The Cancer Imaging Archive (TCIA) Public Access

Space shortcuts

Child pages
  • Publications

Versions Compared

Old Version 164

changes.mady.by.user Sean Berryman

Saved on

compared with

New Version 165

changes.mady.by.user Sean Berryman

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

  1. Prior, F., Smith, K., Sharma, A., Kirby, J., Tarbox, L., Clark, K., Bennett, W., Nolan, T., Freymann, J. (2017). The public cancer radiology imaging collections of The Cancer Imaging Archive. Nature Scientific Data, 4; 1-7. doi:10.1038/sdata.2017.124 

  2. Kohli, M., Morrison, J. J., Wawira, J., Morgan, M. B., & Hostetter, J., Genereaux, B., Hussain, M., Langer S. G. (2017). Creation and curation of the society of imaging informatics in medicine hackathon dataset. Journal of Digital Imaging, 1-4. doi:10.1007/s10278-017-0003-5

  3. Williamson, J.F., Das, S.K., Goodsitt, M.S., Deasy, J.O. (2017). Introducing the Medical Physics Dataset Article. Med. Phys. 44(2); 349-350. doi: 10.1002/mp.12003
  4. Nida, N; Khan, M. (2016). Efficient Colorization of Medical Imaging based on Colour Transfer Method. U.G. Proceedings of the Pakistan Academy of Sciences: B. Life and Environmental Sciences, 53(4); 253-261. (link)
  5. Kalpathy-Cramer, J., Zhao, B., Goldgof, D., Gu, Y., Wang, X., Yang, H., Tan, Y., Gillies, R., Napel, S. (2016). A Comparison of Lung Nodule Segmentation Algorithms: Methods and Results from a Multi-institutional Study. J Digit Imaging 29(4):476-487. DOI: 10.1007/s10278-016-9859-z

  6. Parks, C.L., Monson, K.L. (2016). Automated Facial Recognition of Computed Tomography-Derived Facial Images: Patient Privacy Implications. Journal of Digital Imaging. 1-11. DOI: 10.1007/s10278-016-9932-7

  7. Huang, B.E., Mulyasasmita, W., Rajagopal, G. (2016). The Path from Big Data to Precision Medicine. Expert Review of Precision Medicine and Drug Development, 1(2):129-143. (link)

