The hMRI analysis toolbox for quantitative MRI and in vivo histology using MRI (hMRI)

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 - myelin, iron and water concentration. We introduce the hMRI toolbox, an easy-to-use open-source tool for handling 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 (longitudinal and transverse relaxation rates R 1 and R 2 *, 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 (git repository). The reference documentation is available as a WIKI on the git repository, including installation instructions, example dataset, tutorial and detailed description of the functionalities implemented