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Radiation Oncology
Deformable Registration

Piper JW. Evaluation of An Intensity-Based Free-Form Deformable Registration Algorithm. Medical Physics. June 2007;34(6):2353-2354.

Nelson AS, Duchateau M, Piper JW, Verellen D, De Ridder M. Evaluation of a Free-Form Intensity Based Deformable Registration Method Using the POPI Model. Med Phys 2014; 41:202.

Pirozzi S, Piper J, Nelson A, Duchateau M, Verellen D, De Ridder M. A Novel Framework for Deformable Registration Evaluation and Quality Assurance. IJROBP 2013; 87(2):S719.

Pirozzi S, Piper J, Nelson A, Duchateau M, Verellen D, De Ridder M. A Novel Framework for User-Intervened Correction of Deformable Registration. IJROBP 2013; 87(2):S144.

Nelson AS, Duchateau M, Piper WJ, Verellen D, De Ridder M. Deformable Dose Mapping Accuracy Using a Framework for User-Intervened Correction of Deformable Registration. Med Phys 2014; 41:207.

Fogh SE, Kubicek GJ, Axelrod R, Keane WM, Piper JW, Xiao Y, Machtay M. Utility of Deformable PET Fusion Gross Tumor Volumes in Head & Neck Malignancies. ASTRO Translational Advances in Radiation Oncology and Cancer Imaging 2008 Poster Presentation.

Piper JW. Evaluation of a CT to Cone-Beam CT Deformable Registration Algorithm. IJROBP. 2007;69(3 Suppl S):S418-419.

Nelli Flavio Enrico, Harwood Jeffrey Roy. A Method for Assessing the Dosimetric Consistency of Single Phase 4DCT Dose Accumulation Based on Deforming Image Registration. Physica Medica September 2016; 32(3):275.

Jason Pukala, Perry B. Johnson, Amish P. Shah, Katja M. Langen, Frank J. Bova, Robert J. Staton, Rafael R. Mañon, Patrick Kelly, and Sanford L. Meeks. Benchmarking of Five Commercial Deformable Image Registration Algorithms for Head and Neck Patients. Journal of Applied Clinical Medical Physics, VOLUME 17, NUMBER 3, 2016.

Perry B. Johnson, Kyle R. Padgett, Kuan L. Chen, Nesrin Dogan. Evaluation of the Tool "Reg Refine" for User-Guided Deformable Image Registration. Journal of Applied Clinical Medical Physics, VOLUME 17, NUMBER 3, 2016. *Some details about the deformation algorithm are incorrect and will be corrected in a future correction in the journal.

Piper J, Nelson A, Harper J.  Deformable Image Registration in MIM Maestro® Evaluation and Description.  March 2018. (White Paper)

Nelson AD.  Validation of Manual and Assisted Alignment Techniques.  June 2018. (White Paper)

Piper JW, Richmond JH, Nelson AS. VoxAlign Deformation Engine®. July 2018. (White Paper)

Adaptive Radiotherapy

Hu, K, Surapaneni, A. Value of Kilovoltage Cone Beam CT (CBCT) to Track Dose in the Adaptive Radiation Treatment of Head and Neck Cancer. RSNA 2008 Scientific Assembly and Annual Meeting, Feb 18 - Feb 20, 2008, Chicago IL.

Li W, Vassil A, Zhong Y, Xia P. Evaluation of Atlas-Based Auto-Segmentation on Daily In-Room CT for Prostate Cancer. Med Phys 2012; 39:3676.

Fragoso RC, Piper JW, Nelson AS, Harrison AS, Machtay M, Xiao Y. Evaluation of a Deformable Re-Contouring Method for Adaptive Therapy. ACRO Annual Meeting 2008 Poster Presentation.

Dyess A, Seuntjens J, Poon E, Parker W. Dosimetric Assessment of Treatment Using CBCT Images. Med Phys 2012; 39:3700.

Louise S. H. Bendall, Maria Najim, Rachel Stensmyr, Emily Flower, Shan Yau, David I. Thwaites & Jonathan R. Sykes (2015) Performance Evaluation of Head and Neck Contour Adaptation with Cone Beam CT Using Two Commercial Software Systems. Acta Oncologica, 54:9, 1693-1697.

