1 / 35

Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer

Slicer3 Training Compendium. Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer. Jeffrey Yap, PhD Ron Kikinis, MD Wendy Plesniak, PhD. Materials. This tutorial requires the following installation:

piper-jacobs
Download Presentation

Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Slicer3 Training Compendium Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer Jeffrey Yap, PhD Ron Kikinis, MD Wendy Plesniak, PhD

  2. Materials • This tutorial requires the following installation: • • 3D Slicer version 3.5 Software, which can be installed from • http://www.na-mic.org/Slicer/Download/Snapshots/win32/Slicer3-3.5-RSNA-2009-11-06-win32.exe • Tutorial data can be downloaded from: • http://wiki.na-mic.org/Wiki/images/d/de/RECIST-Tutorial-Data.zip 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. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -1-

  3. Tutorial data Unzip the tutorial dataset to find the following files: RECIST-TutorialScene-With-Snapshots.mrml (Scene file) RECIST-TutorialScene.mrml (Scene file) 2006-spgr.nrrd Axial 3D SPGR T1 post Gadolinium scan (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256 2006-spgr-label.nrrd(pre-generated label map file) 2007-spgr.nrrd Axial 3D SPGR T1 post Gadolinium scan (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256 2007-spgr-label.nrrd(pre-generated label map file) FiducialList.fcsv(fiducial list containing two fiducial markers) vtkMRMLLinearTransformNode4.tfm(registration matrix) If all of these files are not present, please try downloading the tutorial dataset again. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -2-

  4. Clinical context Baseline: June 2006 Follow-up: June 2007 • Baseline radiologist’s impression: • a large falcine lesion is identified. • present on both sides of the anterior falx adjacent to the frontal lobes. • measures 3.1 cm anteroposteriorly, 3.05 cm from side-to-side, and almost 3.5 cm in height. • minimal brain edema. • enhances moderately on post gadolinium imaging. • consistent with meningioma. • ventricular system and subarachnoid spaces are within normal limits. • Follow-up radiologist’s impression: • left frontal lobe mass appears unchanged on all series. • measures 3.3 x 3.2 cm in maximum dimension. • no other intracranial masses, mass-effect, midline shift, edema, or extra-axial collections present. • enhances moderately on post gadolinium imaging. • consistent with meningioma. • ventricular system and subarachnoid spaces are within normal limits. • Has the tumor grown? Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -3-

  5. Response Evaluation Criteria in Solid Tumors (RECIST) • Methodologies: • Assessment criteria: • CR (complete response) = disappearance of all target lesions • PR (partial response) = 30% decrease in the sum of the longest diameter of target lesions • PD (progressive disease) = 20% increase in the sum of the longest diameter of target lesions • SD (stable disease) = small changes that do not meet above criteria Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -4-

  6. Learning objective Following this tutorial, you’ll be able to use 3D Slicer to: Load a MRML Scene file, Visually assess the response to therapy, Make quantitative linear measurements across tumor cross sections, and Make quantitative volume measurements of tumor anatomy Assess according to RECIST criteria. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -5-

  7. Workflow Overview Workflow for linear and volumetric measurements • Load two post-treatment datasets • Compare volumetric measures of tumor using label map statistics. • Identify tumor cross section containing largest diameter • Compare opposing diameters of largest tumor cross section using fiducial markers. • Assess changes. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -6-

  8. Quick overview of Slicer3 GUI Menu Toolbar 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 3DViewer Module GUI Panel Slice Viewer Slice and 3D View Controller Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -7-

  9. Loading data using a MRML scene file Using File->Load Scene: • Raises the Load Scene Interface • select the RECIST-Tutorial-Scene-With-Snapshots.mrml file • double click the file, or click “Open” * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -8-

  10. fyi: What is “MRML”? • MRML (pronounced mur-muhl) stands for the "Medical Reality Markup Language"; and is an XML-based representation of a MRML Scene. • MRML Scene is the collection of datasets and their current state, viewing parameters, semantic descriptions, and algorithm parameterization. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -9-

  11. Loading data: quick look at both image volumes The image volume “2006-spgr” should be displayed in the background (BG) layer. The image volume “2007-spgr” should be displayed in the foreground (FG) layer. Use the FG/BG toggle button and the Fade Slider to see both volumes. Toggle BGonly Fade FGonly * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -10-

  12. Make volume measurements Using Modules Menubutton: Expose the menu and select the “LabelStatistics” module under the “Statistics” group. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -11-

  13. Make volume measurements: Baseline study Use the “Scene Snapshots” menubutton to restore the “2006FourUp” snapshot. This snapshot displays the baseline study and a tumor mask in the label layer. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -12-

