Publications

• M Shao, T Tasdizen, S Joshi (2024). Analyzing the Domain Shift Immunity of Deep Homography Estimation. IEEE. Published, 01/2024.
• Surojit Saha, Sarang Joshi, Ross Whitaker (2023). Matching aggregate posteriors in the variational autoencoder. arXiv preprint arXiv:2311.07693. Published, 11/13/2023.
• Sara Johnson & Blake Zimmerman, Henrik Odéen, Jill Shea, Nicole Winkler, Rachel Factor, Sarang Joshi, Allison Payne (2023). A non-contrast multi-parametric MRI biomarker for assessment of MR-guided focused ultrasound thermal therapies. IEEE. Published, 08/09/2023.
• Haocheng Dai, Martin Bauer, P Thomas Fletcher, Sarang Joshi (2023). Modeling the Shape of the Brain Connectome via Deep Neural Networks. Springer Nature Switzerland. Published, 06/08/2023.
• Haocheng Dai, Michael Penwarden, Robert M Kirby, Sarang Joshi (2023). Neural Operator Learning for Ultrasound Tomography Inversion. arXiv preprint arXiv:2304.03297. Published, 04/06/2023.
• Haocheng Dai, Vikren Sarkar, Christian Dial, Markus Foote, Sarang Joshi, Bill J Salter (2023). High Fidelity, CT on Rails-based Characterization of Total Delivered Dose Variation for Conformal Head and Neck Treatment: With evaluation of adaptive replanning time-point implications. medRxiv. Published, 04/2023.
• Mathias Højgaard Jensen, Sarang Joshi, Stefan Sommer (2022). Discrete-Time Observations of Brownian Motion on Lie Groups and Homogeneous Spaces: Sampling and Metric Estimation. Algorithms. Published, 08/17/2022.
• MH Jensen, S Joshi, S Sommer (2022). Discrete-Time Observations of Brownian Motion on Lie Groups and Homogeneous Spaces: Sampling and Metric Estimation. Algorithms. Vol. 15. Published, 08/2022.
• H Dai, M Bauer, PT Fletcher, SC Joshi (2022). Deep Learning the Shape of the Brain Connectome. arXiv preprint arXiv:2203.06122. Published, 03/2022.
• Kristen M Campbell, Haocheng Dai, Zhe Su, Martin Bauer, P Thomas Fletcher, Sarang C Joshi (2022). Integrated Construction of Multimodal Atlases with Structural Connectomes in the Space of Riemannian Metrics. The journal of machine learning for biomedical imaging. Published, 01/2022.
• Mathias Højgaard Jensen, Lennard Hilgendorf, Sarang Joshi, Stefan Sommer (2021). Bridge Simulation and Metric Estimation on Lie Groups and Homogeneous Spaces. Cornell University. Published, 12/2021.
• Mathias Højgaard Jensen, Lennard Hilgendorf, Sarang Joshi, Stefan Sommer (2021). Bridge Simulation on Lie Groups and Homogeneous Spaces with Application to Parameter Estimation. Cornell University. Published, 12/2021.
• Markus D Foote, Philip E Dennison, Patrick R Sullivan, Kelly B O'Neill, Andrew K Thorpe, David R Tho (2021). Impact of scene-specific enhancement spectra on matched filter greenhouse gas retrievals from imaging spectroscopy. Remote Sensing of Environment. Published, 10/2021.
• Markus D Foote, Philip E Dennison, Patrick R Sullivan, Kelly B O'Neill, Andrew K Thorpe, David R Tho (2021). Impact of scene-specific enhancement spectra on matched filter greenhouse gas retrievals from imaging spectroscopy. Elsevier. Published, 10/2021.
• Blake E Zimmerman & Sara L Johnson, Henrik A Odéen, Jill E Shea, Rachel E Factor, Sarang C Joshi, Allison H Payne (2021). Histology to 3D in vivo MR registration for volumetric evaluation of MRgFUS treatment assessment biomarkers. Nature Publishing Group UK. 18923. Published, 09/2021.
• Kristen M Campbell (2021). Structural connectome atlas construction in the space of riemannian metrics. Springer, Cham. 291-303. Published, 06/28/2021.
• M Højgaard Jensen, S Joshi, S Sommer (2021). Bridge Simulation and Metric Estimation on Lie Groups. arXiv preprint arXiv:2104.01194. Published, 06/2021.