Christian A. Hvid, Ulrik V. Elstrøm, Kenneth Jensen, Markus Alber & Cai Grau (2016): Accuracy of Software-Assisted Contour Propagation from Planning CT to Cone Beam CT in Head and Neck Radiotherapy. Acta Oncologica.

Atlas Segmentation and Post-Processing

Mariangela La Macchia, Francesco Fellin, Maurizio Amichetti, Marco Cianchetti, Stefano Gianolini, Vitali Paola, Antony J Lomax, Lamberto Widesott. Systematic Evaluation of Three Different Commercial Software Solutions for Automatic Segmentation for Adaptive Therapy in Head-and-Neck, Prostate and Pleural Cancer. Radiation Oncology 2012, 7:160.

Nelson AS, Brockway J, Liu M, Javorek A, Pirozzi S, Piper JW. Evaluation of an Atlas-Based Segmentation Method for Prostate MRI. IJROBP 2014; 90(1):S419-420.

Nelson AS, Piper JW, Javorek AR, Pirozzi SD, Lu M. Comparison of Two Atlas-Based Segmentation Methods for Head and Neck Cancer Including RTOG-Defined Lymph Node Levels. IJROBP 2014; 90(1):S882.

Horvat M, Nelson AS, Pirozzi SD. Time Savings of a Multi-Atlas Approach for Liver Segmentation. J Nucl Med. 2014; 55 (Supplement 1):1523.

Hu K, Lin A, Young A, Kubicek G, Piper JW, Nelson AS, Dolan J, Masino R, Machtay M. Timesavings for Contour Generation in Head and Neck IMRT: Multi-Institutional Experience with an Atlas-Based Segmentation Method. IJROBP. 2008; 72(1) Suppl: S391.

Lin A, Kubicek G, Piper JW, Nelson AS, Dicker AP, Valicenti RK. Atlas-Based Segmentation in Prostate IMRT: Timesavings in the Clinical Workflow. IJROBP. 2008; 72(1) Suppl: S328-329.

Ennis RD, Young AV, Wernick I, Evans AE. Atlas-Based Segmentation Improves Consistency and Decreases Time Required for Contouring Postoperative Endometrial Cancer Nodal Volumes. International Journal of Radiation Oncology * Biology * Physics. 1 November 2009 (Vol. 75, Issue 3, Supplement, Page S367).

Pirozzi SD, Horvat M, Nelson AS, Piper JW. Atlas-Based Segmentation: Evaluation of a Multi-Atlas Approach for Prostate Cancer. Accepted for Presentation at the ASTRO Annual Meeting 2012.

Pirozzi S, Horvat M, Piper J, Nelson AS. Atlas-Based Segmentation: Evaluation of a Multi-Atlas Approach for Lung Cancer. Med Phys 2012; 39:3677.

Pirozzi SD, Nelson AS, Piper JW. Atlas-Based Segmentation: Comparison of Multiple Segmentation Approaches for Lymph Level Targets and Normal Structures in Head and Neck Cancer. International Journal of Radiation Oncology * Biology * Physics 1 October 2011 (Vol.81, Issue 2, Supplement, Page S828).

Landau E, Hu K, Oppenheimer A, Skinner WKJ, Young A, Piper JW, Kalnicki S, Harrison LB. Automatic Contouring of Vital Swallowing Structures Using an Atlas-based Segmentation Method: A Time Saving and Toxicity Assessment. Accepted for Presentation at the ASTRO Annual Meeting 2009.

PET Segmentation

Rohren EM, Etchebehere EC, Araujo JC, Hobbs BP, Swanston NM, Everding M, Moody T, Macapinlac HA. Determination of Skeletal Tumor Burden on 18F-Fluoride PET/CT. J Nucl Med. 2015; 56:1507-1512.

Zhang G, Han D, Ma C, Lu J, Sun T, Liu T, Zhu J, Zhou J, Yin Y. Gradient-Based Delineation of the Primary GTV on FLT PET in Squamous Cell Cancer of the Thoracic Esophagus and Impact on Radiotherapy Planning. Radiation Oncology 2015, 10:11.

Sridhar P, Mercier G, Tan J, Truong MT, Daly B, Subramaniam RM. FDG PET Metabolic Tumor Volume Segmentation and Pathologic Volume of Primary Human Solid Tumors. AJR Am J Roentgenol 2014; 202(5):1114-9.