  14. Make volume measurements for baseline study Specify 2006-spgr as the “Input Greyscale Volume” …and specify 2006spgr-label as the “Input Labelmap” Click “Apply”. Note the volumetric measure for the “green” tumor label (label 6). V2006 = 17432.05 mm3 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -13-

  15. Make volume measurements: follow-up study Use the “Scene Snapshots” menubutton to restore the “2007FourUp” snapshot. This snapshot displays the follow-up study and a tumor mask in the label layer. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -14-

  16. Volume measurements for the follow-up study Select “2007-spgr” as the Input Greyscale Volume. Select “2007-spgr-label” as they Input Labelmap. And click “Apply”. V2007 = 17458.24mm3 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -15-

  17. Record changes for assessment Change in Tumor metrics: LD (mm) CD (mm) V mm3 2006-spgr 17432.05 2007-spgr 17458.24 Move on to make linear measurements at both timepoints… * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -16-

  18. Linear measurements: exploring baseline data Use the “Scene Snapshots” menubutton to restore the “2006FourUp” snapshot again. Scroll in any Slice Viewer through the volume to identify the slice that shows the tumor cross section with largest diameter. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -17-

  19. Linear measurements: exploring baseline data Zoom in/out by clicking the right mouse button inside a Viewer and moving the mouse toward/away from you. Translate by clicking and dragging the middle mouse button in a Viewer. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -18-

  20. Linear measurements: exploring baseline data Note the annotations that report voxel (IJK) coordinates and spatial (RAS) coordinates. Note the magnified cursor view in the bottom-most GUI panel. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -19-

  21. Linear measurements Using LabelDiameterEstimation module (available currently only in the Slicer nightly builds), the following results were obtained for the largest diameter (LD). The tutorial will use these results as a guide for making manual measurements. Baseline: June 2006 Follow-up: June 2007 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -20-

  22. Change layouts (shortcut using scene snapshot) Use the “Scene Snapshots” menubutton to restore the “2006SagOnly” snapshot. This changes the layout to display only the Saggital (Yellow) Slice Viewer… * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -21-

  23. Make linear measurements Using Modules Menubutton: Expose the menu and select the “Fiducials Module”. In this scene, a Fiducial List containing Fiducial points has already been created. Side Note: The Fiducials Module is powerful and functionality-rich. Learn more about it here: http://www.slicer.org/slicerWiki/index.php/Modules:Fiducials-Documentation-3.4 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -22-

  24. Make linear measurements Fiducials ModuleGUI Panel Four fiducial points have been set to “Visible”. Distance is reported between first two selected fiducial points. Each fiducial’s XYZ coordinates are editable. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -23-

  25. Make linear measurements Mouse over fiducial LD-1-2006 or LD-2-2006. When it turns “yellow”, it can be clicked and dragged to adjust its position. Record the linear distance along the longest diameter LD2006 = 37.72mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -24-

  26. Make linear measurements Deselect the top two fiducials and select the next two: CD-1-2006 and CD-2-2006 Determine the opposing diameter (WHO). CD2006= 32.24mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -25-

  27. Change layouts (shortcut using scene snapshot) Use the “Scene Snapshots” menubutton to restore the “2007SagOnly” snapshot. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -26-

  28. Linear measurements… Use the same fiducials to make adjustments and new measurements. LD2007= 36.67mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -27-

  29. Linear measurements… …(WHO) CD2007= 31.97mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -28-

  30. Linear measurements… Use the “Scene Snapshots” menubutton to restore the “2007SagOnly-2” snapshot. This shows a nearby slice in follow-up with longer LD -Registration error? -Tumor growth? * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -29-

  31. Comparing measurements Compare corresponding measurements. Change in Tumor metrics: LD (mm) CD (mm) V mm3 2006-spgr 32.24 17432.05 37.72 2007-spgr 36.67 31.97 17458.24 % change: -2.78% -0.84% 0.15% * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -30-

  32. Assessment (Develop content here: discuss) Using the RECIST assessment criteria: SD (stable disease) = small changes that do not meet above criteria Say something here about efficacy and limitations of RECIST. What can it capture, What does it not capture as well. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -31-

  33. Assessment: Other tools to assess changes in tumor metrics (Develop content here: discuss) Segue into Change Tracker tutorial. Provide a link to the tutorial and tutorial data. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -32-

  34. Summary Summary of activity: • Used interactive interface to load a scene • Performed a workflow to make quantitative measures of tumor response to therapy including: --linear measurements --volume measurements * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -32-

  35. Acknowledgments Harvard Clinical and Translational Science Center National Alliance for Medical Image ComputingNIH U54EB005149 Neuroimage Analysis Center (NAC) National Center for Image-Guided Therapy (NCIGT) Surgical Planning Laboratory, Brigham and Women’s Hospital

More Related