QIICR 2013

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October 22-23, 2013 Brigham and Women's Hospital, Boston, MA http://qiicr.org

Introduction

Imaging has enormous untapped potential to improve cancer research through software to extract and process morphometric and functional biomarkers. In the era of non-cytotoxic treatment agents, multi-modality image-guided ablative therapies and rapidly evolving computational resources, quantitative imaging software can be transformative in enabling minimally invasive, objective and reproducible evaluation of cancer treatment response. Post-processing algorithms are integral to high-throughput analysis and fine- grained differentiation of multiple molecular targets. Software tools used for such analyses must be robust and validated across a range of datasets collected for multiple subjects, timepoints and institutions. Ensuring the validity of this software requires unambiguous specification of analysis protocols, documentation of the analysis results, and clear guidelines for their interpretation.

Yet cancer research data does not exist in formats that facilitate advancement of quantitative analysis and there is lack of an infrastructure to support common data exchange and method sharing. We therefore propose to develop and disseminate interoperable image informatics platform for development of software tools for quantitative imaging biomarker discovery. This platform will enable archival, organization, retrieval, dissemination of the data produced by the novel analysis tools and performance evaluation of quantitative analysis methods. Its functionality will be defined by the needs of the active research projects within the NCI Quantitative Imaging Network (QIN) in quantitative imaging biomarker development for prostate adenocarcinoma, head and neck cancer and glioblastoma multiforme. The infrastructure will be based on 3D Slicer, an NIH funded open source platform for image analysis and visualization, and will be accompanied by sample data and step-by-step documentation.

In the Quantitative Image Informatics for Cancer Research (QIICR) project we will (1) develop software tools encapsulating analysis and data organization workflows for the specific cancer imaging research applications; (2) implement support for interoperable open formats accepted in the community to enable dissemination and sharing of the analysis results; (3) develop interfaces to community cancer imaging repositories to enable archival and dissemination of the analysis results.

Objective

During the QIICR 2013 meeting in Boston we will:

• review the project as funded,
• hear updates on the current status of the DICOM standard and its support in major open source toolkits and platforms such as ITK and Slicer
• plan the project activities among the participants
• discuss how to communicate and coordinate among the participants

Program

Day 1 (Oct 22): Public Workshop on DICOM Support for Quantitative Imaging Trials

This meeting is co-organized with NAC, NCIGT, NA-MIC.

Times in Eastern Daylight Time (EDT). 13:30 EDT = 19:30 Central European Summer Time (CEST)

• noon: networking and brown bag working lunch (i.e. bring your own lunch - there are many nearby places to buy food) - coffee will be served
• 1:30pm-2:00pm QIICR introduction (Andrey Fedorov) Slides
• 2:00pm-2:30pm Existing support of DICOM in 3D Slicer and CTK (Steve Pieper) Slides
• 2:30pm-2:55pm DICOM aspects of SlicerRT project (Andras Lasso) Slides
• 2:55pm-3:05pm break
• 3:05pm-3:30pm Overview of the relevant capabilities of DCMTK (Michael Onken) Slides
• 3:30pm-4:25pm Overview of the relevant parts of DICOM (David Clunie) Slides
• 4:25pm-4:35pm break
• 4:35pm-5:30pm Structured Report templates for Cancer Clinical Trials DICOM (David Clunie) Slides
• 5:30pm-6:30pm Open discussion
  • Workflow engine
• 7:30pm Group dinner (everyone pays for their own, location TBD. Please notify Katie if you will join kmast@bwh.harvard.edu) (Elephant Walk, 900 Beacon St, http://elephantwalk.com/)

Day 2 (Oct 23): QIICR Participants Only

• 

  The internal meeting in full swing (photo by Ron)

(this day will be devoted to administrative, logistic, and other details. QIICR funded investigators are required to attend, if you are not a QIICR funded investigator and would like to attend, contact the program committee)