Nelson AS, Faulhaber PF, Pirozzi SD, Harper JW, Piper JW. Comparison of Gradient PET Segmentation from a Multi-Modality PET/CT Measurement Tool to Gradient PET Segmentation Alone. J Nucl Med. 2014; 55 (Supplement 1):1522.

Werner-Wasik M, Nelson D, Choi W, Arai Y, Faulhaber P, Kang P, Almeida F, Xiao Y, Ohri N, Brockway K, Piper J, Nelson A. What is the Best Way to Contour Lung Tumors on PET Scans: Multi-Observer Validation of a Gradient-Based Method Using a NSCLC Digital PET Phantom. IJROBP 2012; 82(3):1164-1171.

Fogh S, Karancke J, Nelson AS, McCue P, Axelrod R, Werner-Wasik W. Pathologic Correlation of PET-CT Based Auto-Contouring for Radiation Planning in Lung Cancer. Presented at the World Conference on Lung Cancer Meeting in 2009.

Werner-Wasik M, Kang P, Choi W, Ohri N, Faulhaber P, Nelson D, Nelson A, Piper J, Shen Z, Pirozzi S. Comparison of PET Contouring Methods in Patients With Early-Stage Resected Non-Small Cell Lung Cancer (NSCLC): A Pathologic–Imaging Correlation IJROBP 2013; 87(2):S540.

Nelson AS, Werner-Wasik M, Choi W, et al. Evaluation of Gradient PET Segmentation for Total Lesion Glycolysis Compared to Thresholds and Manual Contouring. J Nucl Med. 2011; 52 (Supplement 1):2077.

Nelson AD, Nelson AS. Tissue Segmentation in PET Image Volumes. June 2018. (White Paper)

PET Treatment Response

Etchebehere EC, Araujo JC, Fox PS, Swanston NM, Macapinlac HA, Rohren EM. Prognostic Factors in Patients Treated with 223Ra: The Role of Skeletal Tumor Burden on Baseline 18F-Fluoride PET/CT in Predicting Overall Survival. J Nucl Med. 2015; 56:1177-1184.

Yu J, Cooley T, Truong MT, Mercier G, Subramaniam RM. Head and Neck Squamous Cell Cancers (Stages III and IV) Induction Chemotherapy Assessment: Value of FDG Volumetric Imaging Parameters. J Med Imaging Radiat Oncol 2014; 58(1):18-24.

Davison J, Mercier G, Russo G, Subramaniam RM. PET-Based Primary Tumor Volumetric Parameters and Survival of Patients with Non-Small Cell Lung Carcinoma. AJR Am J Roentgenol 2013; 200(3):635-40.

Shah B, Srivastava N, Hirsch AE, et al. Intra-Reader Reliability of FDG PET Volumetric Tumor Parameters: Effects of Primary Tumor Size and Segmentation Methods. Ann Nucl Med. 2012 Nov;26(9):707-14.

Liao S, Penney BC, Wroblewski K, et al. Prognostic Value of Metabolic Tumor Burden on 18FFDG PET in Nonsurgical Patients with Non-Small Cell Lung Cancer. Eur J Nucl Med Mol Imaging 2012; 39(1):27-38.

Clinical Trials

Deep Learning Auto-Contouring

C Halley*, H Wan, A Kruzer, D Pittock, D Darkow, M Butler, N Cole, M Bending, P Jacobs, AS Nelson. Improved Auto-Segmentation for CT Male Pelvis: Comparison of Deep Learning to Traditional Atlas Segmentation Methods. 2020 Joint AAPM | COMP Virtual Meeting Poster Presentation.

NM Cole*, H Wan, J Niedbala, YK Dewaraja, A Kruzer, D Pittock, C Halley, AS Nelson. Impact of a 3D Convolution Neural Network Method On Liver Segmentation: An Accuracy and Time-Savings Evaluation. 2020 Joint AAPM | COMP Virtual Meeting Poster Presentation.

A Kruzer*, H Wan, M Bending, C Halley, D Darkow, D Pittock, N Cole, P Jacobs, AS Nelson. Comparison of a 3D Convolutional Neural Network Segmentation Method to Traditional Atlas Segmentation for CT Head and Neck Contours. 2020 Joint AAPM | COMP Virtual Meeting Poster Presentation.

Biological Effective Dose

Jacobs. P, Nelson A, Liu I.  Biological Effective Dose and Tumor Control Probability Modeling. January 2022. (White Paper)