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Standard Response Evaluation Criteria in Solid Tumors (RECIST) using 3D Slicer Slicer3 Training Compendium Jeffrey Yap, PhD Ron Kikinis, MD Wendy Plesniak, PhD Slide 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- Slide 3 Tutorial data Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -2- 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. Slide 4 Clinical context Baseline radiologists 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 radiologists 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- Baseline: June 2006 Follow-up: June 2007 Slide 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- Slide 6 Learning objective Following this tutorial, youll 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- Slide 7 Workflow Overview 1.Load two post-treatment datasets 2.Compare volumetric measures of tumor using label map statistics. 3.Identify tumor cross section containing largest diameter 4.Compare opposing diameters of largest tumor cross section using fiducial markers. 5. Assess changes. Workflow for linear and volumetric measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -6- * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 8 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 Quick overview of Slicer3 GUI Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -7- Slide 9 Loading data using a MRML scene file Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -8- 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 Slide 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. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -9- * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 11 Loading data: quick look at both image volumes Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -10- * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary 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 Slide 12 Make volume measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -11- 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 Slide 13 Make volume measurements: Baseline study Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -12- 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 Slide 14 Make volume measurements for baseline study Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -13- 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). V 2006 = 17432.05 mm 3 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 15 Make volume measurements: follow-up study Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -14- 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 Slide 16 Volume measurements for the follow-up study Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -15- Select 2007-spgr as the Input Greyscale Volume. Select 2007-spgr- label as they Input Labelmap. And click Apply. V 2007 = 17458.24mm 3 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 17 Record changes for assessment Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -16- Change in Tumor metrics: 2007-spgr 2006-spgr V mm 3 CD (mm)LD (mm) 17458.24 17432.05 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 Slide 18 Linear measurements: exploring baseline data Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -17- 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 Slide 19 Linear measurements: exploring baseline data Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -18- 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 Slide 20 Linear measurements: exploring baseline data Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -19- 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 Slide 21 Linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -20- Using LabelDiameterEstimation module (available currently only in the Slicer nightly builds), the following results were obtained for the largest diameter (LD). Baseline: June 2006 Follow-up: June 2007 The tutorial will use these results as a guide for making manual measurements. * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 22 Change layouts (shortcut using scene snapshot) Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -21- 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 Slide 23 Make linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -22- 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 Slide 24 Make linear measurements Four fiducial points have been set to Visible. Distance is reported between first two selected fiducial points. Each fiducials XYZ coordinates are editable. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -23- Fiducials Module GUI Panel * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 25 Make linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -24- 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 LD 2006 = 37.72mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 26 Make linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -25- Determine the opposing diameter (WHO). CD 2006 = 32.24mm Deselect the top two fiducials and select the next two: CD-1-2006 and CD-2-2006 * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 27 Change layouts (shortcut using scene snapshot) Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -26- 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 Slide 28 Linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -27- Use the same fiducials to make adjustments and new measurements. LD 2007 = 36.67mm * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 29 Linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -28- CD 2007 = 31.97mm (WHO) * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 30 Linear measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -29- 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 Slide 31 Comparing measurements Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -30- Compare corresponding measurements. Change in Tumor metrics: 2007-spgr 2006-spgr V mm 3 CD (mm)LD (mm) 17458.24 17432.05 31.9736.67 32.24 37.72 % 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 Slide 32 Assessment 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. Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -31- (Develop content here: discuss) * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 33 Assessment: Other tools to assess changes in tumor metrics Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -32- Segue into Change Tracker tutorial. Provide a link to the tutorial and tutorial data. (Develop content here: discuss) * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 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 Yap J, Kikinis R, Plesniak W: Harvard CTSC at RSNA2009 -32- * Load a MRML scene * Compare volumetric measurements * Switch layouts & make linear measurements * Switch layouts & analyze follow-up * Assessment * Summary Slide 35 Acknowledgments Harvard Clinical and Translational Science Center National Alliance for Medical Image Computing NIH U54EB005149 Neuroimage Analysis Center (NAC) National Center for Image-Guided Therapy (NCIGT) Surgical Planning Laboratory, Brigham and Womens Hospital