• A Singh & M Bauer, S Joshi (2021). Physics Informed Convex Artificial Neural Networks (PICANNs) for Optimal Transport based Density Estimation. arXiv preprint arXiv:2104.01194. Published, 04/02/2021.
• Line Kühnel & Tom Fletcher, Sarang Joshi, Stefan Sommer (2021). Latent Space Geometric Statistics. Springer, Cham. Published, 01/10/2021.
• Markus D Foote, Philip E Dennison, Andrew K Thorpe, David R Thompson, Siraput Jongaramrungruang, Chr (2020). Fast and accurate retrieval of methane concentration from imaging spectrometer data using sparsity prior. IEEE. Vol. 58(9), 6480-6492. Published, 12/03/2020.
• Markus D Foote, & Sarang C Joshi, Philip E Dennison, Patrick R Sullivan, Andrew K Thorpe, Daniel Cusworth, Riley Duren (2020). Reducing Error in Airborne Imaging Spectrometer Retrieval of Greenhouse Gas Emissions Due to Geometric and Atmospheric Effects. AGU. Published, 12/2020.
• Philip E Dennison, & Markus D Foote, Patrick R Sullivan, Kelly O'Neill, Sarang C Joshi, Andrew K Thorpe, Daniel Cusworth, David R Thompson, Riley M Duren (2020). A Benchmark Dataset for Retrieval of Point Source CH4 and CO2 Plumes from Imaging Spectrometer Data. AGU. Published, 12/2020.
• Patrick R Sullivan & Philip E Dennison, John C Lin, Logan Mitchell, Ryan Bares, Markus D Foote, Sarang C Joshi, Daniel Cusworth, Andrew K Thorpe, Riley Duren (2020). Mapping Methane Point Sources in an Urban Airshed Using Imaging Spectroscopy. AGU. Published, 12/2020.
• Blake E. Zimmerman & Blake E Zimmerman, Sara L Johnson, Henrik A Odéen, Jill E Shea, Rachel E Factor, Sarang C Joshi, Allison H Payne (2020). Histology to 3D In Vivo MR Registration for Volumetric Evaluation of MRgFUS Treatment Assessment Biomarkers. arXiv preprint arXiv:2011.10708. Published, 11/2020.
  https://arxiv.org/abs/2011.10708
• Blake E Zimmerman & Sara Johnson, Henrik Odéen, Jill Shea, Markus D Foote, Nicole Winkler, Sarang C Joshi, Allison Payne (2020). Learning Multiparametric Biomarkers for Assessing MR-Guided Focused Ultrasound Treatment of Malignant Tumors. IEEE. Vol. 68(5), 1737-1747. Published, 09/18/2020.
• Blake Zimmerman & Blake Zimmerman, Sara Johnson, Henrik Odeen, Jill Shea, Markus D Foote, Nicole Winkler, Sarang Joshi, Allison Payne (2020). Learning Multiparametric Biomarkers for Assessing MR-Guided Focused Ultrasound Treatments. IEEE Transactions on Biomedical Engineering. Published, 09/2020.
• Markus D Foote & Markus D Foote, Philip E Dennison, Andrew K Thorpe, David R Thompson, Siraput Jongaramrungruang, Christian Frankenberg, Sarang C Joshi (2020). Fast and accurate retrieval of methane concentration from imaging spectrometer data using sparsity prior. IEEE Transactions on Geoscience and Remote Sensing. Vol. 58, 6480-6492. Published, 03/2020.
  https://ieeexplore.ieee.org/abstract/document/9034...
• Martin Bauer & Sarang Joshi, Klas Modin (2020). Diffeomorphic density registration. (pp. 577-603). Academic Press. Published, 01/2020.
  https://www.sciencedirect.com/science/article/pii/...
• M. Bauer & S. Joshi, and K. Modin (2020). Diffeomorphic density registration. Academic Press. Published, 01/2020.
• Alana Ayasse, & Philip E Dennison, Andrew K Thorpe, Dar A Roberts, Markus D Foote, Sarang C Joshi, Riley M Duren (2019). Point Source Methane Mapping with Future Satellite Imaging Spectrometers. AGU. GC51E-1123. Published, 12/2019.
  https://ui.adsabs.harvard.edu/abs/2019AGUFMGC51E11...
