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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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 Urheber:
Tabelow, Karsten1, Autor
Balteau, Evelyne2, Autor
Ashburner, John3, Autor
Callaghan, Martina F.3, Autor
Draganski, Bogdan4, 5, Autor           
Helms, Gunther6, Autor
Kherif, Ferath6, Autor
Leutritz, Tobias7, Autor           
Lutti, Antoine4, Autor
Philips, Christophe2, Autor
Reimer, Enrico7, Autor           
Ruthotto, Lars8, Autor
Seif, Maryam9, Autor
Weiskopf, Nikolaus7, Autor           
Ziegler, Gabriel10, Autor
Mohammadi, Siawoosh11, Autor
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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Schlagwörter: Quantitative MRI; In-vivo histology; Microstructure; Multi-Parameter Mapping; Relaxometry; SPM toolbox
 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2018-12-212018-09-072019-01-102019-01-212019-07-01
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: 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
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1016/j.neuroimage.2019.01.029
PMID: 30677501
PII: S1053-8119(19)30029-1
Anderer: Epub ahead of print
 Art des Abschluß: -

Veranstaltung

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Projektinformation

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Projektname : Non-Invasive In-Vivo Histology in Health and Disease Using Magnetic Resonance Imaging (MRI) / HMRI
Grant ID : 616905
Förderprogramm : Horizon 2020 (H2020)
Förderorganisation : European Commission (EC)
Projektname : 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
Förderprogramm : Horizon 2020 (H2020)
Förderorganisation : European Commission (EC)
Projektname : -
Grant ID : 15.0137
Förderprogramm : -
Förderorganisation : Swiss State Secretariat for Education, Research and Innovation (SERI)
Projektname : -
Grant ID : -
Förderprogramm : European Regional Development Fund
Förderorganisation : European Commission (EC)
Projektname : BIOMED-HUB
Grant ID : -
Förderprogramm : -
Förderorganisation : Belgian Walloon Government
Projektname : -
Grant ID : MO 2397/4-1
Förderprogramm : DFG Emmy Noether Stipend
Förderorganisation : German Research Foundation (DFG)
Projektname : 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
Förderprogramm : ERA-NET NEURON
Förderorganisation : German Federal Ministry of Education and Research (BMBF)
Projektname : NCCR Synapsy
Grant ID : 32003B_159780
Förderprogramm : -
Förderorganisation : Swiss National Science Foundation
Projektname : -
Grant ID : -
Förderprogramm : -
Förderorganisation : Leenaards Foundation
Projektname : ERA-NET NEURON
Grant ID : MR/R000050/1
Förderprogramm : -
Förderorganisation : Medical Research Council (MRC)
Projektname : -
Grant ID : 203147/Z/16/Z
Förderprogramm : -
Förderorganisation : Wellcome Trust
Projektname : -
Grant ID : -
Förderprogramm : -
Förderorganisation : F.R.S. - FNRS, Belgium
Projektname : -
Grant ID : -
Förderprogramm : -
Förderorganisation : Emory University’s Research Council
Projektname : -
Grant ID : NT 2014-6193
Förderprogramm : -
Förderorganisation : Swedish Research Council

Quelle 1

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Titel: NeuroImage
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: Orlando, FL : Academic Press
Seiten: - Band / Heft: 194 Artikelnummer: - Start- / Endseite: 191 - 210 Identifikator: ISSN: 1053-8119
CoNE: https://pure.mpg.de/cone/journals/resource/954922650166