Our publications

2019

Improved white matter response function estimation for 3-tissue constrained spherical deconvolution Dhollander, T.; Mito, R.; Raffelt, D. & Connelly, A. Proc Intl Soc Mag Reson Med, 2019, 555
Complex diffusion-weighted image estimation via matrix recovery under general noise models Cordero-Grande, L.; Christiaens, D.; Hutter, J.; Price, A.N.; Hajnal, J.V. NeuroImage, 2019, 200, 391-404, doi: 10.1016/j.neuroimage.2019.06.039
MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H.; Connelly, A. NeuroImage, 2019, 116137

2017

Investigating White Matter Fibre Density and Morphology using Fixel-Based Analysis Raffelt, D.; Tournier, JD/; Smith, RE.; Vaughan, DN.; Jackson, G.; Ridgway, GR. Connelly, A. NeuroImage, 2017, 144, 58-73, doi: 10.1016/j.neuroimage.2016.09.029

2016

Diffusion MRI noise mapping using random matrix theory Veraart, J.; Fieremans, E. & Novikov, D.S. Magn. Res. Med., 2016, 76(5), 1582-1593, doi: 10.1002/mrm.26059
Denoising of diffusion MRI using random matrix theory Veraart, J.; Novikov, D.S.; Christiaens, D.; Ades-aron, B.; Sijbers, J. & Fieremans, E. NeuroImage, 2016, 142, 394-406, doi: 10.1016/j.neuroimage.2016.08.016
Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image Dhollander T, Raffelt D, Connelly A. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 2016, 5

2015

Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres Raffelt, D.; Smith, RE.; Ridgway, GR.; Tournier, JD.; Vaughan, DN.; Rose, S.; Henderson, R.; Connelly, A. NeuroImage, 2015, 15(117):40-55
Global tractography of multi-shell diffusion-weighted imaging data using a multi-tissue model Christiaens, D.; Reisert, M.; Dhollander, T.; Sunaert, S.; Suetens, P. & Maes, F. NeuroImage, 2015, 123, 89-101
SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. NeuroImage, 2015, 119, 338-351
Panchromatic sharpening of FOD-based DEC maps by structural T1 information Dhollander T, Raffelt D, Smith RE, Connelly A. Proc Intl Soc Mag Reson Med, 2015, 23, 566
Time to move on: an FOD-based DEC map to replace DTI's trademark DEC FA Dhollander T, Smith RE, Tournier JD, Jeurissen B, Connelly A. Proc Intl Soc Mag Reson Med, 2015, 23, 1027

2014

Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI Jeurissen, B.; Leemans, A.; Sijbers, J. Medical Image Analysis, 2014, 18(7), 953-962
Recursive calibration of the fiber response function for spherical deconvolution of diffusion MRI data Tax, C. M.; Jeurissen, B.; Vos, S. B.; Viergever, M. A. & Leemans, A. NeuroImage, 2014, 86, 67-80
Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography Dhollander, T., Emsell, L., Van Hecke, W., Maes, F., Sunaert, S., Suetens, P. NeuroImage, 2014, 94, 312-336
Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data Jeurissen, B; Tournier, J-D; Dhollander, T; Connelly, A & Sijbers, J. NeuroImage, 2014, 103, 411-426

2013

Determination of the appropriate b-value and number of gradient directions for high-angular-resolution diffusion-weighted imaging Tournier, J.-D.; Calamante, F. & Connelly, A. NMR Biomedicine, 2013, 26, 1775-1786
Weighted linear least squares estimation of diffusion MRI parameters: strengths, limitations, and pitfalls Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B. NeuroImage, 2013, 81, 335-346;
SIFT: Spherical-deconvolution informed filtering of tractograms Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. NeuroImage, 2013, 67, 298-312

2012

A generalised framework for super-resolution track-weighted imaging Calamante, F.; Tournier, J.-D.; Smith, R. E. & Connelly, A. NeuroImage, 2012, 59, 2494-2503
Incorporating directional information in diffusion tractography derived maps: angular track imaging (ATI) Pannek, K., Raffelt, D., Salvado, O., Rose, S. In Proc. ISMRM, 2012, 20, 1912
MRtrix: Diffusion tractography in crossing fiber regions Tournier, J.-D.; Calamante, F. & Connelly, A. Int. J. Imaging Syst. Technol., 2012, 22, 53-66
Anatomically-constrained tractography:Improved diffusion MRI streamlines tractography through effective use of anatomical information Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A. NeuroImage, 2012, 62, 1924-1938
Apparent Fibre Density: a novel measure for the analysis of diffusion-weighted magnetic resonance images Raffelt, D.; Tournier, J.-D.; Rose, S.; Ridgway, G.R.; Henderson, R.; Crozier, S.; Salvado, O.; Connelly, A.; NeuroImage, 2012, 15;59(4), 3976-94
Reorientation of fiber orientation distributions using apodized point spread functions Raffelt, D.; Tournier, J.-D.; Crozier, S.; Connelly, A. & Salvado, O. Magnetic Resonance in Medicine, 2012, 67, 844-855

2011

A novel paradigm for automated segmentation of very large whole-brain probabilistic tractography data sets Smith, R.E., Tournier, J-D., Calamante, F., Connelly, A. In proc. ISMRM, 2011, 19, 673
Symmetric diffeomorphic registration of fibre orientation distributions Raffelt, D.; Tournier, J.-D.; Fripp, J; Crozier, S.; Connelly, A. & Salvado, O. NeuroImage, 2011, 56(3), 1171-1180

