Semi-automated Basal Ganglia Segmentation Using Large Deformation Diffeomorphic Metric Mapping. - Ali R. Khan; Elizabeth H. Aylward; Patrick Barta; Michael I. Miller; Mirza Faisal Beg (MICCAI, 2005)

Computing an average anatomical atlas using LDDMM and geodesic shooting. - Mirza Faisal Beg; Ali R. Khan (ISBI, 2006)

Symmetric Data Attachment Terms for Large Deformation Image Registration. - Mirza Faisal Beg; Ali R. Khan (IEEE Trans. Medical Imaging, 2007)

Representation of time-varying shapes in the large deformation diffeomorphic framework. - Ali R. Khan; Mirza Faisal Beg (ISBI, 2008)

FreeSurfer-initiated fully-automated subcortical brain segmentation in MRI using Large Deformation Diffeomorphic Metric Mapping. - Ali R. Khan; Lei Wang 032; Mirza Faisal Beg (NeuroImage, 2008)

A Combined Surface And VOlumetric Registration (SAVOR) Framework to Study Cortical Biomarkers and Volumetric Imaging Data. - Eli Gibson; Ali R. Khan; Mirza Faisal Beg (MICCAI (1), 2009)

Robust Atlas-Based Brain Segmentation Using Multi-structure Confidence-Weighted Registration. - Ali R. Khan; Moo K. Chung; Mirza Faisal Beg (MICCAI (1), 2009)

Freesurfer-initialized large deformation diffeomorphic metric mapping with application to Parkinson's disease. - Jingyun Chen; Samantha J. Palmer; Ali R. Khan; Martin J. McKeown; Mirza Faisal Beg (Image Processing, 2009)

External landmark and head-shape-based functional data normalization. - Mirza Faisal Beg; Stephen Wong; Ali R. Khan; Teresa Cheung; Naznin Virji-Babul; Anthony T. Herdman (Comput. Medical Imaging Graph., 2009)

Momentum-based morphometric analysis with application to Parkinson's disease. - Jingyun Chen; Ali R. Khan; Martin J. McKeown; Mirza Faisal Beg (Image-Guided Procedures, 2011)

Optimal weights for local multi-atlas fusion using supervised learning and dynamic information (SuperDyn): Validation on hippocampus segmentation. - Ali R. Khan; Nicolas Cherbuin; Wei Wen; Kaarin Anstey; Perminder S. Sachdev; Mirza Faisal Beg (NeuroImage, 2011)

Use of a Mixed-Reality System to Improve the Planning of Brain Tumour Resections: Preliminary Results. - Kamyar Abhari; John S. H. Baxter; Elvis C. S. Chen; Ali R. Khan; Chris Wedlake; Terry M. Peters; Sandrine de Ribaupierre; Roy Eagleson (AE-CAI, 2012)

Robust registration of sparsely sectioned histology to ex-vivo MRI of temporal lobe resections. - Maged Goubran; Ali R. Khan; Cathie Crukley; Susan Buchanan; Brendan Santyr; Sandrine de Ribaupierre; Terry M. Peters (Image Processing, 2012)

The Role of Augmented Reality in Training the Planning of Brain Tumor Resection. - Kamyar Abhari; John S. H. Baxter; Elvis C. S. Chen; Ali R. Khan; Chris Wedlake; Terry M. Peters; Roy Eagleson; Sandrine de Ribaupierre (AE-CAI, 2013)

Image registration of ex-vivo MRI to sparsely sectioned histology of hippocampal and neocortical temporal lobe specimens. - Maged Goubran; Cathie Crukley; Sandrine de Ribaupierre; Terence M. Peters; Ali R. Khan (NeuroImage, 2013)

Multistructure Large Deformation Diffeomorphic Brain Registration. - Ali R. Khan; Lei Wang 032; Mirza Faisal Beg (IEEE Trans. Biomed. Eng., 2013)

