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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

Institution:
1Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA.
2PixelMed Publishing, LLC, Bangor, PA, USA.
3Department of Electrical and Computer Engineering, University of Iowa, Iowa City, IA, USA.
4Iowa Institute for Biomedical Imaging, University of Iowa, Iowa City, IA, USA.
5Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA, USA.
6Harvard Medical School, Harvard University, Boston, MA, USA.
7OpenConnections GmbH, Oldenburg, Germany.
8Freelancer, Oldenburg, Germany.
9Isomics, Inc., Cambridge, MA, USA.
10Department of Radiation Oncology, University of Iowa Carver College of Medicine, Iowa City, IA, USA.
11Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.
Publication Date:
Nov-2015
Journal:
PeerJ PrePrints
Volume Number:
3
Issue Number:
e1921
Citation:
PeerJ PrePrints. 2015 Nov; 3:e1921.
Links:
https://peerj.com/preprints/1541/
Keywords:
bioinformatics, clinical trials, oncology, radiology and medical imaging
Appears in Collections:
SLICER, NAC, SPL
Sponsors:
U24 CA180918/CA/NCI NIH HHS/United States
P41 EB015902/EB/NIBIB NIH HHS/United States
U01 CA140206/CA/NCI NIH HHS/United States
U01 CA151261/CA/NCI NIH HHS/United States
Generated Citation:
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. 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 PrePrints. 2015 Nov; 3:e1921.
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Imaging biomarkers hold tremendous promise in the precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation motivate integration of the clinical and imaging data, and the use of standardized approaches to sharing analysis results and semantics. We develop the methodology and supporting tools to perform these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging Communication in Medicine (DICOM®) international standard and free open source software tools. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor and reference regions of interest (ROI) using manual and semi-automatic approaches, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of encoding via new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited to the QIN-HEADNECK collection of The Cancer Imaging Archive. Supporting tools for data analysis and DICOM conversion are available as free open source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that DICOM standard can be used to represent various types of the analysis results and encode their complex relationships. As a result, the data objects are interoperable with a variety of readily available tools and toolkits, as well as commercial clinical imaging and analysis systems that adopt the DICOM standard virtually universally.

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