1. Surgical Planning Laboratory Brigham and Women’s Hospital Boston, Massachusetts USA a teaching affiliate of Harvard Medical School 3D Slicer And The NA-MIC Kit Ron Kikinis, M.D. Robert Greenes Distinguished Director of Biomedical Informatics Professor of Radiology, Harvard Medical School Founding Director, Surgical Planning Laboratory, Brigham and Women’s Hospital Principal Investigator, National Alliance for Medical Image Computing (a National Center for Biomedical Computing), and Neuroimage Analysis Center (a NCRR National Resource Center) Research Director, National Center for Image Guided Therapy

2. ©2011 Surgical Planning Laboratory, ARR Slide 2 Acknowledgments F. Jolesz, C. Tempany, P. Black, A. Golby, S. Wells, N. Hata, CF. Westin, M. Halle, S. Pieper, F. Talos, W. Schroeder, and many more….

3. ©2011 Surgical Planning Laboratory, ARR Slide 3 Our Science Algorithm research Tool development Biomedical Research Provided by Odonnell, et al. Provided by Kindlmann, et al. Golby, Archip et al.

4. ©2011 Surgical Planning Laboratory, ARR Slide 4 Medical Image Computing Focus is on group analysis in the brain –Where is a function typically located –What is the variability? Fischl, Greve, et al - MGH

5. ©2011 Surgical Planning Laboratory, ARR Slide 5 Personalized Medicine Subject specific analysis –Research in a clinical setting –Interactive Analysis Golby, Pieper, Lemaire, BWH Neurosurgery

6. ©2011 Surgical Planning Laboratory, ARR Slide 6 A Different Style Of Research MIC for personalized medicine –Software runs on your computer (HIPAA) –Fast processing (clinical research) –Subject-specific analysis (pathology) Picture courtesy Raul San Jose

7. ©2011 Surgical Planning Laboratory, ARR Slide 7 Different Communities Neuroimaging –Willing to spend time: calibration of algorithm, learn to use –Automation is very important –Large resources are available Subject specific analysis –Minutes to hours per case –Automation is mostly not available –Limited computational resources

8. ©2011 Surgical Planning Laboratory, ARR Slide 8 Example: Image Guided Therapy (IGT) Use diagnostic imaging to replace/augment direct inspection Requires subject specific analysis of imaging data A very different style of research –Patient specific analysis –Limited resources are available –False positives and false negatives cannot be compensated by adding subjects (you have only one)

9. ©2011 Surgical Planning Laboratory, ARR Slide 9 Augmented Reality

10. ©2011 Surgical Planning Laboratory, ARR Slide 10 The NA-MIC Approach Open community process Modular and extensible software architecture Free open source software (BSD) Works on your computer Picture courtesy Gabor Fichtinger

11. ©2011 Surgical Planning Laboratory, ARR Slide 11 This is Where We are Today Picture courtesy Kapur, Jakab, Kikinis

12. ©2011 Surgical Planning Laboratory, ARR Slide 12 NA-MIC Kit Overview

13. ©2011 Surgical Planning Laboratory, ARR Slide 13 Works on Your Computer Easy download and installation Runs natively on your computer on most common operating systems behind your institutional firewall Training concept: Self guided tutorials Training events Registration and segmentation support Picture courtesy Dominik Meier

14. ©2011 Surgical Planning Laboratory, ARR Slide 14 The 3D Slicer (slicer.org) 3D Slicer is our primary platform for delivering image computing technology for personalized medicine research –Basic and clinical visualization –Longitudinal imaging –Registration –Segmentation Picture courtesy Marianna Jakab

15. ©2011 Surgical Planning Laboratory, ARR Slide 15 Slicer 3.6 Highlights Picture courtesy S. Pieper

16. ©2011 Surgical Planning Laboratory, ARR Slide 16 Slicer 3.6 Highlights (cont) Picture courtesy S. Pieper

17. ©2011 Surgical Planning Laboratory, ARR Slide 17 Slicer 3.6 Highlights (cont) Picture courtesy S. Pieper

18. ©2011 Surgical Planning Laboratory, ARR Slide 18 Slicer 3.6 Highlights (cont) Picture courtesy S. Pieper

19. ©2011 Surgical Planning Laboratory, ARR Slide 19 NA-MIC Image Informatics Today Limited: The tradition in MIC is to chop of the header! Non-standard data as output from research scans Limited Dicom support: ITK/GDCM –Communications layer missing –Many Dicom extensions missing Protoype interfaces to informatics frameworks: –FetchMI in Slicer XNAT Midas

20. ©2011 Surgical Planning Laboratory, ARR Slide 20 XNAT is… The eXtensible Neuroimaging Archive Toolkit. Extensible, free open source software An imaging informatics platform for managing, processing, and sharing imaging and related data. Developed by the Neuroinformatics Research Group at Washington University in St. Louis. Picture courtesy D. Marcus

21. ©2011 Surgical Planning Laboratory, ARR Slide 21 Modular Open Source Architecture Picture courtesy D. Marcus

22. ©2011 Surgical Planning Laboratory, ARR Slide 22 QUARANTINELOCAL USECOLLABORATIONPUBLIC ACCESS IMAGING NON-IMAGING OTHER SOURCES The XNAT Enterprise workflow Data archiving Quality control Data access Security Visualization Automation Integration Data sharing Picture courtesy D. Marcus

23. ©2011 Surgical Planning Laboratory, ARR Slide 23 XNAT Web services RESTful web services API Access to metadata, images, Upload, download Comprehensive search Multiple formats: HTML, XML, CSV, JSON Example clients: XNAT Gateway, PyXNAT, 3D Slicer, Grid Wizard Engine, LONI Pipeline Picture courtesy D. Marcus

24. ©2011 Surgical Planning Laboratory, ARR Slide 24 client applicationsXNAT instance XNAT web services Slicer as a XNAT Client Picture courtesy D. Marcus

25. ©2011 Surgical Planning Laboratory, ARR Slide 25 XNAT Data Sharing Challenges Standards are always behind People don’t use the standards Lots of moving targets Many competing entities (BIRN/ caBIG, DICOM/NIFTI, Java/Python, SOAP/REST/DICOM) Integration with clinical systems is a driving requirement It’s not all about the brain Picture courtesy D. Marcus

26. ©2011 Surgical Planning Laboratory, ARR Slide 26 NA-MIC Kit 2012 ITK v4: –Dicom communication layer, DCMTK –Partial GPU acceleration Slicer 4: Focus on usability –QT, CTK widgets –Support for layouts, hanging protocols are coming –Improved Dicom support –Sceneviews and annotations –Image informatics support XNAT, other –Extended support for plug-ins

27. ©2011 Surgical Planning Laboratory, ARR Slide 27 URL’s National Alliance for Medical Image Computing www.na-mic.org Neuroimage Analysis Center Nac.spl.harvard.edu Surgical Planning Laboratory, Brigham and Women’s Hospital spl.harvard.edu National Center For Image Guided Therapy www.ncigt.org