A Direct Test for Lateralization of Language Activation using fMRI: Comparison with Invasive Assessments in Children with Epilepsy. - Frédérique Liégeois; Alan Connelly; C. H. Salmond; David G. Gadian; Faraneh Vargha-Khadem; Torsten Baldeweg (NeuroImage, 2002)

The Precision of Anatomical Normalization in the Medial Temporal Lobe Using Spatial Basis Functions. - C. H. Salmond; John Ashburner; Faraneh Vargha-Khadem; Alan Connelly; David G. Gadian; Karl J. Friston (NeuroImage, 2002)

Distributional Assumptions in Voxel-Based Morphometry. - C. H. Salmond; John Ashburner; Faraneh Vargha-Khadem; Alan Connelly; David G. Gadian; Karl J. Friston (NeuroImage, 2002)

Diffusion-weighted magnetic resonance imaging fibre tracking using a front evolution algorithm. - Jacques-Donald Tournier; Fernando Calamante; David G. Gadian; Alan Connelly (NeuroImage, 2003)

Cortical lateralization during verb generation: a combined ERP and fMRI study. - Alison Rowan; Frédérique Liégeois; Faraneh Vargha-Khadem; David G. Gadian; Alan Connelly; Torsten Baldeweg (NeuroImage, 2004)

Direct estimation of the fiber orientation density function from diffusion-weighted MRI data using spherical deconvolution. - Jacques-Donald Tournier; Fernando Calamante; David G. Gadian; Alan Connelly (NeuroImage, 2004)

Extra-hippocampal grey matter density abnormalities in paediatric mesial temporal sclerosis. - Francesca Cormack; David G. Gadian; Faraneh Vargha-Khadem; J. Helen Cross; Alan Connelly; Torsten Baldeweg (NeuroImage, 2005)

Cortical abnormalities and language function in young patients with basal ganglia stroke. - Alison Rowan; Faraneh Vargha-Khadem; Fernando Calamante; Jacques-Donald Tournier; Fenella J. Kirkham; Wui K. Chong; Torsten Baldeweg; Alan Connelly; David G. Gadian (NeuroImage, 2007)

Robust determination of the fibre orientation distribution in diffusion MRI: Non-negativity constrained super-resolved spherical deconvolution. - Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (NeuroImage, 2007)

Resolving crossing fibres using constrained spherical deconvolution: Validation using diffusion-weighted imaging phantom data. - Jacques-Donald Tournier; Chun-Hung Yeh; Fernando Calamante; Kuan-Hung Cho; Alan Connelly; Ching-Po Lin (NeuroImage, 2008)

A software tool to generate simulated white matter structures for the assessment of fibre-tracking algorithms. - Thomas G. Close; Jacques-Donald Tournier; Fernando Calamante; Leigh A. Johnston; Iven M. Y. Mareels; Alan Connelly (NeuroImage, 2009)

Track-density imaging (TDI): Super-resolution white matter imaging using whole-brain track-density mapping. - Fernando Calamante; Jacques-Donald Tournier; Graeme D. Jackson; Alan Connelly (NeuroImage, 2010)

The effect of finite diffusion gradient pulse duration on fibre orientation estimation in diffusion MRI. - Chun-Hung Yeh; Jacques-Donald Tournier; Kuan-Hung Cho; Ching-Po Lin; Fernando Calamante; Alan Connelly (NeuroImage, 2010)

Track density imaging (TDI): Validation of super resolution property. - Fernando Calamante; Jacques-Donald Tournier; Robin M. Heidemann; Alfred Anwander; Graeme D. Jackson; Alan Connelly (NeuroImage, 2011)

Symmetric diffeomorphic registration of fibre orientation distributions. - David Raffelt; Jacques-Donald Tournier; Jurgen Fripp; Stuart Crozier; Alan Connelly; Olivier Salvado (NeuroImage, 2011)

A k-space sharing 3D GRASE pseudocontinuous ASL method for whole-brain resting-state functional connectivity. - Xiaoyun Liang 001; Jacques-Donald Tournier; Richard A. J. Masterton; Alan Connelly; Fernando Calamante (Int. J. Imaging Syst. Technol., 2012)

MRtrix: Diffusion tractography in crossing fiber regions. - Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (Int. J. Imaging Syst. Technol., 2012)