• A. Ayasse & P. E. Dennison, A. K. Thorpe, D. A. Roberts, M. D. Foote, S. C. Joshi, and R. M. Duren. (2019). Point Source Methane Mapping with Future Satellite Imaging Spectrometers. AGU. Published, 06/2019.
• M. D. Foote & B. E. Zimmerman, A. Sawant, and S. C. Joshi. (2019). Real-time 2d-3d deformable registration with deep learning and application to lung radiotherapy targeting. Springer. Published, 06/2019.
• M. Ranjbar & P. Sabouri, S. Mossahebi, D. Leiser, M. Foote, J. Zhang, G. Lasio, S. Joshi, and A. Sawant. (2019). Development and prospective in-patient proof-of-concept validation of a surface photogrammetry+ CT-based volumetric motion model for lung radiotherapy. Medical physics. Vol. 46, 5407–5420. Published, 06/2019.
• B. Zimmerman & S. Johnson, H. Ode ́en, J. Shea, M. Foote, N. Winkler, S. Joshi, and A. Payne (2019). Learning Multiparametric Biomarkers for Assessing MR-Guided Focused Ultrasound Treat- ments Using Volume-Conserving Registration. arXiv preprint. Published, 06/2019.
• A. K. Ayasse & P. E. Dennison, M. Foote, A. K. Thorpe, S. Joshi, R. O. Green, R. M. Duren, D. R. Thompson, and D. A. Roberts (2019). Methane Mapping with Future Satellite Imaging Spectrometers. Remote Sensing. Vol. 11, 3054. Published, 06/2019.
• PE Dennison & MD Foote, SC Joshi, AK Thorpe, DR Thompson (2018). Artifact Reduction Strategies in Complex Environments for Trace Gas Retrievals Using Airborne Imaging Spectroscopy. AGU Fall Meeting Abstracts. Published, 12/2018.
• PE Dennison & MD Foote, SC Joshi, AK Thorpe, DR Thompson (2018). Mapping methane plumes in AVIRIS-NG India campaign data and potential for global point source emissions monitoring using imaging spectroscopy. AGU Fall Meeting Abstracts. Published, 12/2018.
• Mark Elliot & Dan Kim, David S Molony, Liam Morris, Habib Samady, Sarang Joshi, Lucas H Timmins (2018). Establishment of an Automated Algorithm Utilizing Optical Coherence Tomography and Micro-Computed Tomography Imaging to Reconstruct the 3D Deformed Stent Geometry. IEEE. Vol. 38, 710 - 720. Published, 09/2018.
  https://ieeexplore.ieee.org/abstract/document/8466...
• P Sabouri & M Ranjbar, S Mossahebi, N Dye, S Joshi, A Sawant (2018). A Generalized Frame-Work for the Validation of Volumetric Motion Models in Thoracic Radiotherapy. AAPM. Published, 09/2018.
• Markus D Foote & Blake Zimmerman, Amit Sawant, Sarang Joshi (2018). Real-Time Patient-Specific Lung Radiotherapy Targeting using Deep Learning. arXiv. Published, 07/2018.
  https://arxiv.org/pdf/1807.08388.pdf
• Martin Bauer (2018). Diffeomorphic density registration. arXiv. Published, 07/2018.
  https://arxiv.org/abs/1807.05505
• Line Kuhnel & Tom Fletcher, Sarang Joshi, Stefan Sommer (2018). Latent Space Non-Linear Statistics. arXiv. Published, 05/2018.
• O Abdullah, & Li Dai, Jacob Tippetts, Blake Zimmerman, Alfred Van Hoek, Sarang Joshi, Edward Hsu (2018). High resolution and high field diffusion MRI in the visual system of primates (P3. 086). (pp. P3. 086). Vol. 90. Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology. Published, 04/2018.
• S Josh & Martin Bauer, Klas Modin (2017). Diffeomorphic random sampling using optimal information transport. Springer, Cham. 135-142. Published, 11/2017.
• Markus Foote & Pouya Sabouri, Amit Sawant, Sarang Joshi (2017). Rank Constrained Diffeomorphic Density Motion Estimation for Respiratory Correlated Computed Tomography. Springer, Cham. 177-185. Published, 09/2017.
• Stefan Sommer & Alexis Arnaudon, Line Kuhnel, Sarang Joshi (2017). Bridge simulation and metric estimation on landmark manifolds. Springer, Cham. 79-91. Published, 09/2017.
