1. Ghassan Hamarneh, Steven Pizer, and Hao (Richard) Zhang, editors. Proceedings of the Geometry for Anatomy (G4A), Banff International Research Station (BIRS) 5-day workshop. Banff, AB, Canada, 8 2011.

1. Daniel Baboiu. Vessel Bifurcation Detection in Scale Space. Master's Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, March 2011.



2. Chris McIntosh. Energy Functionals for Medical Image Segmentation: Choices and Consequences. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, November 2011.



3. Oliver van Kaick. Matching Dissimilar Shapes. Doctoral Thesis, School of Computing Science, Faculty of Applied Sciences, Simon Fraser University, November 2011.

1. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based 3D shape analysis of thigh muscles: Patients with chronic obstructive pulmonary disease versus healthy adults. Academic Radiology, 18(2):155-166, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning.



2. Ghassan Hamarneh, Chris McIntosh, and Mark S. Drew. Perception-based Visualization of Manifold-Valued Medical Images using Distance-Preserving Dimensionality Reduction. IEEE Transactions on Medical Imaging (IEEE TMI), 30(7):1314-1327, 2011. Keyword(s): Color/Multichannel/Vector-valued, Visualization, Diffusion MRI/Tensor-valued, Functional/Molecular/Dynamic Imaging.



3. Preet Jassi and Ghassan Hamarneh. VascuSynth: Vascular Tree Synthesis Software. Insight Journal, January-June:1-12, 2011. Keyword(s): Segmentation, Validation, Shape Modelling and Analysis, Software and Tools, Anatomical Trees and Tubular Structures, Synthesis/Simulation/Augmentation, Datasets.



4. Boris Shabash, Zhi Feng Huang, and Ghassan Hamarneh. Medical Image Analysis with ITK on Apple iOS. Kitware Source - Software Developer's Quarterly, (16):3-5, 2011. Keyword(s): Software and Tools.



5. Andrea Tagliasacchi, Matt Olson, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. VASE: Volume-Aware Surface Evolution for Surface Reconstruction from Incomplete Point Clouds. Computer Graphics Forum (CGF) (Special Issue of Symposium on Geometry Processing 2011), 30(5):1563-1571, 2011. Keyword(s): Deformable Models, Shape Modelling and Analysis.



6. Azadeh Yazdanpanah, Ghassan Hamarneh, Ben Smith, and Marinko Sarunic. Automated Segmentation of Intra-Retinal Layers from Optical Coherence Tomography Images using an Active Contour Approach. IEEE Transactions on Medical Imaging (IEEE TMI), 30(2):484-496, 2011. Keyword(s): Segmentation, Deformable Models.



7. Oliver van Kaick, Andrea Tagliasacchi, Oana Sidi, Hao (Richard) Zhang, Daniel Cohen-Or, Lior Wolf, and Ghassan Hamarneh. Prior Knowledge for Part Correspondence. Computer Graphics Forum (CGF) (Special Issue of Eurographics 2011), 30(2):1-10, 2011. Keyword(s): Segmentation, Registration and Matching, Shape Modelling and Analysis.



8. Oliver van Kaick, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. A Survey on Shape Correspondence. Computer Graphics Forum (CGF) (extended version of Eurographics 2010 STAR), 30(6):1681-1707, 2011. Keyword(s): Survey/Review, Registration and Matching, Shape Modelling and Analysis.

1. Shawn Andrews, Ghassan Hamarneh, Azadeh Yazdanpanah, Bahareh HajGhanbari, and W. Darlene Reid. Probabilistic Multi-Shape Segmentation of Knee Extensor and Flexor Muscles. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6893, pages 651-658, 2011. Keyword(s): Segmentation, Uncertainty, Optimization.



2. Shawn Andrews, Chris McIntosh, and Ghassan Hamarneh. Convex Multi-Region Probabilistic Segmentation with Shape Prior in the Isometric Logratio Transformation Space. In IEEE International Conference on Computer Vision (IEEE ICCV), pages 2096-2103, 2011. Keyword(s): Optimization, Segmentation, Uncertainty.



3. Brian G. Booth and Ghassan Hamarneh. Consistent Information Content Estimation for Diffusion Tensor MR Images. In IEEE Conference on Healthcare Informatics, Imaging and Systems Biology (IEEE HISB), pages 166-173, 2011. Keyword(s): Diffusion MRI/Tensor-valued.



