1. Pohl K, Konukoglu E -1- National Alliance for Medical Image Computing Measuring Volume Change in Tumors Kilian M Pohl, PhD Ender Konugolu Slicer3 Training Compendium

2. Pohl K, Konukoglu E -2- National Alliance for Medical Image Computing Material This course requires the following installation: The current version of Slicer 3 Software, which can be installed from http://www.na-mic.org/Slicer/Download/Snapshots/ /Slicer3-3.3-alpha-2008-09-11-* The TumorGrowth-Tutorial-Data.xcat, which can be downloaded from http://www.na-mic.org/Wiki/index.php/Slicer3:Training A reliable internet connection for downloading the data Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules. The module described in this tutorial was tested on Axial 3D SPGR T1 post Gadolinium scans (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256)

3. Pohl K, Konukoglu E -3- National Alliance for Medical Image Computing Data This course is built upon two scans of a patient with meningioma: MR Scan 1MR Scan 2

4. Pohl K, Konukoglu E -4- National Alliance for Medical Image Computing Learning objective Following this tutorial, you’ll be able to load two scans into Slicer3, and measure and visualize the change in volume of the meningioma between the two scans.

5. Pohl K, Konukoglu E -5- National Alliance for Medical Image Computing Overview Loading a scene Measuring volume change in tumors

6. Pohl K, Konukoglu E -6- National Alliance for Medical Image Computing Part 1: Loading the tutorial data via a scene file

7. Pohl K, Konukoglu E -7- National Alliance for Medical Image Computing Slicer3 GUI The Graphical User Interface (GUI) of Slicer3 integrates five components: the Menu Toolbar the Module GUI Panel the 3D Viewer the Slice Viewer the Slice and 3D View Controller Slice Viewer 3DViewer Module GUI Panel Slice and 3D View Controller Menu Toolbar

8. Pohl K, Konukoglu E -8- National Alliance for Medical Image Computing Loading a Scene Select File  Load Scene in the Main Menu. Load the file ChangeTracker-Tutorial- Data.xcat Data is downloaded from www.xnat.org

9. Pohl K, Konukoglu E -9- National Alliance for Medical Image Computing Loading a Scene The MRML Tree in the Data module shows the two scans ( 2006-spgr and 2007-spgr) in this scene.

10. Pohl K, Konukoglu E -10- National Alliance for Medical Image Computing Modifying Layout of Viewer Select and Four-up layout.

11. Pohl K, Konukoglu E -11- National Alliance for Medical Image Computing New Layout of Viewer Slice Viewers 3D Viewer Modify size of windows as needed

12. Pohl K, Konukoglu E -12- National Alliance for Medical Image Computing Part 2: Measuring Volume Change

13. Pohl K, Konukoglu E -13- National Alliance for Medical Image Computing New Layout of Viewer Select Modules Select ChangeTracker

14. Pohl K, Konukoglu E -14- National Alliance for Medical Image Computing Workflow Wizard The Workflow Wizard of Slicer3 guides the user through a sequence of steps and is defined by the following components: the Step Panel the User Panel the Navigation Panel Step Panel User Panel Navigation Panel

15. Pohl K, Konukoglu E -15- National Alliance for Medical Image Computing Select Scans Select 2006-spgr and 2007-spgr Press Next

16. Pohl K, Konukoglu E -16- National Alliance for Medical Image Computing Identify Volume of Interest Move sliders to see tumor

17. Pohl K, Konukoglu E -17- National Alliance for Medical Image Computing Identify Volume of Interest Identify VOI by clicking left mouse button inside tumor Press Show VOI to view region

18. Pohl K, Konukoglu E -18- National Alliance for Medical Image Computing Identify Volume of Interest VOI is shown in blue Lower and Upper bound of VOI

19. Pohl K, Konukoglu E -19- National Alliance for Medical Image Computing Identify Volume of Interest Move sliders or enter: X: 105 155 Y: 76 121 Z: 62 90 Press Next

20. Pohl K, Konukoglu E -20- National Alliance for Medical Image Computing Segment Tumor Slice Viewers show VOI with current Segmentation 3D Viewer shows model of tumor with additional structures Change Segmentation by moving Slider to 125

