Introduction to Magnetic Resonance Spectroscopy Acquisition and Analysis

Magnetic resonance spectroscopy is a fantastically flexible, quantitative and non-invasive way to study the complex biochemistry of the human brain. However, MRS is renowned as a difficult technique to master. Researchers who want to use MRS may find themselves unable to call upon much advice and support, even from experienced scanner operators, radiologists and technicians. This book aims to close this gap, by providing an accessible description of the principles of acquiring MRS and how to successfully analyse MRS data. This is crucial for choosing acquisition parameters, designing and performing appropriate experiments, and correctly interpreting the results.

The text covers the fundamentals of what MRS is, the choices that go into selecting an acquisition approach, and how to analyse MRS data. Later chapters describe in detail how to plan, pilot, and acquire high quality data. Illustrated examples show common artefacts and how to mitigate them by performing careful scanner calibration. This is all supplemented with online datasets and examples to enable the reader to obtain hands-on experience working with real data. The book provides a practical and approachable introduction for those new to the MRS field.

As it does not require any background knowledge beyond basic mathematics and physics, this primer is essential reading for anyone wanting to work with MRS in neuroimaging or grasp the results coming from this highly flexible non-invasive imaging modality.

The Oxford Neuroimaging Primers are short texts aimed at new researchers or advanced undergraduates from the biological, medical or physical sciences. Written to provide a stand-alone introduction to magnetic resonance spectroscopy, this primer also works with other texts in the Oxford Neuroimaging Primers series to provide a comprehensive overview of the increasingly influential field of neuroimaging.

William Clarke, Wellcome Career Development Fellow, Nuffield Department of Clinical Neurosciences, University of Oxford,Adam Berrington, Royal Academy of Engineering Research Fellow, Sir Peter Mansfield Imaging Centre, School of Physics and Astronomy, University of Nottingham,Saad Jbabdi, Professor of Biomedical Engineering, University of Oxford

Dr William Clarke is a Wellcome Career Development Fellow at the University of Oxford. He and his group specialises in developing novel acquisition and analysis tools for MR spectroscopy of the human brain. Having trained in cardiac phosphorus spectroscopy, and spent time working in ultra-high field neuroimaging, he brings experience from a wide range of MRI systems and applications. Dr Clarke has extensive experience in helping clinical and basic science researchers use cutting-edge MRS methods for their own research.


Dr Adam Berrington is a Royal Academy of Engineering Research Fellow at the Sir Peter Mansfield Imaging Centre in the University of Nottingham. His research focuses on developing robust methods for MR spectroscopy with a particular interest in ultra-high field acquisition. He completed his DPhil at the University of Oxford in 2017, which was followed by postdoctoral work at Johns Hopkins University, USA. He has experience developing MRS for a wide range of applications, e.g. in brain tumours and cognitive studies, as well as harmonising scans across platforms.

Prof Jbabdi is a Wellcome Senior Research Fellow at the University of Oxford, and a Senior Research Fellow at St Hilda's College, Oxford. He trained in Engineering and Applied Mathematics at Ecole Centrale Paris, where he also obtained his PhD in 2006. He has wide ranging contributions to research in imaging methodology development, particularly in diffusion MRI, functional MRI, and spectroscopy.