2016 Winter Project Week/Breakout Sessions/QIICRTools

QIICR Tools

Goal

Give an overview of the various tools from the Quantitative Image Informatics for Cancer Research (QIICR) project that are available now or are being developed.

Participants

The session is aimed at the users and developers interested in the scope of QIICR work. Anyone interested is welcome to attend this session.

Project members expected to attend:

• Andrey Fedorov, BWH
• Ethan Ulrich, U. Iowa
• Xiao Da, MGH
• Michael Onken, Open Connections GmbH
• Nicole Aucoin, BWH
• Christian Herz, BWH

Outline

Slide sets and summary documents:

• Introduction to QIICR (slides from CI4CC Faill 2015 symposium)
• Quantitative imaging: Structured reporting in 3D Slicer and beyond (slides from RSNA 2015 course)
• Quantitative image analysis tools: Communicating quantitative image analysis results (slides from RSNA 2015 course)
• Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2015) 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 3:e1921 https://doi.org/10.7287/peerj.preprints.1541v1

QIICR imaging biomarker analysis tools

• MRI / prostate cancer (Andrey Fedorov)
  • DCE MRI modeling
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling
  • DWI MRI modeling
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWModeling
  • Multiparametric MRI annotation workflow
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/mpReview

• PET/CT / head and neck cancer (Ethan Ulrich)
  • PET SUV correction
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PETStandardUptakeValueComputation
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOMPETSUVPlugin
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DICOMRWVMPlugin
  • PET tumor and hot node segmentation
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PETTumorSegmentation
  • PET quantitative index extraction
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/QuantitativeIndicesTool
  • PET analysis workflow (PET-IndiC)
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PET-IndiC

• MRI / glioblastoma (Xiao Da)
  • DSC MRI modeling
    • http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DSC_MRI_Analysis
  • DCE MRI modeling
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/PkModeling
  • T1 mapping
    • http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/T1Mapping

DICOM informatics tools

• DCMTK API
  • http://support.dcmtk.org/docs-snapshot/mod_dcmseg.html
• Command-line conversion tools (supporting use case in [1])
  • conversion of SEG, RWVM, SR (TID 1500 Measurement report) DICOM objects: https://github.com/QIICR/Iowa2DICOM
  • conversion of SEG, integrated with Slicer: https://github.com/QIICR/Reporting/tree/master/SEGSupport
• User-level access to The Cancer Imaging Archive: https://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/TCIABrowser

DICOM learning, supporting tools, interoperability activities

• A Searchable Index of the DICOM Base Standard: https://fedorov.cloudant.com/dicom_search/.site/index.html
• dicom-dump plugin for Atom editor: click interface to DCMTK dcmdump and dsrdump
• DICOM SEG "connectathon" at RSNA 2015, poster: https://goo.gl/0WGmqm

DICOM datasets

• QIN-HEADNECK collection on TCIA: longitudinal PET/CT of head and neck cancer patients: includes CT, PET, RWVM, SEG, SR objects

References

[1] Fedorov A, Clunie D, Ulrich E, Bauer C, Wahle A, Brown B, Onken M, Riesmeier J, Pieper S, Kikinis R, Buatti J, Beichel RR. (2015) 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 3:e1921 https://doi.org/10.7287/peerj.preprints.1541v1