• Sarang Joshi & M Jorge Cardoso, Tal Arbel, Enzo Ferrante, Xavier Pennec, Adrian V Dalca, Sarah Parisot (2017). Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics:. Springer. Published, 09/2017.
• Sarang Joshi & Martin Bauer, Klas Modin (2017). On geodesic completeness for Riemannian metrics on smooth probability densities. Springer Berlin Heidelberg. Vol. 56, 113. Published, 08/2017.
• Xavier Pennec & X Pennec, S Joshi, M Nielsen, T Fletcher, S Durrleman (2017). Preface MFCA 2017. Vol. 10551. Springer Verlag. Published, 08/2017.
• P Sabouri & M Foote, M Ranjbar, M Tajdini, S Mossahebi, S Joshi, A Sawant (2017). a Novel Method Using Surface Monitoring to Capture Breathing-induced Cycle-to-cycle Variations with 4dct. Medical Physics. Vol. 44, 3312. Published, 06/2017.
• Diffeomorphic Density Registration in Thoracic Computed Tomography. Published, 10/2016.
  https://link.springer.com/chapter/10.1007/978-3-31...
• Deformation Estimation with Automatic Sliding Boundary Computation,. Published, 10/2016.
  https://link.springer.com/chapter/10.1007/978-3-31...
• Hierarchical geodesic models in diffeomorphisms,International Journal of Computer Vision. Published, 03/2016.
  https://link.springer.com/article/10.1007/s11263-0...
• Mobile C-arm 3D Reconstruction in the Presence of Uncertain Geometry C Rottman, L McBride, A Cheryauka, R Whitaker, S Joshi Medical Image Computing and Computer-Assisted Intervention--MICCAI 2015, 692-699. Published, 10/2015.
• Hierarchical Geodesic Models in Diffeomorphisms N Singh, J Hinkle, S Joshi, PT Fletcher International Journal of Computer Vision, 1-23. Published, 08/2015.
• Diffeomorphic density matching by optimal information transport M Bauer, S Joshi, K Modin SIAM Journal on Imaging Sciences 8 (3), 1718-1751. Published, 08/2015.
• Multiscale MRF optimization for robust registration of 2D biological data JS Preston, S Joshi, R Whitaker Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on, 302-305. Published, 04/2015.
• Cardenas, Valerie A., Chao, Linda L., Fletcher, P. Thomas, Joshi, Sarang, Schuff, Norbert, Tosun, Duygu & Weiner, Michael W. (2014). Voxel-Wise Co-analysis of Macro- and Microstructural Brain Alteration in Mild Cognitive Impairment and Alzheimer's Disease Using Anatomical and Diffusion MRI. Wiley-Blackwell. , no-no. Published, 2014.
• Cheung, Y, Hinkle, J, Joshi, S & Sawant, A (2014). SU-E-J-170: Beyond Single-Cycle 4DCT: Maximum a Posteriori (MAP) Reconstruction-Based Binning-Free Multicycle 4DCT for Lung Radiotherapy. American Association of Physicists in Medicine (AAPM). Vol. 41(6), 195-196. Published, 2014.
• Joshi, Sarang, King, Richard D., Marron, J.S., Samuel Preston, J., Singh, Nikhil, Thomas Fletcher, P. & Weiner, Michael W. (2014). Quantifying anatomical shape variations in neurological disorders. Elsevier BV. Vol. 18(3), 616-633. Published, 2014.
• Joshi, Sarang, Tosun, Duygu & Weiner, Michael W. (2014). Multimodal MRI-based imputation of the A β + in early mild cognitive impairment. Wiley-Blackwell. Vol. 1(3), 160-170. Published, 2014.
• Charon, Nicolas, Durrleman, Stanley, Gerig, Guido, Joshi, Sarang, Korenberg, Julie R., Prastawa, Marcel & Trouvé, Alain (2014). Morphometry of anatomical shape complexes with dense deformations and sparse parameters. Elsevier BV. Vol. 101, 35-49. Published, 2014.
• Hinkle, Jacob, Fletcher, P. Thomas & Joshi, Sarang (2014). Intrinsic Polynomials for Regression on Riemannian Manifolds. Springer Science + Business Media. Vol. 50(1-2), 32-52. Published, 2014.
