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  hMRI: A toolbox for quantitative MRI in neuroscience and clinical research

Tabelow, K., Balteau, E., Ashburner, J., Callaghan, M. F., Draganski, B., Helms, G., et al. (2019). hMRI: A toolbox for quantitative MRI in neuroscience and clinical research. NeuroImage, 194, 191-210. doi:10.1016/j.neuroimage.2019.01.029.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0002-D44F-7 Version Permalink: http://hdl.handle.net/21.11116/0000-0003-91D7-6
Genre: Journal Article

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 Creators:
Tabelow, Karsten1, Author
Balteau, Evelyne2, Author
Ashburner, John3, Author
Callaghan, Martina F.3, Author
Draganski, Bogdan4, 5, Author              
Helms, Gunther6, Author
Kherif, Ferath6, Author
Leutritz, Tobias7, Author              
Lutti, Antoine4, Author
Philips, Christophe2, Author
Reimer, Enrico7, Author              
Ruthotto, Lars8, Author
Seif, Maryam9, Author
Weiskopf, Nikolaus7, Author              
Ziegler, Gabriel10, Author
Mohammadi, Siawoosh11, Author
Affiliations:
1Weierstrass Institute for Applied Analysis and Stochastics, Berlin, Germany, ou_persistent22              
2GIGA Institute, University of Liège, Belgium, ou_persistent22              
3Wellcome Trust Centre for Neuroimaging, Institute of Neurology, University College London, United Kingdom, ou_persistent22              
4Laboratoire de Recherche en Neuroimagerie (LREN), Centre hospitalier universitaire vaudois, Lausanne, Switzerland, ou_persistent22              
5Department Neurology, MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_634549              
6Department of Clinical Sciences, Lund University, Sweden, ou_persistent22              
7Department Neurophysics (Weiskopf), MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_2205649              
8Emory University, Atlanta, GA, USA, ou_persistent22              
9University of Zurich, Switzerland, ou_persistent22              
10Institute of Cognitive Neurology and Dementia Research, Otto von Guericke University Magdeburg, Germany, ou_persistent22              
11University Medical Center Hamburg-Eppendorf, Germany, ou_persistent22              

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Free keywords: Quantitative MRI; In-vivo histology; Microstructure; Multi-Parameter Mapping; Relaxometry; SPM toolbox
 Abstract: Neuroscience and clinical researchers are increasingly interested in quantitative magnetic resonance imaging (qMRI) due to its sensitivity to microstructural properties of brain tissue such as axon, myelin, iron and water concentration. We introduce the hMRI-toolbox, an open-source, easy-to-use tool available on GitHub, for qMRI data handling and processing, presented together with a tutorial and example dataset. This toolbox allows the estimation of high-quality multi-parameter qMRI maps (longitudinal and effective transverse relaxation rates R 1 and R 2 ? , proton density PD and magnetisation transfer MT saturation) that can be used for quantitative parameter analysis and accurate delineation of subcortical brain structures. The qMRI maps generated by the toolbox 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. Thus, the current version of the toolbox is a first step towards in vivo histology using MRI (hMRI) and is being extended further in this direction. Embedded in the Statistical Parametric Mapping (SPM) framework, it benefits from the extensive range of established SPM tools for high-accuracy spatial registration and statistical inferences and can be readily combined with existing SPM toolboxes for estimating diffusion MRI parameter maps. From a user’s perspective, the hMRI-toolbox is an efficient, robust and simple framework for investigating qMRI data in neuroscience and clinical research.

