All Outputs (72)

Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project (2018)
Journal Article
Bastiani, M., Andersson, J. L., Cordero-Grande, L., Murgasova, M., Hutter, J., Price, A. N., …Sotiropoulos, S. N. (2019). Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project. NeuroImage, 185, 750-763. https://doi.org/10.1016/j.neuroimage.2018.05.064

The developing Human Connectome Project is set to create and make available to the scientific community a 4-dimensional map of functional and structural cerebral connectivity from 20 to 44 weeks post-menstrual age, to allow exploration of the genetic... Read More about Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project.

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, Article e35237. https://doi.org/10.7554/eLife.35237

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 about Whole brain comparative anatomy using connectivity blueprints.

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, https://doi.org/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 about A gyral coordinate system predictive of fibre orientations.

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, https://doi.org/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 about Bayesian optimization of large-scale biophysical networks.

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), Article e1006007. https://doi.org/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 about A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks.

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, https://doi.org/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 about Image processing and Quality Control for the first 10,000 brain imaging datasets from UK Biobank.

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, Article e20178. https://doi.org/10.7554/eLife.20178

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 about The heritability of multi-modal connectivity in human brain activity.

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, https://doi.org/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 about Subthalamic deep brain stimulation sweet spots and hyperdirect cortical connectivity in Parkinson’s disease.

Estimation of white matter fiber parameters from compressed multiresolution diffusion MRI using sparse Bayesian learning (2017)
Journal Article
Pisharady, P. K., Sotiropoulos, S. N., Duarte-Carvajalino, J. M., Sapiro, G., & Lenglet, C. (in press). Estimation of white matter fiber parameters from compressed multiresolution diffusion MRI using sparse Bayesian learning. NeuroImage, https://doi.org/10.1016/j.neuroimage.2017.06.052

We present a sparse Bayesian unmixing algorithm BusineX: Bayesian Unmixing for Sparse Inference-based Estimation of Fiber Crossings (X), for estimation of white matter fiber parameters from compressed (under-sampled) diffusion MRI (dMRI) data. Busine... Read More about Estimation of white matter fiber parameters from compressed multiresolution diffusion MRI using sparse Bayesian learning.

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, https://doi.org/10.1016/j.neuroimage.2017.06.050

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 about Improved tractography using asymmetric fibre orientation distributions.

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, https://doi.org/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 about Building connectomes using diffusion MRI: why, how and but.

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, https://doi.org/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 about Evaluating fibre orientation dispersion in white matter: comparison of diffusion MRI, histology and polarized light imaging.

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. https://doi.org/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 about Time-efficient and flexible design of optimized multishell HARDI diffusion.

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, https://doi.org/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 about Image quality transfer and applications in diffusion MRI.

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), https://doi.org/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 about Studying neuroanatomy using MRI.

Multimodal population brain imaging in the UK Biobank prospective epidemiological study (2016)
Journal Article
Miller, K. L., Alfaro-Almagro, F., Bangerter, N. K., Thomas, D. L., Yacoub, E., Xu, J., …Smith, S. M. (2016). Multimodal population brain imaging in the UK Biobank prospective epidemiological study. Nature Neuroscience, 19(11), https://doi.org/10.1038/nn.4393

Medical imaging has enormous potential for early disease prediction, but is impeded by the difficulty and expense of acquiring data sets before symptom onset. UK Biobank aims to address this problem directly by acquiring high-quality, consistently ac... Read More about Multimodal population brain imaging in the UK Biobank prospective epidemiological study.

The Human Connectome Project's neuroimaging approach (2016)
Journal Article
Glasser, M. F., Smith, S. M., Marcus, D. S., Andersson, J. L., Auerbach, E. J., Behrens, T. E., …Van Essen, D. C. (2016). The Human Connectome Project's neuroimaging approach. Nature Neuroscience, 19(9), https://doi.org/10.1038/nn.4361

Noninvasive human neuroimaging has yielded many discoveries about the brain. Numerous methodological advances have also occurred, though inertia has slowed their adoption. This paper presents an integrated approach to data acquisition, analysis and s... Read More about The Human Connectome Project's neuroimaging approach.

Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images (2016)
Journal Article
Andersson, J. L., Graham, M. S., Zsoldos, E., & Sotiropoulos, S. N. (2016). Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images. NeuroImage, 141, https://doi.org/10.1016/j.neuroimage.2016.06.058

Despite its great potential in studying brain anatomy and structure, diffusion magnetic resonance imaging (dMRI) is marred by artefacts more than any other commonly used MRI technique. In this paper we present a non-parametric framework for detecting... Read More about Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images.

Using Diffusion Tractography to Predict Cortical Connection Strength and Distance: A Quantitative Comparison with Tracers in the Monkey (2016)
Journal Article
Donahue, C. J., Sotiropoulos, S. N., Jbabdi, S., Hernandez-Fernandez, M., Behrens, T. E., Dyrby, T. B., …Glasser, M. F. (2016). Using Diffusion Tractography to Predict Cortical Connection Strength and Distance: A Quantitative Comparison with Tracers in the Monkey. Journal of Neuroscience, 36(25), 6758-6770. https://doi.org/10.1523/JNEUROSCI.0493-16.2016

Tractography based on diffusion MRI offers the promise of characterizing many aspects of long-distance connectivity in the brain, but requires quantitative validation to assess its strengths and limitations. Here, we evaluate tractography's ability t... Read More about Using Diffusion Tractography to Predict Cortical Connection Strength and Distance: A Quantitative Comparison with Tracers in the Monkey.

Fusion in diffusion MRI for improved fibre orientation estimation: an application to the 3T and 7T data of the Human Connectome Project (2016)
Journal Article
Sotiropoulos, S. N., Hernández-Fernández, M., Vu, A. T., Andersson, J. L., Moeller, S., Yacoub, E., …Jbabdi, S. (2016). Fusion in diffusion MRI for improved fibre orientation estimation: an application to the 3T and 7T data of the Human Connectome Project. NeuroImage, 134, 396-409. https://doi.org/10.1016/j.neuroimage.2016.04.014

Determining the acquisition parameters in diffusion magnetic resonance imaging (dMRI) is governed by a series of trade-offs. Images of lower resolution have less spatial specificity but higher signal to noise ratio (SNR). At the same time higher angu... Read More about Fusion in diffusion MRI for improved fibre orientation estimation: an application to the 3T and 7T data of the Human Connectome Project.