  8. Chatellier, G., Varlet, V., Blachier-Poisson, C. (2016). "Big data" and "open data": What kind of access should researchers enjoy? Therapie. 71(1); 97-105, 107-114.(link)
  9. Benedict, S.H., Hoffman K., Martel, M.K., Abernethy, A.P., Asher, A.L., Capala, J., Chen, R.C., Chera, B., Couch, J., Deye, J., Efstathiou, J.A., Ford, E., Fraass, B.A., Gabriel, P.E., Huser, V., Kavanagh, B.D., Khuntia, D., Marks, L.B., Mayo, C., McNutt, T., Miller, R.S., Moore, K.L., Prior, F., Roelofs, E., Rosenstein, B.S., Sloan, J., Theriault, A., Vikram, B. (2016). Overview of the American Society for Radiation Oncology–National Institutes of Health–American Association of Physicists in Medicine Workshop 2015: Exploring Opportunities for Radiation Oncology in the Era of Big Data. International Journal of Radiation Oncology: Biology, Physics. 95(3):873-879 (link)
  10. Toga, A.W., Dinov, I.D. (2015). Sharing big biomedical data. Journal of Big Data. 2(1); 1-12. (link)
  11. Moore, S.M., Maffitt, D.R., Smith, K.E., Kirby, J.S., Clark, K.W., Freymann, J.B., Vendt, B.A., Tarbox, L.R., Prior, F.W. (2015). De-identification of Medical Images with Retention of Scientific Research Value. RadioGraphics. 35(3); 727-35. doi: 10.1148/rg.2015140244.
  12. Mayo, C.S., Deasy, J.O., Chera, B.S., Freymann, J., Kirby, J.S., Hardenberg, P.H. (2016). How Can We Effect Culture Change Toward Data-Driven Medicine? International Journal of Radiation Oncology: Biology, Physics. 95(3); 916-21. (link)
  13. Kirby, J., Tarbox, L., Freymann, J., Jaffe, C., Prior, F. (2015). "TU-AB-BRA-03: The Cancer Imaging Archive: Supporting Radiomic and Imaging Genomic Research with Open-Access Data Sets." Medical physics 42(6): 3587-3587.  DOI: 10.1118/1.4925508
  14. GIllies, R.J., Kinahan, P.E., Hricak, H., (2016). Radiomics: Images Are More than Pictures, They Are Data. Radiology, 278(2); 563-77. (link)
  15. Fedorov, A., Clunie, D., Ulrich, E., Bauer, C., Wahle, A., Brown, B., Onken, M., Riesmeier, J., Pieper, S., Kikinis, R., Buatti, J., Beichel, R.R. (2016). DICOM for quantitative imaging biomarker development: A standards based approach to sharing of clinical data and structured PET/CT analysis results in head and neck cancer research. PeerJ, 4(e2057). (link)
  16. Commean, P.K., Rathmell, J.M., Clark, K.W., Maffitt, D.R., Prior, F.W. (2015). A Query Tool for Investigator Access to the Data and Images of the National Lung Screening Trial. Journal of Digital Imaging. 1-9. (paper)
  17. Bourne, P.E. (2015). DOIs for DICOM Raw Images: Enabling Science Reproducibility. Radiology. 275(1); 3-4. link. 
  18. Armato, S.G., Hadjiiski, L., Tourassi, G.D., Drukker, K., Giger, M.L., Li, F., Redmond, G., Farahani, K., Kirby, J.S., Clarke, L.P. (2015). Special Section Guest Editorial: LUNGx Challenge for computerized lung nodule classification: reflections and lessons learned. Journal of Medical Imaging. 2(2); 10.1117/1.JMI.2.2.020103
  19. Herskovits, E.H. (2014). Quantitative Radiology: Applications to Oncology. Emerging Applications of Molecular Imaging to Oncology. 124; 1-30. (link)
  20. Gutman, D.A., Dunn Jr., W.D., Cobb, J., Stoner, R.M., Kalpathy-Cramer, J., Erickson, B. (2014) Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer. Frontiers in Neuroinformatics. 8. (paper)
  21. Erickson, B.J., Fajnwaks, P., Langer, S.G., and Perry, J. (2014) Multisite Image Data Collection and Management Using the RSNA Image Sharing Network., Translational oncology, 7(1); 36-39. (paper)
  22. Prior, F.W., Clark, K., Commean, P., Freymann, J., Jaffe, C., Kirby, J., Moore, S., Smith, K., Tarbox, L., Vendt, B. (2013) TCIA: an information resource to enable open science. Engineering in Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE. (paper)
  23. Gutman, D.A., Cobb, J., Somanna, D., Park, Y., Wang, F., Kurc, T., Saltz, J.H., Brat, D.J., Cooper, L.A. (2013) Cancer Digital Slide Archive: an informatics resource to support integrated in silico analysis of TCGA pathology data. Journal of the American Medical Informatics Association. 20(6); 1091-1098. doi: 10.1136/amiajnl-2012-001469 (paper)
  24. Clark, K., Vendt, B., Smith, K., Freymann, J., Kirby, J., Koppel, P., Moore, S., Phillips, S., Maffitt, D., Pringle, M., Tarbox, L., Prior, F. (2013). The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository, Journal of Digital Imaging, 26(6), 1045-1057. (paper)
  25. Villani, L., and Prati, R.C. (2012). Classificação Multirrótulo na Anotação Automática de Nódulo Pulmonar Solitário. Congresso Brasileiro de Informática em Saúde, Citado na. (paper)
  26. Mongkolwat, P., Channin, D.S., Kleper, V., Rubin, D.L. (2012). Informatics in Radiology: An Open-Source and Open-Access Cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder. Radiographics, 32(4); 1223-32. (paper).
  27. Jaffe, C.C. (2012). Imaging and Genomics: Is There a Synergy? Radiology. 264(2); 329-31.(paper).