2010

Track-density imaging (TDI): Super-resolution white matter imaging using whole-brain track-density mapping Calamante, F.; Tournier, J.-D.; Jackson, G. D. & Connelly, A. NeuroImage, 2010, 53, 1233-1243
Improved probabilistic streamlines tractography by 2nd order integration over fibre orientation distributions Tournier, J.-D.; Calamante, F. & Connelly, A. Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 1670

2007

Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution Tournier, J.-D.; Calamante, F. & Connelly, A. NeuroImage, 2007, 35, 1459-1472

2004

Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution Tournier, J.-D.; Calamante, F., Gadian, D.G. & Connelly, A. NeuroImage, 2004, 23, 1176-1185

External publications

2019

Automated quality control for within and between studies diffusion MRI data using a non-parametric framework for movement and distortion correction Bastiani, M.; Cottaar, M.; Fitzgibbon, S.P.; Suri, S.; Alfaro-Almagro, F.; Sotiropoulos, S.N.; Jbabdi, S.; Andersson, J.L.R. NeuroImage, 2019, 184, 801-812
Intrinsic non-stationarity correction for Fixel-Based Analysis Smith, RE.; Dimond, D; Vaughan, D.; Parker, D.; Dhollander, T.; Jackson, G.; Connelly, A. In Proc OHBM 2019 M789

2017

Towards a comprehensive framework for movement and distortion correction of diffusion MR images: Within volume movement Andersson, J. L. R.; Graham, M. S.; Drobnjak, I.; Zhang, H.; Filippini, N. & Bastiani, M. NeuroImage, 2017, 152, 450-466

2016

Incorporating outlier detection and replacement into a non-parametric framework for movement and distortion correction of diffusion MR images Andersson, J. L. R.; Graham, M. S.; Zsoldos, E. & Sotiropoulos, S. N. NeuroImage, 2016, 141, 556-572

2015

An integrated approach to correction for off-resonance effects and subject movement in diffusion MR imaging Andersson, J. L. & Sotiropoulos, S. N. NeuroImage, 2015, 125, 1063-1078

2014

Beyond Fractional Anisotropy: Extraction of bundle-specific structural metrics from crossing fibre models Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R. NeuroImage, 2014, 100, 176-191

2011

A Bayesian model of shape and appearance for subcortical brain segmentation Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M. NeuroImage, 2011, 56, 907-922
The average pathlength map: A diffusion MRI tractography-derived index for studying brain pathology Pannek, K.; Mathias, J. L.; Bigler, E. D.; Brown, G.; Taylor, J. D. & Rose, S. E. NeuroImage, 2011, 55, 133-141
Adjusting the effect of nonstationarity in cluster-based and TFCE inference Salimi-Khorshidi, G. Smith, S.M. Nichols, T.E. NeuroImage, 2011, 54(3), 2006-19

2010

Jacobian weighting of distortion corrected EPI data Skare, S. & Bammer, R. Proceedings of the International Society for Magnetic Resonance in Medicine, 2010, 5063

2009

Threshold-free cluster enhancement: Addressing problems of smoothing, threshold dependence and localisation in cluster inference Smith, S. M. & Nichols, T. E. NeuroImage, 2009, 44, 83-98
Issues with threshold masking in voxel-based morphometry of atrophied brains Ridgway, G. R.; Omar, R.; Ourselin, S.; Hill, D. L.; Warren, J. D. & Fox, N. C. NeuroImage, 2009, 44, 99-111

2008

Tractography Gone Wild: Probabilistic Fibre Tracking Using the Wild Bootstrap With Diffusion Tensor MRI Jones, D. IEEE Transactions on Medical Imaging, 2008, 27, 1268-1274
Probabilistic fibre tracking: Differentiation of connections from chance events Morris, D. M.; Embleton, K. V. & Parker, G. J. NeuroImage, 2008, 42, 1329-1339

2004

Advances in functional and structural MR image analysis and implementation as FSL Smith, S. M.; Jenkinson, M.; Woolrich, M. W.; Beckmann, C. F.; Behrens, T.E.; Johansen-Berg, H.; Bannister, P. R.; De Luca, M.; Drobnjak, I.; Flitney, D. E.; Niazy, R. K.; Saunders, J.; Vickers, J.; Zhang, Y.; De Stefano, N.; Brady, J. M. & Matthews, P. M. NeuroImage, 2004, 23, S208-S219

2003

How to correct susceptibility distortions in spin-echo echo-planar images: application to diffusion tensor imaging Andersson, J. L.; Skare, S. & Ashburner, J. NeuroImage, 2003, 20, 870-888

2002

Fast robust automated brain extraction Smith, S. M. Human Brain Mapping, 2002, 17, 143-155

2001

Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm Zhang, Y.; Brady, M. & Smith, S. IEEE Transactions on Medical Imaging, 2001, 20, 45-57

2000

Minimal gradient encoding for robust estimation of diffusion anisotropy Papadakis, N. G.; Murrills, C. D.; Hall, L. D.; Huang, C. L.-H. & Adrian Carpenter, T. Magnetic Resonance Imaging, 2000, 18: 671-679
In vivo fiber tractography using DT-MRI data Basser, P. J.; Pajevic, S.; Pierpaoli, C.; Duda, J. & Aldroubi, A. Magnetic Resonance in Medicine, 2000, 44, 625-632

1999

Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging Jones, D.; Horsfield, M. & Simmons, A. Magnetic Resonance in Medicine, 1999, 42: 515-525
Three-dimensional tracking of axonal projections in the brain by magnetic resonance imaging Mori, S.; Crain, B. J.; Chacko, V. P. & van Zijl, P. C. M. Annals of Neurology, 1999, 45, 265-269