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Language(s): eng - English
 Dates: 2018-12-212018-09-072019-01-102019-01-212019-07-01
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: 1. Introduction
2. Background
2.1. The MPM protocol
2.2. Overview theory of MPM signal model
3. Methods
3.1. Toolbox documentation and installation
3.2. MPM example dataset
3.3. Organisation of the toolbox
3.4. Configure toolbox module
3.5. DICOM import module
3.6. Auto-reorient module
3.7. Create hMRI maps module
3.7.1. Multi-parameter input images
3.7.2. B1 (transmit) bias correction
3.7.3. Receiver RF sensitivity bias correction
3.7.4. Output
3.8. Process hMRI maps module
3.9. Statistical analysis
4. Discussion and outlook
Acknownledgements
Appendix A. Summary of the model for MPM
A.1. R1 and PD estimation
A.2. Estimation of the magnetisation transfer
A.3. The ESTATICS model and R2* estimation
A.4. Corrections for transmit and receive field inhomogeneities
A.5. Spoiling corrections
Appendix B. DICOM import and JSON metadata
B.1. DICOM to NIfTI conversion
B.2. DICOM to NIfTI conversion – SPM Batch
B.3. The metadata structure
B.4. Metadata handling
B.5. General usage of the metadata and BIDS compatibility
Appendix C. Detailed description of the hMRI modules
C.1. Configure toolbox module
C.2. Auto-reorient module
C.3. B1 transmit field corrections
C.4. Receive (RF) sensitivity bias correction
C.5. Process hMRI maps module
C.5.1. Segmentation
C.5.2. Diffeomorphic registration
C.5.3. Tissue-weighted smoothing
C.5.4. Integrated pipeline
References
 Rev. Method: Peer
 Identifiers: DOI: 10.1016/j.neuroimage.2019.01.029
PMID: 30677501
PII: S1053-8119(19)30029-1
Other: Epub ahead of print
 Degree: -

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Project information

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Project name : Non-Invasive In-Vivo Histology in Health and Disease Using Magnetic Resonance Imaging (MRI) / HMRI
Grant ID : 616905
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : Antibodies against Nogo-A to enhance plasticity, regeneration and functional recovery after acute spinal cord injury, a multicenter European clinical proof of concept trial / NISCI
Grant ID : 681094
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : -
Grant ID : 15.0137
Funding program : -
Funding organization : Swiss State Secretariat for Education, Research and Innovation (SERI)
Project name : -
Grant ID : -
Funding program : European Regional Development Fund
Funding organization : European Commission (EC)
Project name : BIOMED-HUB
Grant ID : -
Funding program : -
Funding organization : Belgian Walloon Government
Project name : -
Grant ID : MO 2397/4-1
Funding program : DFG Emmy Noether Stipend
Funding organization : German Research Foundation (DFG)
Project name : NEURON-Verbund hMRTofSchl: Entschlüsselung der pathophysiologischen Prozesse induziert durch eine Querschnittlähmung: Anwendung von MRT basierter in vivo und ex vivo Histologie / ERA-NET NEURON
Grant ID : 01EW1711A
Funding program : ERA-NET NEURON
Funding organization : German Federal Ministry of Education and Research (BMBF)
Project name : NCCR Synapsy
Grant ID : 32003B_159780
Funding program : -
Funding organization : Swiss National Science Foundation
Project name : -
Grant ID : -
Funding program : -
Funding organization : Leenaards Foundation
Project name : ERA-NET NEURON
Grant ID : MR/R000050/1
Funding program : -
Funding organization : Medical Research Council (MRC)
Project name : -
Grant ID : 203147/Z/16/Z
Funding program : -
Funding organization : Wellcome Trust
Project name : -
Grant ID : -
Funding program : -
Funding organization : F.R.S. - FNRS, Belgium
Project name : -
Grant ID : -
Funding program : -
Funding organization : Emory University’s Research Council
Project name : -
Grant ID : NT 2014-6193
Funding program : -
Funding organization : Swedish Research Council

Source 1

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Title: NeuroImage
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Orlando, FL : Academic Press
Pages: - Volume / Issue: 194 Sequence Number: - Start / End Page: 191 - 210 Identifier: ISSN: 1053-8119
CoNE: https://pure.mpg.de/cone/journals/resource/954922650166