The “hMRI Toolbox” for quantitative imaging & in vivo histology using MRI

Abstract

Quantitative magnetic resonance imaging (qMRI) finds increasing application in neuroscience and clinical research due to its greater specificity and its sensitivity to microstructural properties of brain tissue, such as myelin, iron and water concentration. We introduce the “hMRI Toolbox”, an easy-to-use open-source tool for generating and processing quantitative MRI data. This toolbox is embedded in the SPM framework, profiting from the high accuracy spatial registration in common space and the variety of available statistical analyses. It allows the estimation of quantitative MRI maps, precisely longitudinal (R 1 =1/T 1 ) and transverse (R 2 *=1/T 2 *) relaxation rates, proton density (PD) and magnetization transfer (MT), followed by spatial registration in common space for statistical analysis. It also offers flexibility for calculation of novel MRI biomarkers of tissue microstructure. The hMRI toolbox can be downloaded from http://hmri.info. The Readme.md and Wiki of the Git repository provide : • reference documentation, including installation instructions, example dataset, tutorial and detailed description of the functionalities implemented; • a link to a pre-print paper describing the hMRI toolbox