  28. Freymann, J.B., Kirby, J.S., Perry, J.H., Clunie, D.A., Jaffe, C.C. (2012). Image data sharing for biomedical research—meeting HIPAA requirements for de-identification. Journal of Digital Imaging, 25(1). 14-24. (paper)

Radiogenomics

  1. Smits, M., & van den Bent, M. J. (2017). Imaging correlates of adult glioma genotypes. Radiology, 284(2). http://dx.doi.org/10.1148/radiol.2017151930

  2. Lehrer, M., Bhadra, A., Ravikumar, V., Chen, J. Y., Wintermark, M., Hwang, S. N., Holder, C. A., Huang, E. P., Fevrier-Sullivan, B., Freymann, J. B., Rao, A., & TCGA Glioma Phenotype Research Group. (2017). Multiple-response regression analysis links magnetic resonance imaging features to de-regulated protein expression and pathway activity in lower grade glioma. Oncoscience, 4, 57-66. doi:10.18632/oncoscience.353

  3. Demerath, T., Simon-Gabriel, C.P., Kellner, E., Schwarzwald, R., Lange, T., Heiland, D.H., Reinacher, P., Staszewski, O., Mast, H., Kiselev, V.G., Egger, K., Urbach, H., Weyerbrock, A., Mader, I. (2017). Mesoscopic imaging of glioblastomas: Are diffusion, perfusion and spectroscopic measures influenced by the radiogenetic phenotype? Neuroradiology Journal, 30(1); 36-47. doi: 10.1177/1971400916678225

  4. Liu, T.T., Achrol, A.S., Mitchell, L.A., Rodriguez, S.A., Feroze, A., Iv, M., Kim, C., Chaudhary, N., Gevaert, O., Stuart, J.M., Harsh, G.R., Chang, S.D., Rubin, D.L. (2016). Magnetic resonance perfusion image features uncover an angiogenic subgroup of glioblastoma patients with poor survival and better response to antiangiogenic treatment. Neuro-Oncology, 1-11. doi: 10.1093/neuonc/now270

  5. Schrock, M., Batar, B., Lee, J., Druck, T., Ferguson, B., Cho, J., Akakpo, K., Hagrass, H., Heerema, N., Xia, F. (2016). Wwox–Brca1 interaction: role in DNA repair pathway choice. Oncogene, 1-13. doi: 10.1038/onc.2016.389.

  6. Song, S.E., Bae, M.S., Chang, J.M., Cho, N., Ryu, H.S., Moon, W.K. (2016). MR and mammographic imaging features of HER2-positive breast cancers according to hormone receptor status: a retrospective comparative study. Acta Radiologica. 58(7), 792-799.  doi: 10.1177/0284185116673119

  7. McCann, S.M., Jiang, Y., Fan, X., Wang, J. Antic, T., Prior, F., VanderWeele, D., Oto, A. Quantitative Multiparametric MRI Features and PTEN Expression of Peripheral Zone Prostate Cancer: A Pilot Study. American Journal of Roentgenology 206(3); 559-565 doi: 10.2214/AJR.15.14967

  8. Katrib, A., Hsu, W., Bui, A., Xing, Y. (2016). “Radiotranscriptomics”: A synergy of imaging and transcriptomics in clinical assessment.Quantitative Biology. 1-12. doi: 10.1007/s40484-016-0061-6

  9. Bai, H.X., Lee, A.M., Yang, L., Zhang, P., Davatzikos, C., Maris, J.M., Diskin, S.J. (2016). Imaging genomics in cancer research: Limitations and promises.The British Journal of Radiology, 89(1061); doi: 10.1259/bjr.20151030

