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.
Introduction to Magnetic Resonance Spectroscopy Acquisition and Analysis
Key publications
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
Creatine kinase rate constant in the human heart measured with 3D-localization at 7 tesla.
Journal article
Clarke WT. et al, (2017), Magn Reson Med, 78, 20 - 32
Recent publications
MR Spectroscopy without Water Suppression using the Gradient Impulse Response Function
Preprint
Bacon JB. et al, (2026)
deep autoencoder for fast spectral-temporal fitting of dynamic deuterium metabolic imaging data at 7T.
Journal article
Osburg AP. et al, (2025), Neuroimage, 324
Repeatability of Rapid Human Cardiac Phosphorus MRSI (31P-MRSI) Using Concentric Ring Trajectory Readouts at 7 T.
Journal article
Mózes FE. et al, (2025), Magn Reson Med
Brain and muscle chemistry in myalgic encephalitis/chronic fatigue syndrome (ME/CFS) and long COVID: a 7T magnetic resonance spectroscopy study.
Journal article
Godlewska BR. et al, (2025), Mol Psychiatry, 30, 5215 - 5226
Diffusion MRS tracks distinct trajectories of neuronal development in the cerebellum and thalamus of rat neonates.
Preprint
Ligneul C. et al, (2025)