Smoothness parameter tuning for generalized hierarchical continuous max-flow segmentation. - John S. H. Baxter; Martin Rajchl; A. Jonathan McLeod; Ali R. Khan; Jing Yuan 001; Terry M. Peters (Image Processing, 2014)

RANCOR: Non-Linear Image Registration with Total Variation Regularization. - Martin Rajchl; John S. H. Baxter; Wu Qiu; Ali R. Khan; Aaron Fenster; Terry M. Peters; Jing Yuan 001 (CoRR, 2014)

MRBrainS Challenge: Online Evaluation Framework for Brain Image Segmentation in 3T MRI Scans. - Adriënne M. Mendrik; Koen L. Vincken; Hugo J. Kuijf; Marcel Breeuwer; Willem H. Bouvy; Jeroen de Bresser; Amir Alansary; Marleen de Bruijne; Aaron Carass; Ayman El-Baz; Amod Jog; Ranveer Katyal; et al. (Comput. Intell. Neurosci., 2015)

Detection of temporal lobe epilepsy using support vector machines in multi-parametric quantitative MR imaging. - Diego Cantor-Rivera; Ali R. Khan; Maged Goubran; Seyed M. Mirsattari; Terry M. Peters (Comput. Medical Imaging Graph., 2015)

Visual Enhancement of MR Angiography Images to Facilitate Planning of Arteriovenous Malformation Interventions. - Kamyar Abhari; John S. H. Baxter; Ali R. Khan; Terry M. Peters; Sandrine de Ribaupierre; Roy Eagleson (ACM Trans. Appl. Percept., 2015)

Training for Planning Tumour Resection: Augmented Reality and Human Factors. - Kamyar Abhari; John S. H. Baxter; Elvis C. S. Chen; Ali R. Khan; Terry M. Peters; Sandrine de Ribaupierre; Roy Eagleson (IEEE Trans. Biomed. Eng., 2015)

Fast Deformable Image Registration with Non-smooth Dual Optimization. - Martin Rajchl; John S. H. Baxter; Wu Qiu; Ali R. Khan; Aaron Fenster; Terry M. Peters; Daniel Rueckert; Jing Yuan 001 (CVPR Workshops, 2016)

Single slice US-MRI registration for neurosurgical MRI-guided US. - Utsav Pardasani; John S. H. Baxter; Terry M. Peters; Ali R. Khan (Image-Guided Procedures, 2016)

Generation and evaluation of an ultra-high-field atlas with applications in DBS planning. - Brian T. Wang; Stefan Poirier; Ting Guo; Andrew G. Parrent; Terry M. Peters; Ali R. Khan (Image Processing, 2016)

Individual feature maps: a patient-specific analysis tool with applications in temporal lobe epilepsy. - Diego Cantor-Rivera; John S. H. Baxter; Sandrine de Ribaupierre; Jonathan C. Lau; Seyed M. Mirsattari; Maged Goubran; Jorge G. Burneo; David A. Steven; Terry M. Peters; Ali R. Khan (Int. J. Comput. Assist. Radiol. Surg., 2016)

Hierarchical max-flow segmentation framework for multi-atlas segmentation with Kohonen self-organizing map based Gaussian mixture modeling. - Martin Rajchl; John S. H. Baxter; A. Jonathan McLeod; Jing Yuan 001; Wu Qiu; Terry M. Peters; Ali R. Khan (Medical Image Anal., 2016)

Unfolding the hippocampus: An intrinsic coordinate system for subfield segmentations and quantitative mapping. - Jordan DeKraker; Kayla M. Ferko; Jonathan C. Lau; Stefan Köhler 001; Ali R. Khan (NeuroImage, 2018)

Quantification of local geometric distortion in structural magnetic resonance images: Application to ultra-high fields. - Jonathan C. Lau; Ali R. Khan; Tony Y. Zeng; Keith W. MacDougall; Andrew G. Parrent; Terry M. Peters (NeuroImage, 2018)