  10. Zhu, Y., H. Li, et al. (2015). TU-CD-BRB-06: Deciphering Genomic Underpinnings of Quantitative MRI-Based Radiomic Phenotypes of Invasive Breast Carcinoma.Medical physics 42(6): 3603-3603. doi: 10.1118/1.4925591

  11. Tomczak, K., Czerwińska, P., Wiznerowicz, M. (2015). The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.Contemp Oncol (Pozn). 19(1A); A68-A77. doi: 10.5114/wo.2014.47136

  12. Shinegare, A.B., Vikram, R., Jaffe, C., Akin, O., Kirby, J., Huang, E., Freymann, J., Sainani, N.I., Sadow, C.A., Bathala, T.K., Rubin, D.L., Oto, A., Heller, M.T., Surabhi, V.R., Katabathina, V., Silverman, S.G. (2015). Radiogenomics of clear renal cell carcinoma: Preliminary Findings of The Cancer Genome Atlas-Renal Cell Carcinoma (TCGA-RCC) Imaging Research Group.Abdominal Imaging, 40(6). 1684-1692. doi: 10.1007/s00261-015-0386-z

  13. Pope, W.B. (2015). Genomics of Brain Tumor Imaging. Neuroimaging Clinics of North America. 25(1); 105-19. doi: 10.1016/j.nic.2014.09.006

  14. Gutman, D.A., Dunn Jr., W.D., Grossmann, P., Cooper, L.A., Holder, C.A., Ligon, K.L., Alexander, B.M., Aerts, H.J. (2015). Somatic mutations associated with MRI-derived volumetric features in glioblastoma.Neuroradiology, 57(12); 1227-1237. doi: 10.1007/s00234-015-1576-7

  15. Feldman, M., Piazza, M.G., Edwards, N.A., Ray, Chaudhury, A., Maric, D., Merrill, M.J., Zhuang, Z., Chittiboina, P. (2015). 137 Somatostatin Receptor Expression on VHL-Associated Hemangioblastomas Offers Novel Therapeutic Target.Neurosurgery 62. (CN_suppl_1); 209-210. doi: 10.1227/01.neu.0000467099.84064.25

  16. Colen R, Foster I, Gatenby R, Giger ME, Gillies R, Gutman D, Heller M, Jain R, Madabhushi A, Madhavan S, Napel S, Rao A, Saltz J, Tatum J, Verhaak R, Whitman G. (2014). NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures. Translational Oncology. 7(5); 556-69. doi: 10.1016/j.tranon.2014.07.007.
  17. Rao A. (2013).  Exploring relationships between multivariate radiological phenotypes and genetic features: A case-study in Glioblastoma using the Cancer Genome Atlas, Global Conference on Signal and Information Processing (GlobalSIP), doi: 10.1109/GlobalSIP.2013.6736815

  18. Gevaert, O., Xu, J., Hoang, C.D., Leung, A.N., Xu, Y., Quon, A., Rubin, D.L., Napel, S., Plevritis, S.K. (2012) Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results. Radiology. 264(2); 387-96. doi: 10.1148/radiol.12111607

Radiomics

  1. Sutton, E. J., Huang, E. P., Drukker, K., Burnside, E. S., Li, H., Net, J. M., Rao, A., Whitman, G. J., Zuley, M., Ganott, M., Bonaccio, E., Giger, M. L., Morris, E. A. (2017). Breast MRI radiomics: Comparison of computer- and human-extracted imaging phenotypes. European Radiology Experimental.  http://dx.doi.org/10.1186/s41747-017-0025-2

  2. Vani, N., Swomya, A., & Jayamma, N. (2017). MRI Brain tumor classification using support vector machine. International Research Journal of Engineering and Technology, 1724-1729. doi: 10.1109/SCEECS.2014.6804439