Comment on time-varying eddy currents effects on diffusion-weighting echo-planar imaging. - Fernando Calamante; Alan Connelly (NeuroImage, 2012)

Super-resolution track-density imaging studies of mouse brain: Comparison to histology. - Fernando Calamante; Jacques-Donald Tournier; Nyoman D. Kurniawan; Zhengyi Yang 004; Erika Gyengesi; Graham J. Galloway; David C. Reutens; Alan Connelly (NeuroImage, 2012)

A generalised framework for super-resolution track-weighted imaging. - Fernando Calamante; Jacques-Donald Tournier; Robert E. Smith 002; Alan Connelly (NeuroImage, 2012)

Apparent Fibre Density: A novel measure for the analysis of diffusion-weighted magnetic resonance images. - David Raffelt; Jacques-Donald Tournier; Stephen E. Rose; Gerard R. Ridgway; Robert D. Henderson; Stuart Crozier; Olivier Salvado; Alan Connelly (NeuroImage, 2012)

Anatomically-constrained tractography: Improved diffusion MRI streamlines tractography through effective use of anatomical information. - Robert E. Smith 002; Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (NeuroImage, 2012)

Classification Forests and Markov Random Field to Segment Chronic Ischemic Infarcts from Multimodal MRI. - Jhimli Mitra; Pierrick Bourgeat; Jurgen Fripp; Soumya Ghose; Stephen E. Rose; Olivier Salvado; Alan Connelly; Bruce Campbell 004; Susan Palmer; Gagan Sharma; Soren Christensen; Leeanne Carey (MBIA, 2013)

Track-weighted functional connectivity (TW-FC): A tool for characterizing the structural-functional connections in the brain. - Fernando Calamante; Richard A. J. Masterton; Jacques-Donald Tournier; Robert E. Smith 002; Lisa Willats; David Raffelt; Alan Connelly (NeuroImage, 2013)

SIFT: Spherical-deconvolution informed filtering of tractograms. - Robert E. Smith 002; Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (NeuroImage, 2013)

Identification and interpretation of microstructural abnormalities in motor pathways in adolescents born preterm. - Samuel Groeschel; Jacques-Donald Tournier; Gemma B. Northam; Torsten Baldeweg; John Wyatt; Brigitte Vollmer; Alan Connelly (NeuroImage, 2014)

Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data. - Ben Jeurissen; Jacques-Donald Tournier; Thijs Dhollander; Alan Connelly; Jan Sijbers (NeuroImage, 2014)

Graph analysis of resting-state ASL perfusion MRI data: Nonlinear correlations among CBF and network metrics. - Xiaoyun Liang 001; Alan Connelly; Fernando Calamante (NeuroImage, 2014)

Lesion segmentation from multimodal MRI using random forest following ischemic stroke. - Jhimli Mitra; Pierrick Bourgeat; Jurgen Fripp; Soumya Ghose; Stephen E. Rose; Olivier Salvado; Alan Connelly; Bruce Campbell 004; Susan Palmer; Gagan Sharma; Soren Christensen; Leeanne Carey (NeuroImage, 2014)

Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and super-resolution track density imaging. - Kay Richards; Fernando Calamante; Jacques-Donald Tournier; Nyoman D. Kurniawan; Farnoosh Sadeghian; Alexander R. Retchford; Gabriel Davis Jones; Christopher A. Reid; David C. Reutens; Roger J. Ordidge; Alan Connelly; Steven Petrou (NeuroImage, 2014)

Quantification of track-weighted imaging (TWI): Characterisation of within-subject reproducibility and between-subject variability. - Lisa Willats; David Raffelt; Robert E. Smith 002; Jacques-Donald Tournier; Alan Connelly; Fernando Calamante (NeuroImage, 2014)

Voxel-Wise Functional Connectomics Using Arterial Spin Labeling Functional Magnetic Resonance Imaging: The Role of Denoising. - Xiaoyun Liang 001; Alan Connelly; Fernando Calamante (Brain Connect., 2015)

Quantification of voxel-wise total fibre density: Investigating the problems associated with track-count mapping. - Fernando Calamante; Robert E. Smith 002; Jacques-Donald Tournier; David Raffelt; Alan Connelly (NeuroImage, 2015)