• Fletcher, P. Thomas, Hinkle, Jacob, Joshi, Sarang & Singh, Nikhil (2014). An efficient parallel algorithm for hierarchical geodesic models in diffeomorphisms. . , 341-344. Published, 2014.
• Alley, Marcus, Hinkle, Jacob, Joshi, Sarang, Keall, Paul, Loo Jr., Billy W., Pauly, Kim Butts, Sawant, Amit & Vasanawala, Shreyas (2014). Investigating the Feasibility of Rapid MRI for Image-Guided Motion Management in Lung Cancer Radiotherapy. Hindawi Publishing Corporation. Vol. 2014, 1-6. Published, 06/2014.
• Allassonnière, Stéphanie, Durrleman, Stanley & Joshi, Sarang (2013). Sparse Adaptive Parameterization of Variability in Image Ensembles. Springer Science + Business Media. Vol. 101(1), 161-183. Published, 2013.
• Joshi, Sarang, Tosun, Duygu & Weiner, Michael W. (2013). Neuroimaging predictors of brain amyloidosis in mild cognitive impairment: sMRI Predictors of Amyloidosis. Wiley-Blackwell. , n/a-n/a. Published, 2013.
• Anderton, Larry, Cheryauka, Arvidas, Joshi, Sarang, Preston, J. Samuel, Rottman, Caleb & Whitaker, Ross T. (2013). Multi-layer Deformation Estimation for Fluoroscopic Imaging. Springer Science + Business Media. Vol. 7917, 123-134. Published, 2013.
• Joshi, Sarang, Nielsen, Mads & Pennec, Xavier (2013). Mathematical Methods for Medical Imaging. Springer Science + Business Media. Vol. 105(2), 109-110. Published, 2013.
• Hinkle, Jacob & Joshi, Sarang (2013). IDiff: Irrotational Diffeomorphisms for Computational Anatomy. Springer Science + Business Media. Vol. 7917, 754-765. Published, 2013.
• Fletcher, P. Thomas, Hinkle, Jacob, Joshi, Sarang & Singh, Nikhil (2013). A Hierarchical Geodesic Model for Diffeomorphic Longitudinal Shape Analysis. Springer Science + Business Media. Vol. 7917, 560-571. Published, 2013.
• Fletcher, P. Thomas, Hinkle, Jacob, Joshi, Sarang & Singh, Nikhil (2013). A vector momenta formulation of diffeomorphisms for improved geodesic regression and atlas construction. Institute of Electrical & Electronics Engineers (IEEE). , 1219-1222. Published, 2013.
• Sparse Adaptive Parameterization of Variability in Image Ensembles S Durrleman, S Allassonnière, S Joshi International Journal of Computer Vision, 1-23. Published, 01/2013.
  http://link.springer.com/article/10.1007%2Fs11263-...
• Tissue characterization using a phantom to validate four-dimensional tissue deformation M Szegedi, P Rassiah-Szegedi, V Sarkar, J Hinkle, B Wang, YH Huang, H Zhao ... Medical physics 39, 6065. Published, 10/2012.
  http://online.medphys.org/resource/1/mphya6/v39/i1...
• Genetic, Structural and Functional Imaging Biomarkers for Early Detection of Conversion from MCI to AD N Singh, A Wang, P Sankaranarayanan, P Fletcher, S Joshi Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012, 132-140. Published, 07/2012.
  http://link.springer.com/chapter/10.1007%2F978-3-6...
• Topology Preserving Atlas Construction from Shape Data without Correspondence Using Sparse Parameters S Durrleman, M Prastawa, J Korenberg, S Joshi, A Trouvé, G Gerig Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012, 223-230. Published, 06/2012.
  http://link.springer.com/chapter/10.1007%2F978-3-6...
• Metamorphic Geodesic Regression Y Hong, S Joshi, M Sanchez, M Styner, M Niethammer Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012, 197-205. Published, 06/2012.
  http://link.springer.com/chapter/10.1007%2F978-3-6...
• ISP: An Optimal Out-of-Core Image-Set Processing Streaming Architecture for Parallel Heterogeneous Systems LK Ha, J Kruger, JLD Comba, CT Silva, S Joshi Visualization and Computer Graphics, IEEE Transactions on 18 (6), 838-851. Published, 06/2012.
  http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumb...
