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

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

Slicer3 Training Compendium

Jeffrey Yap, PhDRon Kikinis, MDWendy Plesniak, PhD

Materials

This tutorial requires the following installation:

• 3D Slicer version 3.5 Software, which can be installed fromhttp://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

DisclaimerIt 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-

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.

Clinical context

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?


Baseline: June 2006 Follow-up: June 2007

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


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.


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


* Load a MRML scene* Compare volumetric measurements* Switch layouts & make linear measurements* Switch layouts & analyze follow-up* Assessment* Summary

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

3DViewerModule GUI Panel

Slice and 3D View

Controller

Menu Toolbar

Quick overview of Slicer3 GUI


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”


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.



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

Make volume measurements


Using Modules Menubutton:

Expose the menu and select the “LabelStatistics” module under the “Statistics” group.


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.


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


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.


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


Record changes for assessment


Change in Tumor metrics:

2007-spgr

2006-spgr

V mm3CD (mm)LD (mm)

17458.24

17432.05

Move on to make linear measurements at both timepoints…


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.




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.




Note the annotations that report voxel (IJK) coordinates and spatial (RAS) coordinates.

Note the magnified cursor view in the bottom-most GUI panel.


Linear measurements


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.


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…


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



Four fiducial points have been set to “Visible”.

Distance is reported between first two selected fiducial points.

Each fiducial’s XYZ coordinates are editable.


Fiducials Module GUI Panel




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




Determine the opposing diameter (WHO).

CD2006= 32.24mm

Deselect the top two fiducials and select the next two:CD-1-2006 and CD-2-2006


Change layouts (shortcut using scene snapshot)


Use the “Scene Snapshots” menubutton to restore the “2007SagOnly” snapshot.


Linear measurements…


Use the same fiducials to make adjustments and new measurements.

LD2007= 36.67mm




CD2007= 31.97mm

…(WHO)




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?


Comparing measurements


Compare corresponding measurements.

Change in Tumor metrics:

2007-spgr

2006-spgr

V mm3CD (mm)LD (mm)

17458.24

17432.05

31.9736.67

32.2437.72

% change: -2.78% -0.84% 0.15%


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.


(Develop content here: discuss)


Assessment: Other tools to assess changes in tumor metrics


Segue into Change Tracker tutorial.

Provide a link to the tutorial and tutorial data.

(Develop content here: discuss)


SummarySummary 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



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

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

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