IJCARS: MICCAI 2019 special issue. - Terry M. Peters; Caroline Essert; Ali R. Khan (Int. J. Comput. Assist. Radiol. Surg., 2020)

Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological features in 3D BigBrain. - Jordan DeKraker; Jonathan C. Lau; Kayla M. Ferko; Ali R. Khan; Stefan Köhler 001 (NeuroImage, 2020)

Effects of MP2RAGE B1+ sensitivity on inter-site T1 reproducibility and hippocampal morphometry at 7T. - Roy A. M. Haast; Jonathan C. Lau; Dimo Ivanov; Ravi S. Menon; Kâmil Uludag; Ali R. Khan (NeuroImage, 2021)

Image Guidance in Deep Brain Stimulation Surgery to Treat Parkinson's Disease: A Comprehensive Review. - Yiming Xiao; Jonathan C. Lau; Dimuthu Hemachandra; Greydon Gilmore; Ali R. Khan; Terry M. Peters (IEEE Trans. Biomed. Eng., 2021)

Corrections to "Image Guidance in Deep Brain Stimulation Surgery to Treat Parkinson's Disease: A Comprehensive Review". - Yiming Xiao; Jonathan C. Lau; Dimuthu Hemachandra; Greydon Gilmore; Ali R. Khan; Terry M. Peters (IEEE Trans. Biomed. Eng., 2021)

Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults. - Jason Kai; Ali R. Khan (Frontiers Neuroinformatics, 2022)

Mapping the subcortical connectome using in vivo diffusion MRI: Feasibility and reliability. - Jason Kai; Ali R. Khan; Roy A. M. Haast; Jonathan C. Lau (NeuroImage, 2022)

Funcmasker-flex: An Automated BIDS-App for Brain Segmentation of Human Fetal Functional MRI data. - Emily S. Nichols; Susana Correa; Peter Van Dyken; Jason Kai; Tristan Kuehn; Sandrine de Ribaupierre; Emma G. Duerden; Ali R. Khan (Neuroinformatics, 2023)

bids-specification. - Aaron Oliver-Taylor; Adam Li; Adam G. Thomas; Adeen Flinker; Adina S. Wagner; Agah Karakuzu; Aki Nikolaidis; Alberto Lazari; Alejandro de la Vega; Alessio Giacomel; Alexander Rockhill; Alexander Jones; et al. (Zenodo, 2023)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Yaroslav O. Halchenko; Rémi Gau; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Yaroslav O. Halchenko; Rémi Gau; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

MRI-degad: toward accurate conversion of gadolinium-enhanced T1w MRIs to non-contrast-enhanced scans using CNNs. - Feyi Ogunsanya; Alaa Taha; Greydon Gilmore; Jason Kai; Tristan Kuehn; Arun Thurairajah; Mauricio C. Tenorio; Ali R. Khan; Jonathan C. Lau (Int. J. Comput. Assist. Radiol. Surg., 2024)

The Brain Imaging Data Structure (BIDS) Specification. - Aaron Oliver-Taylor; Adam Li; Adam G. Thomas; Adeen Flinker; Adina S. Wagner; Agah Karakuzu; Aki Nikolaidis; Alberto Lazari; Alejandro de la Vega; Alessio Giacomel; Alexander Rockhill; Alexander Jones; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Rémi Gau; Yaroslav O. Halchenko; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Rémi Gau; Yaroslav O. Halchenko; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Rémi Gau; Yaroslav O. Halchenko; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Rémi Gau; Yaroslav O. Halchenko; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2024)

PyBIDS: Python tools for BIDS datasets. - Tal Yarkoni; Christopher J. Markiewicz; Alejandro de la Vega; Krzysztof J. Gorgolewski; Taylor Salo; Rémi Gau; Yaroslav O. Halchenko; Dimitri Papadopoulos Orfanos; Oscar Esteban; Quinten McNamara; Krista DeStasio; Jean-Baptiste Poline; et al. (Zenodo, 2025)