1. Colin J. Brown. Modelling and Prediction of Neurodevelopment in Preterm Infants using Structural Connectome Data. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, April 2017. [bibtex-key = phd2017brown]

1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample \(\zeta\)-mixup: Richer, More Realistic Synthetic Samples from a \(p\)-Series Interpolant. Journal of Big Data, 11(43):1-41, March 2024. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation, Classification, Dermatology. [bibtex-key = jbd2024]



2. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive connectome subnetwork extraction with anatomical and connectivity priors. Computerized Medical Imaging and Graphics (CMIG), 71(January):67-78, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = cmig2018b]



3. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Convolutional Neural Networks for Brain Networks; Towards Predicting Neurodevelopment (Brown and Kawahara: Joint first authors). NeuroImage, 146(1):1038-1049, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning. [bibtex-key = neuroimage2017]



4. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Christina Aquino-Parsons, and Ingrid Spadinger. Association of Bladder Dose with Late Urinary Side Effects in Cervical Cancer High-Dose-Rate Brachytherapy. Brachytherapy, 16(6):1175-1183, 2017. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = brachy2017]



5. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Christina Aquino-Parsons, and Ingrid Spadinger. Bladder Accumulated Dose in Image-Guided High-Dose-Rate Brachytherapy for Locally Advanced Cervical Cancer and its Relation to Urinary Toxicity. Physics in Medicine and Biology (PMB), 1(24):8408-8424, 2016. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = pmb2016]



6. Brian G. Booth, Steven Miller, Colin J. Brown, Kenneth Poskitt, Vann Chau, Ruth Grunau, Anne Synnes, and Ghassan Hamarneh. STEAM - Statistical Template Estimation for Abnormality Mapping: a Personalized DTI Analysis Technique with Applications to the Screening of Preterm Infants. NeuroImage, 125:705-723, 2015. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Datasets, Synthesis/Simulation/Augmentation. [bibtex-key = neuroimage2015]



7. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, and Ingrid Spadinger. Validation of non-rigid point-set registration methods using a porcine bladder pelvic phantom. Physics in Medicine and Biology (PMB), 61(2):825-854, 2015. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = pmb2015]



8. Colin J. Brown, Steven Miller, Brian G. Booth, Shawn Andrews, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Structural Network Analysis of Brain Development in Young Preterm Neonates. NeuroImage, 101(0):667-680, 2014. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome. [bibtex-key = neuroimage2014]



9. Roja Zakariaee, Colin J. Brown, Ghassan Hamarneh, Christina Parsons, and Ingrid Spadinger. Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration. Medical Physics (also appeared in COMP 2014), 41(3):1, 2014. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = mp2014]

1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. $\zeta$-mixup: Richer, More Realistic Mixing of Multiple Images. In Medical Imaging with Deep Learning (MIDL), pages 1-5, 2023. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = midl2023]



2. Kayleigh Campbell, Colin J. Brown, Ghassan Hamarneh, Steven Miller, and Tim Oberlander. Disrupted structural network topology of the neonatal brain following prenatal SSRI antidepressant exposure, and its relationship with later infant neurodevelopment and behaviour at 2-years of age. In International Society for Developmental Psychobiology (ISDP), 2022. Keyword(s): Neurodevelopment, Diffusion MRI/Tensor-valued. [bibtex-key = isdp2022]



3. Mia McLean, Lynne Williams, Colin J. Brown, Ghassan Hamarneh, Cecil Chau, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Neonatal Pain-related Stress, Neonatal Structural Brain Subnetworks, Cortisol and Behavior at 4 years in Children Born Very Preterm. In 54th Annual Meeting of the International Society for Developmental Psychobiology, Chicago, USA, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = isdp2021]



4. Mia McLean, Lynne Williams, Jeremy Kawahara, Colin J. Brown, Ghassan Hamarneh, Joanne Weinberg, Anne Synnes, Steven Miller, and Ruth Grunau. Associations Between Neonatal Pain-Related Stress, Neonatal Brain Structural Connectome, and Behavior at School Age in Children Born Very Preterm. In 6th Annual Research Day Brain, Behaviour and Development (BB&D), Vancouver, Canada, pages 1, 2021. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning. [bibtex-key = bcbbd2021]



5. Jeremy Kawahara, Colin J. Brown, and Ghassan Hamarneh. Connectome Priors in Deep Neural Networks to Predict Autism (Kawahara and Brown: Joint first authors). In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 110-113, 2018. Keyword(s): Diffusion MRI/Tensor-valued, Autism, Connectome, Machine Learning, Deep Learning, Classification. [bibtex-key = isbi2018c]



6. Colin J. Brown, Kathleen Moriarty, Steven Miller, Brian G. Booth, Vann Chau, Anne Synnes, Ruth Grunau, and Ghassan Hamarneh. Prediction of Brain Network Age and Factors of Delayed Maturation in Very Preterm Infants. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 10433, pages 84-91, 2017. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = miccai2017b]



7. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Artificial Convolutional Neural Networks for Connectomes. In 2nd Annual Health Technology Symposium, Vancouver, Canada, pages 1, 2017. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning, Classification. [bibtex-key = healthtech2017c]



8. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = neuroscix2016b]



9. Colin J. Brown, Steven Miller, Brian G. Booth, Jill Zwicker, Ruth Grunau, Anne Synnes, Vann Chau, and Ghassan Hamarneh. Predictive Subnetwork Extraction with Structural Priors for Infant Connectomes. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9900, pages 175-183, 2016. Keyword(s): Neurodevelopment, Machine Learning. [bibtex-key = miccai2016b]



10. Jeremy Kawahara, Colin J. Brown, Steven Miller, Brian G. Booth, Vann Chau, Ruth Grunau, Jill Zwicker, and Ghassan Hamarneh. BrainNetCNN: Artificial Convolutional Neural Networks for Connectomes. In Annual Neuroscience Extravaganza, Centre for Brain Health, BC, Canada, 2016. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment, Connectome, Machine Learning, Deep Learning. [bibtex-key = neuroscix2016a]



11. Roja Zakariaee, Christina Aquino-Parsons, Ghassan Hamarneh, Colin J. Brown, Marc Gaudet, Peter Lim, and Ingrid Spadinger. Can Bladder Late Complications be predicted in Cervical Cancer HDR Brachytherapy?. In World Congress of Brachytherapy (WCB), 2016. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = wcb2016]



12. Colin J. Brown, Steven Miller, Brian G. Booth, Ken Poskitt, Vann Chau, Anne Synnes, Jill Zwicker, Ruth Grunau, and Ghassan Hamarneh. Prediction of Motor Function in Very Preterm Infants using Connectome Features and Local Synthetic Instances. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 9349, pages 69-76, 2015. Keyword(s): Neurodevelopment, Machine Learning, Synthesis/Simulation/Augmentation. [bibtex-key = miccai2015a]



13. Jenna Smith-Forrester, Naama Rotem-Kohavi, Colin J. Brown, Ghassan Hamarneh, and Naznin Virji-Babul. Changes in Structural Brain Connectivity Following Concussion. In The 9th Annual Canadian Neuroscience Meeting (CAN-ACN). Symposium: Vision and Movement Order and Disorder: From Bench to Bedside, 2015. Keyword(s): Diffusion MRI/Tensor-valued. [bibtex-key = can-acn2015]



14. Roja Zakariaee, Ghassan Hamarneh, Colin J. Brown, and Ingrid Spadinger. Phantom Validation of a Point-Set Deformable Registration Method using Pig Bladder. In World Congress on Medical Physics and Biomedical Engineering (WCMPBE), 2015. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = wcmpbe2015]



15. Colin J. Brown, Steven Miller, Brian G. Booth, Shawn Andrews, Vann Chau, Ken Poskitt, and Ghassan Hamarneh. Analysis of Structural Connectome Development in Healthy Preterm Neonates. In Annual Neuroscience Extravaganza, Brain Research Centre, UBC, 2014. Keyword(s): Diffusion MRI/Tensor-valued, Neurodevelopment. [bibtex-key = neuroscix2014]



16. Roja Zakariaee, Colin J. Brown, Ghassan Hamarneh, Christina Parsons, and Ingrid Spadinger. Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration. In Canadian Organization of Medical Physicists 60th Annual Scientific Meeting (COMP), 2014. Keyword(s): Registration and Matching, Brachytherapy. [bibtex-key = comp2014]



17. Colin J. Brown, Brian G. Booth, and Ghassan Hamarneh. K-Confidence: Assessing Uncertainty in Tractography using k Optimal Paths. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 250-253, 2013. Keyword(s): Diffusion MRI/Tensor-valued, Optimization, Uncertainty. [bibtex-key = isbi2013a]



18. Colin J. Brown, Brian G. Booth, and Ghassan Hamarneh. Uncertainty in Tractography via Tract Confidence Regions. In Medical Image Computing and Computer-Assisted Intervention Workshop on Computational Diffusion MRI (MICCAI CDMRI), pages 13-22, 2013. Keyword(s): Uncertainty, Diffusion MRI/Tensor-valued. [bibtex-key = miccai_cdmri2013]

1. Kumar Abhishek, Colin J. Brown, and Ghassan Hamarneh. Multi-Sample \(\zeta\)-mixup: Richer, More Realistic Synthetic Samples from a \(p\)-Series Interpolant. Technical report arXiv:2204.03323, 4 2022. Keyword(s): Machine Learning, Deep Learning, Synthesis/Simulation/Augmentation. [bibtex-key = arxiv:2204.03323]



2. Colin J. Brown and Ghassan Hamarneh. Machine Learning on Human Connectome Data from MRI. Technical report arxiv:1611.08699, 11 2016. Keyword(s): Survey/Review, Machine Learning, Connectome, Diffusion MRI/Tensor-valued. [bibtex-key = arxiv:1611.08699]

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