Research groups
Open-source MRS Software
FSL-MRS - End to end MRS analysis software
FSLeyes (+ plugin): MRS and MRSI visualisation
Spec2nii: Multi-format in vivo MR spectroscopy conversion to NIFTI
- NIfTI-MRS software tools and standard
William Clarke
Wellcome Career Development Fellow
Advanced, open tools for MR Spectroscopy
My work focusses on developing new methods for magnetic resonance spectroscopy (MRS). Using similar methods to MR imaging (MRI), MRS allows us to quantify the concentrations and chemical kinetics of many neurochemicals in the human brain. Furthermore, by using neurochemicals as endogenous probes we can also map cell-type-specific microstructure. My work seeks to develop new ways of acquiring multi-voxel spectroscopic information to measure chemical dynamics and cellular microstructure across the brain. I have released the open-science MRS analysis tool FSL-MRS and created a range of open-source tools for the MRS community. I am a cofounder of the educational website MRSHub.
In 2023 I started a spectroscopy group at WIN funded by a Wellcome Career Development Award. Previously I have worked as spectroscopist in the Physiological Neuroimaging Group and as a post-doctoral researcher in the UK7T Network. Prior to working in neuroimaging, I completed my doctorate in cardiovascular magnetic resonance spectroscopy. This work focused on the high-energy phosphorus metabolism of the human myocardium.
I am open to consulting on acquisition and analysis of MR spectroscopy for clinical trials, and have previously done so for third-party CROs.
OxCIN MRS Group
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Jason Lyu
DPhil Student
Introduction to Magnetic Resonance Spectroscopy Acquisition and Analysis
Key publications
NIfTI-MRS: A standard data format for magnetic resonance spectroscopy
Journal article
CLARKE W. et al, (2022), Magnetic Resonance in Medicine
FSL‐MRS: An end‐to‐end spectroscopy analysis package
Journal article
Clarke WT. et al, (2021), Magnetic Resonance in Medicine, 85, 2950 - 2964
Multi-site harmonization of 7 tesla MRI neuroimaging protocols
Journal article
Clarke WT. et al, (2020), NeuroImage, 206, 116335 - 116335
Creatine kinase rate constant in the human heart measured with 3D‐localization at 7 tesla
Journal article
Clarke WT. et al, (2017), Magnetic Resonance in Medicine, 78, 20 - 32
Recent publications
Noradrenaline causes a spread of association in the hippocampal cognitive map
Journal article
Koolschijn RS. et al, (2026), Nature Communications
The Impact of BOLD Induced Linewidth Modulation on Functional 1 H MRS Analysis
Preprint
Wilson M. et al, (2026)
MR Spectroscopy without Water Suppression using the Gradient Impulse Response Function
Preprint
Bacon JB. et al, (2026)
Repeatability of Rapid Human Cardiac Phosphorus MRSI ( 31 P ‐ MRSI ) Using Concentric Ring Trajectory Readouts at 7 T
Journal article
Mózes FE. et al, (2025), Magnetic Resonance in Medicine