• Special Section on the Eurographics Symposium on Parallel Graphics and Visualization (EGPGV)-ISP: An Optimal Out-of-Core Image-Set Processing Streaming Architecture for Parallel Heterogeneous Systems L Khanh Ha, J Krüger, JL Dihl Comba, CT Silva, S Joshi IEEE Transactions on Visualization and Computer Graphics 18 (5), 838. Published, 02/2012.
• Detection of crossing white matter fibers with high-order tensors and rank-k decompositions, F Jiao, Y Gur, C Johnson, S Joshi Information Processing in Medical Imaging, 538-549. Published, 07/2011.
  http://scholar.google.com/citations?view_op=view_c...
• Efficient probabilistic and geometric anatomical mapping using particle mesh approximation on GPUs,Linh Ha, Marcel Prastawa, Guido Gerig, John H Gilmore, Cláudio T Silva, Sarang Joshi,Journal of Biomedical Imaging, 2011. Published, 01/01/2011.
  http://scholar.google.com/citations?view_op=view_c...
• Gerber S, Tasdizen T, Thomas Fletcher P, Joshi S, Whitaker R; Alzheimers Disease Neuroimaging Initiative (ADNI). Manifold modeling for brain population analysis. Med Image Anal. 2010 Oct;14(5):643-53. Epub 2010 Jun 4. PubMed PMID: 20579930; PubMed Central PMCID: PMC3020141. Published, 10/2010.
• Singh N, Fletcher PT, Preston JS, Ha L, King R, Marron JS, Wiener M, Joshi S. Multivariate statistical analysis of deformation momenta relating anatomical shape to neuropsychological measures. Med Image Comput Comput Assist Interv. 2010;13(Pt 3):529-37. PubMed PMID: 20879441. Published, 09/2010.
• Ha L, Prastawa M, Gerig G, Gilmore JH, Silva CT, Joshi S. Image registration driven by combined probabilistic and geometric descriptors. Med Image Comput Comput Assist Interv. 2010;13(Pt 2):602-9. PubMed PMID: 20879365. Published, 09/2010.
• Davis BC, FletcherP, BulittE, JoshiS. Population Shape Regression from Random Design Data . International Journal of Computer Vision. 2010; 90(2):255-266. Published, 07/2010.
• Henninger HB, Maas SA, Shepherd JH, Joshi S, Weiss JA, Transversely isotropic distribution of sulfated glycosaminoglycans in human medial collateral ligament: a quantitative analysis. J Struct Biol 2009 Mar;165(3):176-83. Published, 03/01/2009.
• Fletcher PT, Venkatasubramanian S, Joshi S, The geometric median on Riemannian manifolds with application to robust atlas estimation. Neuroimage 2009 Mar;45(1 Suppl):S143-52. Published, 03/01/2009.

Presentations

• Bridge Simulation and Metric Estimation on Lie Groups and Orbit Spaces,Isaac Newton Institute for Mathematical Sciences, Workshop on Shape analysis and computational anatomy. Invited Talk/Keynote, Presented, 11/2017.
• Metric Estimation on Landmark Manifolds, Workshop on Applications-Driven Geometric Functional Data Analysis, . Invited Talk/Keynote, Presented, 10/2017.
• Samuel Gerber, Tolga Tasdizen, Sarang Joshi, Ross Whitaker, "On the Manifold Structure of the Space of Brain Images", In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2009). Conference Paper, Other, 09/11/2009.
• Jacob Hinkle, P. Thomas Fletcher, Brian Wang, Bill Salter, and Sarang Joshi. 4D MAP Image Reconstruction Incorporating Organ Motion. Proceedings of Information Processing in Medical Imaging, 21st International Conference (IPMI), 2009, Williamsburg, VA, USA, July 5-10, 2009. Conference Paper, Other, 07/30/2009.
• Jacob Hinkle, P. Thomas Fletcher, Brian Wang, Bill Salter, and Sarang Joshi. 4D MAP Image Reconstruction Incorporating Organ Motion. Proceedings of Information Processing in Medical Imaging, 21st International Conference (IPMI), 2009, Williamsburg, VA, USA, July 5-10, 2009. Conference Paper, Presented, 07/30/2009.
• Jacob Hinkle, P. Thomas Fletcher, Brian Wang, Bill Salter, and Sarang Joshi. 4D MAP Image Reconstruction Incorporating Organ Motion. Proceedings of Information Processing in Medical Imaging, 21st International Conference (IPMI), 2009, Williamsburg, VA, USA, July 5-10, 2009. Conference Paper, Presented, 07/30/2009.
