Study of Connectivity in the Brain Using the Full Diffusion Tensor from MRI. - Philipp G. Batchelor; Derek L. G. Hill; Fernando Calamante; David Atkinson (IPMI, 2001)

Estimation of bolus dispersion effects in perfusion MRI using image-based computational fluid dynamics. - Fernando Calamante; Peter J. Yim; Juan R. Cebral (NeuroImage, 2003)

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

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)

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)

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)

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)

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)

Visualization of mouse barrel cortex using ex-vivo track density imaging. - Nyoman D. Kurniawan; Kay L. Richards; Zhengyi Yang 004; David She; Jeremy F. P. Ullmann; Randal X. Moldrich; Sha Liu; Javier Urriola Yaksic; Gayeshika Leanage; Irina Kharatishvili; Verena Wimmer; Fernando Calamante; et al. (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)

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)

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)

The contribution of geometry to the human connectome. - James A. Roberts 002; Alistair Perry; Anton R. Lord; Gloria M. P. Roberts; Philip B. Mitchell; Robert E. Smith 002; Fernando Calamante; Michael Breakspear (NeuroImage, 2016)

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 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)

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)

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)

TractLearn: A geodesic learning framework for quantitative analysis of brain bundles. - Arnaud Attye; Félix Renard; Monica Baciu; Elise Roger; Laurent Lamalle; Patrick Dehail; Hélène Cassoudesalle; Fernando Calamante (NeuroImage, 2021)

Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset? - Kurt G. Schilling; François Rheault; Laurent Petit; Colin B. Hansen; Vishwesh Nath; Fang-Cheng Yeh; Gabriel Girard; Muhamed Barakovic; Jonathan Rafael-Patino; Thomas Yu; Elda Fischi Gomez; Marco Pizzolato; et al. (NeuroImage, 2021)

Diffusion MRI Fibre Orientation Distribution Inpainting. - Zihao Tang; Xinyi Wang; Mariano Cabezas; Arkiev D'Souza; Fernando Calamante; Dongnan Liu; Michael Barnett 006; Chenyu Wang 001; Tom Weidong Cai (CDMRI@MICCAI, 2022)

MS Lesion Segmentation: Revisiting Weighting Mechanisms for Federated Learning. - Dongnan Liu; Mariano Cabezas; Dongang Wang; Zihao Tang; Lei Bai 001; Geng Zhan; Yuling Luo; Kain Kyle; Linda Ly; James Yu; Chun-Chien Shieh; Aria Nguyen; et al. (CoRR, 2022)

FOD-Net: A deep learning method for fiber orientation distribution angular super resolution. - Rui Zeng; Jinglei Lv; He Wang 016; Luping Zhou; Michael Barnett 006; Fernando Calamante; Chenyu Wang 001 (Medical Image Anal., 2022)

Network communication models narrow the gap between the modular organization of structural and functional brain networks. - Caio Seguin; Sina Mansour L.; Olaf Sporns; Andrew Zalesky; Fernando Calamante (NeuroImage, 2022)

Structural connections between the noradrenergic and cholinergic system shape the dynamics of functional brain networks. - Natasha L. Taylor; Adora M. DSouza; Brandon R. Munn; Jinglei Lv; Laszlo Zaborszky; Eli J. Müller; G. Wainstein; Fernando Calamante; James M. Shine (NeuroImage, 2022)

Hippocampal Neuronal Integrity and Functional Connectivity Within the Default Mode Network in Mild Cognitive Impairment: A Multimodal Investigation. - Marilena M. Demayo; Jinglei Lv; Shantel L. Duffy; Arkiev D'Souza; Loren Mowszowski; Sharon L. Naismith; Fernando Calamante (Brain Connect., 2023)

Enhancing Angular Resolution via Directionality Encoding and Geometric Constraints in Brain Diffusion Tensor Imaging. - Sheng Chen; Zihao Tang; Mariano Cabezas; Xinyi Wang; Arkiev D'Souza; Michael Barnett 006; Fernando Calamante; Weidong Cai 001; Chenyu Wang 001 (ICONIP (4), 2024)

Predicting Human Brain States with Transformer. - Yifei Sun; Mariano Cabezas; Jiah Lee; Chenyu Wang 001; Wei Zhang 090; Fernando Calamante; Jinglei Lv (LDTM/MMMI/ML4MHD/ML-CDS@MICCAI, 2024)

Fibre Population-guided Pre-training for 3D Spatial Super-Resolution on Multimodal Brain Diffusion MR Imaging. - Zihao Tang; Xinyi Wang; Mariano Cabezas; Arkiev D'Souza; Michael Barnett 006; Fernando Calamante; Weidong Cai 001; Chenyu Wang 001 (MMAsia, 2024)

Improving multiple sclerosis lesion segmentation across clinical sites: A federated learning approach with noise-resilient training. - Lei Bai 001; Dongang Wang; Hengrui Wang; Michael Barnett 006; Mariano Cabezas; Weidong Cai 001; Fernando Calamante; Kain Kyle; Dongnan Liu; Linda Ly; Aria Nguyen; Chun-Chien Shieh; et al. (Artif. Intell. Medicine, 2024)

How Much Data are Enough? Investigating Dataset Requirements for Patch-Based Brain MRI Segmentation Tasks. - Dongang Wang; Peilin Liu; Hengrui Wang; Heidi Beadnall; Kain Kyle; Linda Ly; Mariano Cabezas; Geng Zhan; Ryan Sullivan; Tom Weidong Cai; Wanli Ouyang; Fernando Calamante; et al. (CoRR, 2024)

Voxel-Level Brain States Prediction Using Swin Transformer. - Yifei Sun; Daniel Chahine; Qinghao Wen; Tianming Liu 001; Xiang Li 001; Yixuan Yuan; Fernando Calamante; Jinglei Lv (CoRR, 2025)

Age Sensitive Hippocampal Functional Connectivity: New Insights from 3D CNNs and Saliency Mapping. - Yifei Sun; Marshall A. Dalton; Robert D. Sanders; Yixuan Yuan; Xiang Li 001; Sharon L. Naismith; Fernando Calamante; Jinglei Lv (CoRR, 2025)

From Promise to Practical Reality: Transforming Diffusion MRI Analysis with Fast Deep Learning Enhancement. - Xinyi Wang; Michael Barnett 006; Frederique Boonstra; Yael Barnett; Mariano Cabezas; Arkiev D'Souza; Matthew C. Kiernan; Kain Kyle; Meng Law; Lynette Masters; Zihao Tang; Stephen Tisch; et al. (CoRR, 2025)