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The hMRI toolbox is an open-source toolbox that incorporates all the necessary processing tools to obtain quantitative MRI (qMRI) maps (R1, PD, MT and R2*) following the MPM approach (Weiskopf et al. 2008 & 2013). The spatial processing implementation of the toolbox relies on the voxel-based quantification (VBQ) approach developed by Draganski et al. 2011 to preserve the quantitative nature of qMRI maps during processing.
The toolbox is embedded in the SPM framework, profiting from the highly accurate spatial registration in common space and the variety of established statistical inference schemes.
The flexible and modular nature of the toolbox makes it usable for a wide range of data types, from the full MPM protocol to subsets of it, including e.g. single contrast echo trains for mapping R2* or variable flip angle data for R1 and PD mapping using multi-echo or single-echo data. The spatial processing part of the toolbox can be applied to any set of rotationally-invariant qMRI maps, including diffusion MRI scalar parameter maps as well as the standard (R1, PD, MT and R2*) MPM maps.
This wiki is a collection of documentation and information about using the hMRI-Toolbox. It is an on-going project that will be updated regularly.
Please do not print these pages. This online Wiki is meant to be browsed online!!
GET STARTED
Instructions to install the toolbox, examples for setting up the acquisition protocol.
JSON METADATA AND DICOM IMPORT
DICOM to NIFTI conversion retrieving the whole DICOM header, tools for metadata handling (get, set and search tools), to keep track of acquisition and processing parameters at each step of the process.
AUTO-REORIENT
A simple tool to reorient all images towards the MNI space prior to map creation and data processing.
MAP CREATION
Tools to create quantitative and semi-quantitative R1, R2*, MT and PD maps.
PROCESSING
Spatial and statistical processing of the quantitative and semi-quantitative maps.
DEFAULTS & CUSTOMIZATION
Description of the default acquisition and processing parameters provided with the toolbox,
how to customise them and when!
DEBUG TIPS & TRICKS
Guidelines and good practices to make sure your data are processed as expected, with the help of information stored in the metadata associated to the images & maps and in the parameters and messages log files.
DEMO DATASET
A demo dataset is available for download and used in the tutorial and examples.
HELP
A list of help information from each and every script in the toolbox.
REFERENCES
Bibliographical references of interest for the hMRI toolbox.
CONTACT
For bug reporting...