4. Brian G. Booth and Ghassan Hamarneh. Exact Integration of Diffusion Orientation Distribution Functions for Graph-Based Diffusion MRI Analysis. In IEEE International Symposium on Biomedical Imaging (IEEE ISBI), pages 935-938, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Graph based.



5. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. 3D shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Canadian Physiotherapy Association Congress, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning.



6. Bahareh HajGhanbari, Ghassan Hamarneh, Neda Changizi, Aaron Ward, and W. Darlene Reid. MRI-based Three dimensional shape analysis of thigh muscles: people with Chronic Obstructive Pulmonary Disease versus healthy older adults. In Heart+Lung Health Fest, pages 1, 2011. Keyword(s): Shape Modelling and Analysis, Machine Learning.



7. Chris McIntosh, Ghassan Hamarneh, Matt Toom, and Roger Tam. Spinal Cord Segmentation for Volume Estimation in Healthy and Multiple Sclerosis Subjects using Crawlers and Minimal Paths. In IEEE Conference on Healthcare Informatics, Imaging and Systems Biology (IEEE HISB), pages 25-31, 2011. Keyword(s): Artificial Life, Deformable Organisms, Segmentation, Anatomical Trees and Tubular Structures, Multiple Sclerosis, MRI.



8. Hengameh Mirzaalian, Ghassan Hamarneh, Bahareh HajGhanbari, and W. Darlene Reid. 3D Shape Analysis of the Knee Extensor and Flexor Muscles in Patients with COPD using Mesh Projection-based Features. In Medical Image Computing and Computer-Assisted Intervention Workshop on Mesh Processing in Medical Image Analysis (MICCAI MeshMed), pages 1-8, 2011. Keyword(s): Medial-based Shape Representation, Shape Modelling and Analysis.



9. Krishna Nand, Rafeef Abugharbieh, Brian G. Booth, and Ghassan Hamarneh. Detecting Structure in Diffusion Tensor MR Images. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6892, pages 90-97, 2011. Keyword(s): Diffusion MRI/Tensor-valued, Processing, Anatomical Trees and Tubular Structures.



10. Manku Rana, Ghassan Hamarneh, and James Wakeling. Automated methods for determination of 3D muscle fascicle orientation in human muscle using free hand ultrasound. In American Society of Biomechanics (ASB), 2011. Keyword(s): Shape Modelling and Analysis, Tracking.



11. Andrea Tagliasacchi, Matt Olson, Hao (Richard) Zhang, Ghassan Hamarneh, and Daniel Cohen-Or. VASE: Volume-Aware Surface Evolution for Surface Reconstruction from Incomplete Point Clouds. In Symposium on Geometry Processing (SGP) (also appears in the Special Issue of the Journal Computer Graphics Forum), pages 1563-1571, 2011. Keyword(s): Deformable Models, Shape Modelling and Analysis.



12. Lisa Y. W. Tang, Ghassan Hamarneh, and Tim Bressmann. A Machine Learning Approach to Tongue Motion Analysis in 2D Ultrasound Image Sequences. In Medical Image Computing and Computer-Assisted Intervention Workshop on Machine Learning in Medical Imaging (MICCAI MLMI), volume 7009, pages 151-158, 2011. Keyword(s): Tracking, Machine Learning.



13. Andrew Top, Ghassan Hamarneh, and Rafeef Abugharbieh. Active Learning for Interactive 3D Image Segmentation. In Lecture Notes in Computer Science, Medical Image Computing and Computer-Assisted Intervention (MICCAI), volume 6893, pages 603-610, 2011. Keyword(s): Uncertainty, User Interaction, Segmentation.



14. Oliver van Kaick, Andrea Tagliasacchi, Oana Sidi, Hao (Richard) Zhang, Daniel Cohen-Or, Lior Wolf, and Ghassan Hamarneh. Prior Knowledge for Part Correspondence. In Eurographics (also appears in the Special Issue of the Journal Computer Graphics Forum), pages 1-10, 2011. Keyword(s): Segmentation, Registration and Matching, Shape Modelling and Analysis.

1. Shawn Andrews, Chris McIntosh, and Ghassan Hamarneh. Convex Multi-Region Probabilistic Segmentation with Shape Prior in the Isometric Logratio Transformation Space. Technical report TR 2011-03, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, July 2011. Keyword(s): Optimization, Segmentation, Uncertainty.



2. Ghassan Hamarneh. The Optimizability-Fidelty Trade-Off in Image Analysis. Technical report SFU-Summit-10897, School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, 9 2011. Keyword(s): Optimization, Segmentation, Registration and Matching.

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