• S.E. Geneser, R.M. Kirby, B. Wang, B. Salter and S. Joshi. Quantifying Uncertainty in Dose Deposition Resulting from Patient Breathing Variability. Proceedings of American Association of Physicists in Medicine (AAPM) Annual Meeting, Anaheim, CA 2009. Conference Paper, Presented, 07/30/2009.
• J Hinkle, P Fletcher, B Wang, BJ Salter, S Joshi, Development and testing of a novel, Maximum A Posteriori (MAP) image reconstruction algorithm, Proceedings of American Association of Physicists in Medicine (AAPM) Annual Meeting, Anaheim, CA 2009. Conference Paper, Presented, 07/30/2009.
• Statistics of shape: Simple statistics on interesting spaces“,Random Fields and Stochastic Geometry, Banff International Research Station for Mathematical Innovation and Discovery, February 2009. Invited Talk/Keynote, Presented, 02/06/2009.

Languages

• English, fluent.

Software Titles

• Modeling the Shape of the Brain Connectome via Deep Neural Networks. A metric CNN is a simple convolutional encoder-decoder neural network (CEDNN) trained to estimating a Riemannian manifold that represents the brain connectome faithfully using a covariant derivative loss. The network directly maps from multiple vector fields (4D output) to a Riemannian metric field (5D output), acting as the manifold so we can run geodesic tractography on it and also construct connectome Riemannian manifold atlas from tractography data to statistically quantify the geometric variability of structural connectivity across a population. Estimating a Riemannian metric takes less than a few hours and only requires a single GPU, depending on resolution. Inference a Riemannian metric from an optimized MetricCNN takes less than a second, again depending on resolution. Release Date: 06/2022. Inventors: 🏜️ Haocheng Dai, 🐊 Martin Bauer, 🌊 P. Thomas Fletcher, 🏜️ Sarang Joshi.
• Integrated Construction of Multimodal Atlases with Structural Connectomes in the Space of Riemannian Metrics. The structural network of the brain, or structural connectome, can be represented by fiber bundles generated by a variety of tractography methods. While such methods give qualitative insights into brain structure, there is controversy over whether they can provide quantitative information, especially at the population level. In order to enable populationlevel statistical analysis of the structural connectome, we propose representing a connectome as a Riemannian metric, which is a point on an infinite-dimensional manifold. We equip this manifold with the Ebin metric, a natural metric structure for this space, to get a Riemannian manifold along with its associated geometric properties. We then use this Riemannian framework to apply object-oriented statistical analysis to define an atlas as the Fréchet mean of a population of Riemannian metrics. This formulation ties into the existing framework for diffeomorphic construction of image atlases, allowing us to construct a multimodal atlas by simultaneously integrating complementary white matter structure details from DWMRI and cortical details from T1-weighted MRI. We illustrate our framework with 2D data examples of connectome registration and atlas formation. Finally, we build an example 3D multimodal atlas using T1 images and connectomes derived from diffusion tensors estimated from a subset of subjects from the Human Connectome Project. Release Date: 01/2022. Inventors: Kristen M Campbell, Haocheng Dai, Zhe Su, Martin Bauer, P Thomas Fletcher, Sarang C Joshi.
• AtlasWerks. Atlas Development Tools. Release Date: 01/2012. Inventors: Sarang Joshi, Sam Preston, Jacob Hinkel.
• AlasWerks. AtlasWerks is an open-source (BSD license) software package for medical image atlas generation. Such atlases are a widely-used tool for image segmentation, and deformations generated using these techniques are used for statistical analysis of brain shape to identify patterns of change related to disease progression. The AtlasWerks software package provides efficient CPU and GPU implementations of nonlinear deformation algorithms based on the Large Deformation Diffeomorphic Metric Mapping (LDMM) framework for single machines and clusters, command line frontends for atlas and deformation generation, and a number of utility programs for handling 3D medical image data. Release Date: 01/01/2011.
• AtlasWerks. AtlasWerks is a set of high-performance tools for diffeomorphic 3D image registration and atlas building. Applications support atlas building on GPUs, clusters, and clusters of GPUs. Release Date: 05/2010. Inventors: Sarang Joshi, Sam Preston, Linh Ha, Claudio Silva.