1. Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: Measurement WorkFlow 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Standard volumetric measurements

2. Volumetric Analysis using 3D Slicer: Loading Data 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section File->Add Volume …shows a DICOM browser from which data can be loaded into Slicer… Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

3. Volumetric Analysis using 3D Slicer: Loading Data 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Post-TX T1 shown in “Four-up” Layout (Axial, Saggital, Coronal, & 3D)

4. Volumetric Analysis using 3D Slicer: Displaying Data 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumes Module GUIPre-TX study Post-TX study

5. Volumetric Analysis using 3D Slicer: Changing Layouts 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout & Display Pre-TX volume 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

6. Volumetric Analysis using 3D Slicer: Linear Measurement 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Fiducials Module: Create Fiducial List Create two fiducials Click & drag fiducials to endpoints of longest diameter Record distance readout Linear Measurement: D1 pre =48.7073mm

7. Volumetric Analysis using 3D Slicer: Linear Measurement 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Fiducials Module: Click & drag fiducials to endpoints of orthogonal diameter Record distance readout Linear Measurement: D2 pre =48.6839 mm

8. Volumetric Analysis using 3D Slicer: Linear Measurement 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Or: Make only Axial Slice visible in 3D Viewer Select 3D-Only Layout Use Measurements Module to turn on Ruler Widget; click & drag endpoints. (Currently being extended to work in Slice Viewers too) *** Note: gives Different report than fiducials! Off by ~3mm…Discuss with Nicole.

9. Volumetric Analysis using 3D Slicer: Linear Measurement Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Linear Measurement on Post-TX volume: D1 post =26.123mm 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section

10. Volumetric Analysis using 3D Slicer: Linear Measurement Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Linear Measurement on Post-TX volume: D2 post =17.8873mm 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section

11. Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Editor Module: Threshold Paint Tool, configured to capture the greyscale range within tumor. Paint in a few strokes 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section

12. Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Editor Module: Refine if desired: Remove islands, Erase unwanted labels, etc. View ROI: as transparent overlay, or as outline at voxel boundaries. 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Rapid region specification; more accurate than ellipsoid

13. Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Statistics Module: Specify: Study volume Label Map Apply Save output to file Volume Measurement: V pre = 7877.268 mm 3 (computed for single slice) 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section

14. Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Similar workflow applied to Post-TX volume: Volume Measurement: V post = 38.192 mm 3 (computed for single slice) 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section

15. Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Pre- and Post-Treatment Comparisons: 1.Load pre- and post-treatment T1s (or Pre/Post GAD) study 2.Adjust display of both studies in Volumes Module 3.Switch to Axial (Red) Slice Layout 4.Compare opposing diameters of largest tumor cross section 5.Compare region size of largest tumor cross section Post-TX Pre-TX VD2D1 38.192 mm 3 7877.268 mm 3 17.8873mm26.123mm 48.6839 mm 48.7073mm

16. Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: Volume Change Analysis 1.Create left breast volume of interest (for both pre- and post-TX) 2.Mask out background using Editor Tools: 3.Run bias correction (10 iterations): 4.Run histogram equalization: input = preTX, ref = post-TX 5.Run manual, then affine registration with default settings Preparing the data for volumetric change analysis

17. Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: Volume Change Analysis 1.Create left breast volume of interest for pre- and post-TX datasets 2.Mask out background using Editor Tools 3.Run bias correction 4.Run histogram equalization: input = preTX, ref = post-TX 5.Run manual, then affine registration with default settings Converters->ExtractSubvolume Module: Use two fiducial points to mark opposing corners of a subvolume to extract. Pre- and Post-TX subvolumes should contain anatomy in good correspondence. Pre-TXPost-TX

18. Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: Volume Change Analysis 1.Create left breast volume of interest 2.Mask out background using Editor Tools 3.Run bias correction 4.Run histogram equalization: input = preTX, ref = post-TX 4.Run manual, then affine registration with default settings Editor Module: Tools to use: threshold, save island, dilation, island removal, erosion

19. Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: Volume Change Analysis 1.Create left breast volume of interest 2.Mask out background using Editor Tools 3.Run bias correction 4.Run histogram equalization: input = preTX, ref = post-TX 5.Run manual, then affine registration with default settings MRI Bias Field Correction Module: IN parameters = GADParameters2 Input Volume = 10 iterations performed

20. Volumetric Analysis using 3D Slicer: Volume Change Analysis Advanced volumetric analysis: Tumor Segmentation Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

21. Volumetric Analysis using 3D Slicer: Volume Change Analysis Advanced volumetric analysis: Building 3D Models Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

22. Volumetric Analysis using 3D Slicer: Volume Change Analysis Advanced volumetric analysis: Visualization Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

23. Volumetric Analysis using 3D Slicer: Volume Change Analysis Advanced volumetric analysis: Computing Changes Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis