Research Repository

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Whole brain comparative anatomy using connectivity blueprints (2018)
Journal Article
Mars, R. B., Sotiropoulos, S. N., Passingham, R. E., Sallet, J., Verhagen, L., Khrapitchev, A. A., …Jbabdi, S. (in press). Whole brain comparative anatomy using connectivity blueprints. eLife, 7, doi:10.7554/eLife.35237. ISSN 2050-084X

Comparing the brains of related species faces the challenges of establishing homologies whilst accommodating evolutionary specializations. Here we propose a general framework for understanding similarities and differences between the brains of primat... Read More

A gyral coordinate system predictive of fibre orientations (2018)
Journal Article
Cottaar, M., Bastiani, M., Chen, C., Dikranian, K., Van Essen, D., Behrens, T. E., …Jbabdi, S. (2018). A gyral coordinate system predictive of fibre orientations. NeuroImage, 176, doi:10.1016/j.neuroimage.2018.04.040

When axonal fibres approach or leave the cortex, their trajectories tend to closely follow the cortical convolutions. To quantify this tendency, we propose a three-dimensional coordinate system based on the gyral geometry. For every voxel in the brai... Read More

Moving magnetoencephalography towards real-world applications with a wearable system (2018)
Journal Article
Boto, E., Holmes, N., Leggett, J., Roberts, G., Shah, V., Meyer, S. S., …Brookes, M. J. (2018). Moving magnetoencephalography towards real-world applications with a wearable system. Nature, 555, doi:10.1038/nature26147

Imaging human brain function with techniques such as magnetoencephalography1 (MEG) typically requires a subject to perform tasks whilst their head remains still within a restrictive scanner. This artificial environment makes the technique inaccessibl... Read More

Dynamic metabolic patterns tracking neurodegeneration and gliosis following 26S proteasome dysfunction in mouse forebrain neurons (2018)
Journal Article
Geiszler, P. C., Ugun-Klusek, A., Lawler, K., Pardon, M., Yuchun, D., Bai, L., …Bedford, L. (in press). Dynamic metabolic patterns tracking neurodegeneration and gliosis following 26S proteasome dysfunction in mouse forebrain neurons. Scientific Reports, 8, doi:10.1038/s41598-018-23155-2

Metabolite profiling is an important tool that may better capture the multiple features of neurodegeneration. With the considerable parallels between mouse and human metabolism, the use of metabolomics in mouse models with neurodegenerative pathology... Read More

Altered connectivity of the right anterior insula drives the pain connectome changes in chronic knee osteoarthritis (2018)
Journal Article
Cottam, W. J., Iwabuchi, S. J., Drabek, M. M., Reckziegel, D., & Auer, D. P. (2018). Altered connectivity of the right anterior insula drives the pain connectome changes in chronic knee osteoarthritis. PAIN, 159(5), doi:10.1097/j.pain.0000000000001209

Resting-state functional connectivity (FC) has proven a powerful approach to understand the neural underpinnings of chronic pain, reporting altered connectivity in three main networks: the default mode (DMN), central executive (CEN), and the salience... Read More

Bayesian optimization of large-scale biophysical networks (2018)
Journal Article
Hadida, J., Sotiropoulos, S. N., Abeysuriya, R. G., Woolrich, M. W., & Jbabdi, S. (2018). Bayesian optimization of large-scale biophysical networks. NeuroImage, 174, doi:10.1016/j.neuroimage.2018.02.063

The relationship between structure and function in the human brain is well established, but not yet well characterised. Large-scale biophysical models allow us to investigate this relationship, by leveraging structural information (e.g. derived from... Read More

A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks (2018)
Journal Article
Abeysuriya, R. G., Hadida, J., Sotiropoulos, S. N., Jbabdi, S., Becker, R., Hunt, B. A., …Woolrich, M. W. (in press). A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks. PLoS Computational Biology, 14(2), doi:10.1371/journal.pcbi.1006007

Over long timescales, neuronal dynamics can be robust to quite large perturbations, such as changes in white matter connectivity and grey matter structure through processes including learning, aging, development and certain disease processes. One pos... Read More

Patterns of grey matter loss associated with motor subscores in early Parkinson's disease (2017)
Journal Article
Li, X., Xing, Y., Martin-Bastida, A., Piccini, P., & Auer, D. P. (in press). Patterns of grey matter loss associated with motor subscores in early Parkinson's disease. NeuroImage: Clinical, 17, doi:10.1016/j.nicl.2017.11.009

Classical motor symptoms of Parkinson's disease (PD) such as tremor, rigidity, bradykinesia, and axial symptoms are graded in the Movement Disorders Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) III. It is yet to be ascertained whether... Read More

Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank (2017)
Journal Article
Alfaro-Almagro, F., Jenkinson, M., Bangerter, N. K., Andersson, J. L., Griffanti, L., Douaud, G., …Smith, S. M. (2018). Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank. NeuroImage, 166, doi:10.1016/j.neuroimage.2017.10.034

UK Biobank is a large-scale prospective epidemiological study with all data accessible to researchers worldwide. It is currently in the process of bringing back 100,000 of the original participants for brain, heart and body MRI, carotid ultrasound an... Read More