21. Pohl K, Konukoglu E -21- National Alliance for Medical Image Computing Segment Tumor Press Grid to view grid with original voxel size

22. Pohl K, Konukoglu E -22- National Alliance for Medical Image Computing Segment Tumor Press Slice to see the first scan in the 3D Viewer Press Next

23. Pohl K, Konukoglu E -23- National Alliance for Medical Image Computing Choose Metric Type Choice of Metric: Detect change by analyzing intensity pattern (fast)‏ Measure change by analyzing deformation map (slow) Select fast and press Analyze

24. Pohl K, Konukoglu E -24- National Alliance for Medical Image Computing Analysis I: Volume Preserving Registration BeforeAfterwards

25. Pohl K, Konukoglu E -25- National Alliance for Medical Image Computing Analysis II: Normalize Intensities Scan 1Scan 2Scan 2 - Norm

26. Pohl K, Konukoglu E -26- National Alliance for Medical Image Computing PDF of Dormant Tissue Determine probability density function Analysis III: Detect Change – Intensity Based - = Compute statistics of static tissue: Subtract Scan2 from Scan1 Define region of static tissue

27. Pohl K, Konukoglu E -27- National Alliance for Medical Image Computing Analysis III: Detect Change – Intensity Based Mode : Sensitive Moderate Robust False Positive Risk: High Medium Low Growth (mm 3 ) : 1301 547 100 Growth (voxel): 1057 444 81 Analysis Data Konukoglu et al.,“Monitoring Slowly Evolving Tumors”, ISBI, 2008

28. Pohl K, Konukoglu E -28- National Alliance for Medical Image Computing Analysis III: Detect Change–Deformation Map = Determine change via mapping: Compute diffeomorphic mapping between scans Compute Jaccobian Apply mapping to segmentation or Mode : Jaccobian Growth (mm 3 ) : 1291 Growth (voxels): 1049 Mode : Segmentation Growth (mm 3 ) : 1386 Growth (voxels): 1126

29. Pohl K, Konukoglu E -29- National Alliance for Medical Image Computing Show Change in Pathology Define sensitivity of analysis Show change in volume: purple = growth green = shrinkage

30. Pohl K, Konukoglu E -30- National Alliance for Medical Image Computing Define Working Directory Press directory button Select to create directory

31. Pohl K, Konukoglu E -31- National Alliance for Medical Image Computing Define Working Directory Enter tutorial and press OK Select tutorial and press OK

32. Pohl K, Konukoglu E -32- National Alliance for Medical Image Computing Save Screenshot Press Screenshot Screenshot is saved to tutorial directory View TG_Screenshot_001.png

33. Pohl K, Konukoglu E -33- National Alliance for Medical Image Computing Save Analysis Result Press Analysis Outcome of analysis is saved to tutorial directory View AnalysisOutcome.log

34. Pohl K, Konukoglu E -34- National Alliance for Medical Image Computing Save Intermediate Results Press Data Press Save All and Save

35. Pohl K, Konukoglu E -35- National Alliance for Medical Image Computing Finish Workflow Press OK to return to the first step of the workflow

36. Pohl K, Konukoglu E -36- National Alliance for Medical Image Computing Overview Loading a scene Measuring volume change in tumors

37. Pohl K, Konukoglu E -37- National Alliance for Medical Image Computing Summary Conclusion: Interactive interface to load scene Workflow technology to semi-automatically detect change in pathology In-depth description of technology: Konukoglu et al.,“Monitoring Slowly Evolving Tumors”, IEEE ISBI, p. 812 – 815, 2008 http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430 Pohl et al., “Automatic Tumor Growth Detection” in Meningiomas A Comprehensive Text, In Press.

38. Pohl K, Konukoglu E -38- National Alliance for Medical Image Computing Information We tested the tool on Axial 3D SPGR T1 post Gadolinium scans (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256) We expect the tool to work also on set of scans that fulfill the following requirements: –same patient was scanned –scans were acquired with the same acquisition protocol –scans have isotropic resolution

39. Pohl K, Konukoglu E -39- National Alliance for Medical Image Computing Acknowledgments National Alliance for Medical Image Computing NIH U54EB005149 add nac, ncigt and spl acknowledgements Brain Science Foundation INRIA, France