can be found in All-Functions.nb, which is alos availible as a pdf file.