• Closed program
• 8am Working breakfast (bring your own) - coffee will be served
• 8:45am-9:00am Review the agenda for the day (Andrey Fedorov)
• 9am-noon: Presentations from DBPs and brain-storming
  • 9:00am-10:00 am Quantitative MRI of prostate cancer as a biomarker and guide for treatment (Fiona Fennessy, BWH QIN site PI, QIICR investigator) + questions
  • 10:00am-10:10am break
  • 10:10am-11:00am Quantitative MRI of Glioblastoma Response (Jayashree Kalpathy-Cramer, MGH QIN site investigator, QIICR MGH site PI) + questions
  • 11:00am-12:00am Quantitative Imaging to Assess Response in Cancer Therapy Trials (Reinhard Beichel, Iowa QIN site investigator, QIICR Iowa site PI) + questions
• noon-1pm brown-bag lunch
• 1:00pm-1:20pm Discussion of the DBP and related issues
  • Site-specific and common informatics and data organization needs
  • Organization of image-related vs clinical data - interaction between DICOM-based storage and databases
  • Data sharing
  • Integration of structured terminology
  • Near term and end of year deliverables
• 1:20pm-3pm Discussions of day-to-day logistics issues
  • communication means and frequency
    • every other week - Google hangout ? YES - Except during RSNA week
    • perhaps meet at RSNA - with other folks, perhaps Monday 2.00pm-3.00pm (CST) ?? what room
    • perhaps meet at NA-MIC project week Salt Lake City Jan 6-10
    • wiki for status updates, documentation and record-keeping: NA-MIC wiki (http://wiki.na-mic.org/Wiki/index.php/QIICR_2013), github project wiki (https://github.com/QIICR/qiicr.github.io/wiki/QIICR-Wiki-Home) (AF to demo)
    • github issues for project milestones (AF to demo)
      • large binary files on MIDAS http://www.kitware.com/source/home/post/8
    • web-site for publicity: http://qiicr.org (AF to demo)
      • git crash course and links (Slicer-specific, but many useful links) https://www.slicer.org/wiki/Slicer:git-svn
    • face-to-face meetings: NA-MIC project weeks twice a year, do we need more?
  • Development-related activities
    • prioritization of development tasks, SR templates, XML
    • repository of sample DICOM objects (public?)
    • cross-linking of DICOM standard ?
      • related effort: DICOM in XML (~2005) PPT slides. March 2013 update: The Secretary reported that plans are formulated for a 2013 conversion. More discussion will be needed when a more detailed proposal is available. It was noted however that Pts 3 and 16 are available in XML form, now. [DSC meeting minutes
    • means of data sharing (XNAT Central? MIDAS?)

Logistics

Registration

This event is intended for the participants in the grant, but open to others as long as they are willing to participate in the DICOM-related discussions. You must have expertise on one or several of the following topics: quantitative image analysis, open source software development, imaging informatics or related topics.

Unless you received an invitation to attend this event, please fill this form if you are interested to join. Organizing committee (Ron Kikinis, Steve Pieper and Andrey Fedorov) will confirm your registration and you will be added to the registered attendee list.

Registration is open until October 1 so that we can finalize the logistics.

Due to space limitations, the number of attendees is limited. After accommodating the participants in the grant, we have a "first come" policy. Please register early if you are interested in attending!

Where

2nd floor Demo Room, 1249 Boylston street, Boston MA (Google map link)

Room will be finalized subject to the number of attendees registered.

When

October 22 and 23, 2013

Lodging and other considerations

There are many hotel options near 1249 Boylston. Public transportation in Boston is pretty good, and you should not have issues commuting from the neighborhoods like Cambridge and Brookline. Hubway is a popular bike share system that you can use to get around, 24-hour access pass is $6.

Among the nearby choices:

• The Howard Johnson's next door is convenient, but run down.
• Residence Inn is new and looks nice.
• People have said good things about the Hotel Commonwealth
• The Hotel Buckminster has also worked well for visitor.

Please Note: the Red Sox WILL BE in the World Series, which starts at 8:07pm on the second day of our meeting Wednesday, October 23. Because of this exciting event, the neighborhood will be very busy and parking will be impossible. Definitely make your reservations in advance, because rooms will be hard to come by.

The meeting location is easily reachable by cab or bus if the nearby hotels don't work out.

Contact

Andrey Fedorov, Brigham and Women's Hospital

fedorov AT bwh.harvard.edu

Attendees

Day 1

1. Ron Kikinis, Brigham and Women's Hospital
2. Andrey Fedorov, Brigham and Women's Hospital
3. Steve Pieper, Isomics Inc.
4. Jayashree Kalpathy-Cramer, Mass General Hospital
5. Reinhard Beichel, U. of Iowa
6. David Clunie, Pixelmed Publishing
7. Michael Onken, Open Connections GmbH and OFFIS
8. Andras Lasso, Queens U. and OCAIRO
9. Csaba Pinter, Queens U. and OCAIRO
10. Gordon Harris, BWH/MGH Tumor Imaging Metrics Core
11. Greg Sharp, MGH Radiation Oncology
12. Oleg Pianykh, Harvard
13. Leonid Syrkin, DFCI
14. John Evans, MGH
15. Alireza Mehrtash, BWH
16. Tobias Penzkofer, BWH
17. Nathaniel Reynolds, MGH
18. Marco Nolden, DKFZ (by Google hangout)
19. Jean-Christophe Fillion-Robin, Kitware Inc. (by Google hangout)
20. Jörg Riesmeier, Freelancer and DCMTK (by Google hangout)
21. Kevin Wang, Toronto (by Google hangout)

Day 2

1. Ron Kikinis, Brigham and Women's Hospital
2. Andrey Fedorov, Brigham and Women's Hospital
3. Steve Pieper, Isomics Inc.
4. Jayashree Kalpathy-Cramer, Mass General Hospital
5. Reinhard Beichel, U. of Iowa
6. Fiona Fennessy, Brigham and Women's Hospital
7. David Clunie, Pixelmed Publishing
8. Michael Onken, Open Connections GmbH and OFFIS
9. John Evans, MGH
10. Alireza Mehrtash, BWH
11. Yantian Zhang, NCI (by phone)

References

• NCI Quantitative Imaging Network
• NIH Reporter info on QIICR