  3. Beichel, R.R., Smith, B.J., Bauer, C., Ulrich, E.J., Ahmadvand, P., Budzevich, M.M., Gillies, R.J., Goldgof, D., Grkovski, M., Hamarneh, G., Huang, Q., Kinahan, P.E., Laymon, C.M., Mountz, J.M., Muzi, J.P., Muzi, M., Nehmeh, S., Oborski, M.J., Tan, Y., Zhao, B., Sunderland, J.J., Buatti, J.M. (2017). Multi-site quality and variability analysis of 3D FDG PET segmentations based on phantom and clinical image data. Med. Phys. 44(2); 479-496. doi: 10.1002/mp.12041
  4. Vallières, M., Kay-Rivest, E., Perrin, L.J., Liem, X., Furstoss, C., Aerts, H.J.W.L., Khaouam, N., Nguyen-Tan, P.F., Want, C.-S., Sultanem, K., Seuntjens, J., Naqa, I.E. (2017). Radiomics strategies for risk assessment of tumour failure in head-and-neck cancer. Scientific Reports, (arXiv 1703.08516)
  5. Paredes, D., Saha, A., Mazurowski, M.A.(2017). Deep learning for segmentation of brain tumors: can we train with images from different institutions? SPIE Medical Imaging: Computer-Aided Diagnosis, doi: 10.1117/12.2255696
  6. Kumar, S., Dharun. (2017). Combination of fuzzy c-means clustering and texture pattern matrix for brain MRI segmentation. Biomedical Research, 28(5) 
  7. Nabizadeh N, Kubat M. Automatic Tumor Segmentation in Single-Spectral MRI Using A Texture-Based and Contour-Based Algorithm. ScienceDirect, 77: 1-10. doi: 10.1016/j.eswa.2017.01.036

  8. Kaur, T., Saini, B.S., Gupta, S. (2016). A joint intensity and edge magnitude-based multilevel thresholding algorithm for the automatic segmentation of pathological MR brain images. Neural Computing and Applications. 1-24. doi: 10.1007/s00521-016-2751-4

  9. Song, J., Liu, Z., Zhong, W., Huang, Y., Ma, Z., Dong, D., Liang, C., Tian, J. (2016). Non-small cell lung cancer: quantitative phenotypic analysis of CT images as a potential marker of prognosis. Scientific Reports. 6:38282:1-9. doi: 10.1038/srep38282

  10. Crawford, L., Monod, A., Chen, A.X., Mukherjee, S., Rabadán, R. (2016). Topological Summaries of Tumor Images Improve Prediction of Disease Free Survival in Glioblastoma Multiforme. arXiv preprint arXiv:161106818. 

  11. Korfiatis, P., Kline, T.L., Erickson, B.J. (2016). Automated Segmentation of Hyperintense Regions in FLAIR MRI Using Deep Learning. J Tomography, 2(4) 334-340 DOI: 10.18383/j.tom.2016.00166

  12. Zheng, C., Wang, X., Feng, D. (Eds.). (2016). Topology guided demons registration with local rigidity preservation. 2016 IEEE 38th Annual International Conference Engineering in Medicine and Biology Society (EMBC). IEEE. doi: 10.1109/EMBC.2016.7590913

  13. Kotrotsou, A., Zinn, P.O., Colen, R.R. (2016). Radiomics in Brain Tumors: An Emerging Technique for Characterization of Tumor Environment. Magnetic Resonance Imaging Clinics of North America. 24(4); 719-29. doi: 10.1016/j.mric.2016.06.006

