-- ctsa at rsna 2009 pet/ct analysis using 3d slicer jeffrey yap phd ron kikinis md wendy plesniak...

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-- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

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Page 1: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

PET/CT Analysis using 3D Slicer

Jeffrey Yap PhD

Ron Kikinis MD

Wendy Plesniak PhD

Slicer3 Training Compendium

Page 2: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

The Slicer3 software

• An end-user application for image analysis and visualization

• An open-source environment for software development

• A software platform that is both easy to use for clinical researchers and easy to extend for programmers

Page 3: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

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. Slicer is a tool for research, and is not FDA approved.

3D Slicer version 3 is a multi-platform software

running on Windows, Linux, and Mac OSX.

www.slicer.org

Page 4: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Software version

• This workshop uses a “pre-release cut” of Slicer version 3.5 which includes new features.

• Visit the slicer download page for Slicer 3.4 stable release, or for Slicer nightly builds.

Page 5: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

This raises the Load Scene Interface

• select the

PETCTFusion-Tutorial-Scene.mrml file

• double click the file, or click Open

Select File->Load Scene:

Load the MRML Scene

Page 6: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Study Data

•Non small cell lung cancer patient

•Two PET studies: one acquired before and the other 1 month after chemotherapy

•Two non-diagnostic CT images are acquired without the use of contrast

•FDG-PET scans acquired 60 minutes after intravenous injection of approximately 20 mCi of 18FDG

•Two VOIs have been created using Slicer’s Editor Module.

Page 7: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Navigate to the PETCTFusion Module

Using Modules Menubutton: Expose the menu and select the module called “PETCTFusion”.

PETCTFusion is a new and developing module.

Page 8: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Select the Volumes to Display and Analyze

In the Data Fusion panel, select:

CT volume: CT1,

PET volume: PET1,

and Tumor Mask: PET1-label volume.

When the PET volume is selected, a “wait message” will be displayed while parameters are read from DICOM header.

*Note: Click, hold & pull down menus to select…

Page 9: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

In the Display Panel, choose a colorization option for the PET volume from among

Grey, Heat, or Spectrum.

Adjust the window and level for CT1 and PET1 volumes.

Adjust the Slices Fade Scale to jointly display the datasets.

Adjust the combined display of PET and CT data

Page 10: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Explore the dataset

Explore:

in the Slice Viewers, scroll through the slices to locate the green Tumor label and the yellow Liver label

Note: (the yellow label is used only to demonstrate multiple-VOI functionality).

Page 11: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

View Tumor Label in all Slice Viewers

Shortcut: To view the Tumor Label in all Slice Viewers:

Enter –740 in the Axial Slice Viewer’s Slice Number Entry

…and…

-54 (Sagittal)

103 (Coronal)

These are mm positions within the reference frame of the image volumes.

Page 12: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

SUVmax and SUVmean for each VOI (represented by a different color in the label map) will be displayed in the table.

Compute SUV for all VOIs in the pre-treatment study

In the Quantitative Measures panel, click the Compute/Refresh button.

Page 13: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Compute SUVbw for follow-up study.

Now select:

the CT volume CT2, the PET volume PET2 and the Tumor Mask called PET2-label in the Data Fusion Panel.

This dataset contains a green VOI that corresponds to the tumor segmentation the pre-treatment study.

Page 14: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Adjust the display for the follow-up study.

You may want to adjust the Slices Fade Slider and manipulate the 3D View to refresh them.

Adjust display for follow-up study.

Page 15: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Compute SUVbw for follow-up study.

In the “Quantitative Measures” Panel, select Compute/Refresh to compute SUVbw for the green Tumor volume (and yellow liver volume).

Page 16: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Assess response with respect to this VOI

Pre-Treatment Max SUVbw =

Post-Treatment Max SUVbw =

8.0

9.4

+16.61% (SD)

Page 17: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Appropriate use

• Still validating this module against performance of commercial systems.

• Appropriate for DICOM PET studies only

• Not compatible with Philips datasets

Page 18: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

This tutorial has demonstrated:

• Workflow to make quantitative measurements of SUV in PETCTFusion module

Summary

Page 19: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

Slides and Datasets:

Tutorial Data:http://wiki.na-mic.org/Wiki/images/7/73/PETCTFusion-Tutorial-Data.zip

Tutorial Software:http://www.na-mic.org/Slicer/Download/Snapshots/win32/Slicer3-3.5-RSNA-2009-11-06-

win32.exe

More Information:http://www.slicer.org

Summary

Page 20: -- CTSA at RSNA 2009 PET/CT Analysis using 3D Slicer Jeffrey Yap PhD Ron Kikinis MD Wendy Plesniak PhD Slicer3 Training Compendium

--CTSA at RSNA 2009

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