Fourier Tract Sampling (FouTS): A framework for improved inference of white matter tracts from diffusion MRI by explicitly modelling tract volume. - Thomas G. Close; Jacques-Donald Tournier; Leigh A. Johnston; Fernando Calamante; Iven Mareels; Alan Connelly (NeuroImage, 2015)

Reproducibility of multiphase pseudo-continuous arterial spin labeling and the effect of post-processing analysis methods. - Amir Fazlollahi; Pierrick Bourgeat; Xiaoyun Liang 001; Fabrice Mériaudeau; Alan Connelly; Olivier Salvado; Fernando Calamante (NeuroImage, 2015)

Connectivity-based fixel enhancement: Whole-brain statistical analysis of diffusion MRI measures in the presence of crossing fibres. - David A. Raffelt; Robert E. Smith 002; Gerard R. Ridgway; Jacques-Donald Tournier; David N. Vaughan; Stephen E. Rose; Robert D. Henderson; Alan Connelly (NeuroImage, 2015)

The effects of SIFT on the reproducibility and biological accuracy of the structural connectome. - Robert E. Smith 002; Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (NeuroImage, 2015)

SIFT2: Enabling dense quantitative assessment of brain white matter connectivity using streamlines tractography. - Robert E. Smith 002; Jacques-Donald Tournier; Fernando Calamante; Alan Connelly (NeuroImage, 2015)

Correction for diffusion MRI fibre tracking biases: The consequences for structural connectomic metrics. - Chun-Hung Yeh; Robert E. Smith 002; Xiaoyun Liang 001; Fernando Calamante; Alan Connelly (NeuroImage, 2016)

A New MRI-Based Pediatric Subcortical Segmentation Technique (PSST). - Wai Yen Loh; Alan Connelly; Jeanie L. Y. Cheong; Alicia J. Spittle; Jian Chen 031; Christopher L. Adamson; Zohra M. Ahmadzai; Lillian Gabra Fam; Sandra Rees; Katherine J. Lee; Lex W. Doyle; Peter J. Anderson; et al. (Neuroinformatics, 2016)

Investigating white matter fibre density and morphology using fixel-based analysis. - David A. Raffelt; Jacques-Donald Tournier; Robert E. Smith 002; David N. Vaughan; Graeme D. Jackson; Gerard R. Ridgway; Alan Connelly (NeuroImage, 2017)

A Novel Method for Extracting Hierarchical Functional Subnetworks Based on a Multisubject Spectral Clustering Approach. - Xiaoyun Liang 001; Chun-Hung Yeh; Alan Connelly; Fernando Calamante (Brain Connect., 2019)

Is removal of weak connections necessary for graph-theoretical analysis of dense weighted structural connectomes from diffusion MRI? - Oren Civier; Robert Elton Smith; Chun-Hung Yeh; Alan Connelly; Fernando Calamante (NeuroImage, 2019)

MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. - Jacques-Donald Tournier; Robert E. Smith 002; David Raffelt; Rami Tabbara; Thijs Dhollander; Maximilian Pietsch; Daan Christiaens; Ben Jeurissen; Chun-Hung Yeh; Alan Connelly (NeuroImage, 2019)

Connectomes from streamlines tractography: Assigning streamlines to brain parcellations is not trivial but highly consequential. - Chun-Hung Yeh; Robert E. Smith 002; Thijs Dhollander; Fernando Calamante; Alan Connelly (NeuroImage, 2019)

Maturation and interhemispheric asymmetry in neurite density and orientation dispersion in early childhood. - Dennis Dimond; Stella Heo; Amanda Ip; Christiane S. Rohr; Ryann Tansey; Kirk Graff; Thijs Dhollander; Robert E. Smith 002; Catherine Lebel; Deborah Dewey; Alan Connelly; Signe Bray (NeuroImage, 2020)

Early childhood development of white matter fiber density and morphology. - Dennis Dimond; Christiane S. Rohr; Robert E. Smith 002; Thijs Dhollander; Ivy Cho; Catherine Lebel; Deborah Dewey; Alan Connelly; Signe Bray (NeuroImage, 2020)

Characterisation of white matter asymmetries in the healthy human brain using diffusion MRI fixel-based analysis. - Arush Honnedevasthana Arun; Alan Connelly; Robert Elton Smith; Fernando Calamante (NeuroImage, 2021)