  14. Zhao, B., Tan, Y., Tsai, W.Y., Qi, J., Xie, C., Lu, L., Schwartz, L.H. (2016). Reproducibility of radiomics for deciphering tumor phenotype with imaging. Scientific Reports. 6:23428. doi: 10.1038/srep23428
  15. Li, H., Zhu, Y., Burnside, E.S., Huang, E., Drukker, K., Hoadley, K.A., Fan, C., Conzen, S.D., Zuley, M., Net, J.M., Sutton, E., Whitman, G.J., Morris, E., Perou, C.M., Ji, Y., Giger, M.L. (2016). Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set. npj Breast Cancer. doi: 10.1038/npjbcancer.2016.12
  16. Grossmann, P., Gutman, D.A., Dunn Jr., W.D., Holder, C.A., Aerts, H.J.W.L. (2016). Imaging-genomics reveals driving pathways of MRI derived volumetric tumor phenotype features in Glioblastoma. BMC Cancer. 16(611). doi: 10.1186/s12885-016-2659-5
  17. Zhu, Y., Li, H., Guo, W., Drukker, K., Lian, L., Giger, M.L., Ji, Y. (2015). Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma. Scientific Reports. 5(17787). doi: 10.1038/srep17787 
  18. Rajakumar, K., Muttan, S., Deepa, G., Revathy, S., Priya, B.S. (2015). Intelligent texture feature extraction and indexing for MRI image retrieval using curvelet and PCA with HTF. Advances in Natural and Applied Sciences. 9(6 SE) 506-513. doi: (link)

  19. Parmar, C., Leijenaar, R.T.H., Grossmann, P., Valazquez, E.R., Bussink, J., Rietveld, D., Rietbergen, M.M., Haibe-Kains, B., Lambin, P., Aerts, H.J.W.L. (2015). Radiomic feature clusters and Prognostic Signatures specific for Lung and Head &Neck cancer. Scientific Reports. 5(11044) doi: 10.1038/srep11044

  20.  Parmar, C., Grossmann, P., Bussink, J., Lambin, P., Aerts, H.J.W.L. (2015). Machine Learning methods for Quantitative Radiomic Biomarkers. Scientific Reports, 5(13087). doi: 10.1038/srep13087 
  21. Chaddad, A., Tanougast, C. (2015), High-Throughput Quantification of Phenotype Heterogeneity Using Statistical Features. Advances in Bioinformatics, 15(728164). doi: 10.1155/2015/728164
  22. Chaddad, A. (2015). Automated Feature Extraction in Brain Tumor by Magnetic Resonance Imaging Using Gaussian Mixture Models.  International Journal of Biomedical Imaging, 2015(868031). doi: 10.1155/2015/868031
  23. Dhara, A.K., Mukhopadhyay, S., Khandelwal, N. (2013). 3d texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images. Medical Imaging 2013: Computer-Aided Diagnosis, 8670. doi: 10.1117/12.2007016

  24. Dhara, A.K., Mukhopadhyay, S., Alam, N., Khandelwal, N. (2013). Measurement of spiculation index in 3D for solitary pulmonary nodules in volumetric lung CT images.Medical Imaging 2013: Computer-Aided Diagnosis, 8670. doi: 10.1117/12.2006970

...

  1. Meyer JM, Perlewitz KS, Hayden JB, Doung Y-C, Hung AY, Vetto JT, Pommier RF, Mansoor A, Beckett BR, Tudorica A. Phase I trial of preoperative chemoradiation plus sorafenib for high-risk extremity soft tissue sarcomas with dynamic contrast-enhanced MRI correlates. Clinical Cancer Research. 2013;19(24):6902-11.

Collection:  REMBRANDT

  1. Schrock, M. S. (2017). Wwox deficiency in human cancers: Role in treatment resistance. Columbus, OH: The Ohio State University.  Retrieved from https://etd.ohiolink.edu/!etd.send_file?accession=osu1492793625915816&disposition=inline

  2. Babu, B. S., & Varadarajan, S. (2017). Detection of brain tumour in MRI scan images using Tetrolet Transform and SVM classifier. Indian Journal of Science and Technology, 10. doi:10.17485/ijst/2017/v10i19/113721 

Collection: RIDER Collections

...