The heritability of multi-modal connectivity in human brain activity (2017)
Journal Article
Colclough, G. L., Smith, S. M., Nichols, T. E., Winkler, A. M., Sotiropoulos, S. N., Glasser, M. F., …Woolrich, M. W. (in press). The heritability of multi-modal connectivity in human brain activity. eLife, 6, doi:10.7554/eLife.20178. ISSN 2050-084X

Patterns of intrinsic human brain activity exhibit a profile of functional connectivity that is associated with behaviour and cognitive performance, and deteriorates with disease. This paper investigates the relative importance of genetic factors and... Read More

Subthalamic deep brain stimulation sweet spots and hyperdirect cortical connectivity in Parkinson’s disease (2017)
Journal Article
Akram, H., Sotiropoulos, S. N., Jbabdi, S., Georgiev, D., Mahlknecht, P., Hyam, J., …Zrinzo, L. (2017). Subthalamic deep brain stimulation sweet spots and hyperdirect cortical connectivity in Parkinson’s disease. NeuroImage, 158, doi:10.1016/j.neuroimage.2017.07.012

Objectives Firstly, to identify subthalamic region stimulation clusters that predict maximum improvement in rigidity, bradykinesia and tremor, or emergence of side-effects; and secondly, to map-out the cortical fingerprint, mediated by the hyperdire... Read More

Improved tractography using asymmetric fibre orientation distributions (2017)
Journal Article
Bastiani, M., Cottaar, M., Dikranian, K., Ghosh, A., Zhang, H., Alexander, D. C., …Sotiropoulos, S. N. (2017). Improved tractography using asymmetric fibre orientation distributions. NeuroImage, 158, doi:10.1016/j.neuroimage.2017.06.050. ISSN 1053-8119

Diffusion MRI allows us to make inferences on the structural organisation of the brain by mapping water diffusion to white matter microstructure. However, such a mapping is generally ill-defined; for instance, diffusion measurements are antipodally s... Read More

Building connectomes using diffusion MRI: why, how and but (2017)
Journal Article
Sotiropoulos, S. N., & Zalesky, A. (in press). Building connectomes using diffusion MRI: why, how and but. NMR in Biomedicine, doi:10.1002/nbm.3752

Why has diffusion MRI become a principal modality for mapping connectomes in vivo? How do different image acquisition parameters, fiber tracking algorithms and other methodological choices affect connectome estimation? What are the main factors that... Read More

Evaluating fibre orientation dispersion in white matter: comparison of diffusion MRI, histology and polarized light imaging (2017)
Journal Article
Mollink, J., Kleinnijenhuis, M., Cappellen van Walsum, A. V., Sotiropoulos, S. N., Cottaar, M., Mirfin, C., …Miller, K. L. (2017). Evaluating fibre orientation dispersion in white matter: comparison of diffusion MRI, histology and polarized light imaging. NeuroImage, 157, doi:10.1016/j.neuroimage.2017.06.001

Diffusion MRI is an exquisitely sensitive probe of tissue microstructure, and is currently the only non-invasive measure of the brain’s fibre architecture. As this technique becomes more sophisticated and microstructurally informative, there is incre... Read More

Time-efficient and flexible design of optimized multishell HARDI diffusion (2017)
Journal Article
Hutter, J., Tournier, J. D., Price, A. N., Cordero-Grande, L., Hughes, E. J., Malik, S., …Hajnal, J. V. (2018). Time-efficient and flexible design of optimized multishell HARDI diffusion. Magnetic Resonance in Medicine, 79(3), 1276-1292. doi:10.1002/mrm.26765

Purpose: Advanced diffusion magnetic resonance imaging benefits from collecting as much data as is feasible but is highly sensitive to subject motion and the risk of data loss increases with longer acquisition times. Our purpose was to create a maxim... Read More

Image quality transfer and applications in diffusion MRI (2017)
Journal Article
Alexander, D. C., Zikic, D., Ghosh, A., Tanno, R., Wottschel, V., Zhang, J., …Criminisi, A. (2017). Image quality transfer and applications in diffusion MRI. NeuroImage, 152, doi:10.1016/j.neuroimage.2017.02.089

This paper introduces a new computational imaging technique called image quality transfer (IQT). IQT uses machine learning to transfer the rich information available from one-off experimental medical imaging devices to the abundant but lower-quality... Read More

Studying neuroanatomy using MRI (2017)
Journal Article
Lerch, J. P., van der Kouwe, A. J., Raznahan, A., Paus, T., Johansen-Berg, H., Miller, K. L., …Sotiropoulos, S. N. (in press). Studying neuroanatomy using MRI. Nature Neuroscience, 20(3), doi:10.1038/nn.4501

The study of neuroanatomy using imaging enables key insights into how our brains function, are shaped by genes and environment, and change with development, aging, and disease. Developments in MRI acquisition, image processing, and data modelling hav... Read More

In vivo assessment of brainstem depigmentation in Parkinson’s: potential as severity marker for multi-centre studies (2016)
Journal Article
Schwarz, S. T., Xing, Y., Tomar, P., Bajaj, N., & Auer, D. P. (in press). In vivo assessment of brainstem depigmentation in Parkinson’s: potential as severity marker for multi-centre studies. Radiology, doi:10.1148/radiol.2016160662

Purpose: To investigate the pattern of neuromelanin signal intensity loss within the substantia nigra pars compacta (SNpc), locus coeruleus, and ventral tegmental area in Parkinson disease (PD); the specific aims were (a) to study regional magnetic... Read More