Our publications


Improved white matter response function estimation for 3-tissue constrained spherical deconvolution

Dhollander, T.; Mito, R.; Raffelt, D. & Connelly, A.

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.

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.


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.


Diffusion MRI noise mapping using random matrix theory

Veraart, J.; Fieremans, E. & Novikov, D.S.

Denoising of diffusion MRI using random matrix theory

Veraart, J.; Novikov, D.S.; Christiaens, D.; Ades-aron, B.; Sijbers, J. & Fieremans, E.

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.


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.

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.

SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography

Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A.

Panchromatic sharpening of FOD-based DEC maps by structural T1 information

Dhollander T, Raffelt D, Smith RE, Connelly A.

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.


Automated correction of improperly rotated diffusion gradient orientations in diffusion weighted MRI

Jeurissen, B.; Leemans, A.; Sijbers, J.

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.

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.

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.


Weighted linear least squares estimation of diffusion MRI parameters: strengths, limitations, and pitfalls

Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B.

SIFT: Spherical-deconvolution informed filtering of tractograms

Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A.


A generalised framework for super-resolution track-weighted imaging

Calamante, F.; Tournier, J.-D.; Smith, R. E. & Connelly, A.

Incorporating directional information in diffusion tractography derived maps: angular track imaging (ATI)

Pannek, K., Raffelt, D., Salvado, O., Rose, S.

MRtrix: Diffusion tractography in crossing fiber regions

Tournier, J.-D.; Calamante, F. & Connelly, A.

Anatomically-constrained tractography:Improved diffusion MRI streamlines tractography through effective use of anatomical information

Smith, R. E.; Tournier, J.-D.; Calamante, F. & Connelly, A.

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.;

Reorientation of fiber orientation distributions using apodized point spread functions

Raffelt, D.; Tournier, J.-D.; Crozier, S.; Connelly, A. & Salvado, O.


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.

Symmetric diffeomorphic registration of fibre orientation distributions

Raffelt, D.; Tournier, J.-D.; Fripp, J; Crozier, S.; Connelly, A. & Salvado, O.


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.

Improved probabilistic streamlines tractography by 2nd order integration over fibre orientation distributions

Tournier, J.-D.; Calamante, F. & Connelly, A.



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.

External publications


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.

Intrinsic non-stationarity correction for Fixel-Based Analysis

Smith, RE.; Dimond, D; Vaughan, D.; Parker, D.; Dhollander, T.; Jackson, G.; Connelly, A.


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.


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.



Beyond Fractional Anisotropy: Extraction of bundle-specific structural metrics from crossing fibre models

Riffert, T. W.; Schreiber, J.; Anwander, A. & Knosche, T. R.


A Bayesian model of shape and appearance for subcortical brain segmentation

Patenaude, B.; Smith, S. M.; Kennedy, D. N. & Jenkinson, M.

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.

Adjusting the effect of nonstationarity in cluster-based and TFCE inference

Salimi-Khorshidi, G. Smith, S.M. Nichols, T.E.


Jacobian weighting of distortion corrected EPI data

Skare, S. & Bammer, R.


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.


Probabilistic fibre tracking: Differentiation of connections from chance events

Morris, D. M.; Embleton, K. V. & Parker, G. J.


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.



Fast robust automated brain extraction

Smith, S. M.


Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm

Zhang, Y.; Brady, M. & Smith, S.


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.

In vivo fiber tractography using DT-MRI data

Basser, P. J.; Pajevic, S.; Pierpaoli, C.; Duda, J. & Aldroubi, A.


Optimal strategies for measuring diffusion in anisotropic systems by magnetic resonance imaging

Jones, D.; Horsfield, M. & Simmons, A.

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.