View the Project on GitHub hMRI-group/hMRI-toolbox

A toolbox for quantitative MRI and in-vivo histology using MRI (hMRI)


Neuroscience and clinical researchers are increasingly interested in quantitative magnetic resonance imaging (qMRI) due to its sensitivity to micro-structural properties of brain tissue such as axon, myelin, iron and water concentration (Weiskopf et al., 2015).

The hMRI-toolbox is an easy-to-use open-source and flexible tool, for qMRI data handling and processing. It allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R1 and R2*, proton density PD and magnetisation transfer MT saturation) (Weiskopf et al., 2013), followed by spatial registration in common space for statistical analysis (Draganski et al., 2011).

Embedded in the Statistical Parametric Mapping (SPM) framework, it can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps, and it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences.

The qMRI maps generated by the toolbox can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures. They are key input parameters for biophysical models designed to estimate tissue microstructure properties such as the MR g-ratio and to derive standard and novel MRI biomarkers (Mohammadi et al., 2015). The hMRI toolbox is therefore the first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction.


The hMRI-toolbox is free but copyright software, distributed under the terms of the GNU General Public Licence as published by the Free Software Foundation (either version 2, as given in file LICENSE, or at your option, any later version). Further details on "copyleft" can be found here. In particular, the hMRI-toolbox is supplied as is. No formal support or maintenance is provided or implied.


The latest release (and previous releases and pre-releases) of the hMRI-toolbox Matlab code can be downloaded from the releases page. The latest release is v0.2.0 (2018/12/20).

Supporting Material


Online documentation is available as a Wiki. It provides guidelines and instructions for installation and usage of the hMRI-toolbox. These pages are work-in-progress and updated on a regular basis.

hMRI-toolbox Paper & Poster

For a reference on the scientific background, methods and concepts please use this pre-print paper and cite it when publishing results compiled with the hMRI-toolbox. A conference poster is also available here.

Sample Dataset and MRI Acquisition Protocols

A sample dataset is provided as reference and material for exploring the possibilities and functionalities of the hMRI-toolbox. It is publicly available for download here. Several example MRI protocols (standard MPM protocol using customised Siemens sequences, as well MPM protocol implemented using Siemens and Philips product sequences) as well as a setup (for Siemens 3T MRI) and usage tutorial are available at the same URL. Please be aware that we provide these protocols and information without any warranty. They must be considered work-in-progress, possibly non-optimal protocols and information.

E-Mail List

We have created an e-mail list for users of the hMRI-toolbox. Registered users can login to view the message archive at the list home page.

Developers of the hMRI-toolbox

The development of the hMRI-toolbox is an international collaborative effort including the following sites and developers:


Acknowledgments and Funding