Standard and Advanced Tumor Response Analysis using 3D Slicer

Standard and AdvancedTumor Response Analysis

using 3D Slicer

Title change?Images &Acknowledgements…

RECIST and Advanced Tumor Response Analysis in 3D Slicer

Clinical relevance: (jeff)

Tutorial description: (jeff desc. how addresses clinical needs)

RECIST and Advanced Tumor Response Analysis in 3D Slicer

The tutorial has 3 parts:

1. Volumetric analysis using structural MR

2. Perfusion analysis using DCE-MRI

3. Functional image analysis for PET/CT

Part 1: Volumetric Analysis using Structural MR

(image)

Overview

Part I: Volumetric Analysis using structural MR

In Part I, you will learn how to perform volumetric analysis of tumors using both existing and developing tools using 3D Slicer.

• Standard Response Evaluation Criteria in Solid Tumors (RECIST) analysis, and

• Advanced analyses and visualization of tumor response to therapy using Slicer’s ChangeTracker Module.

• Approximate time to complete: 60 minutes??

Learning objective

Following Part I of this tutorial, you’ll be able to…

Part I: Volumetric Analysis using structural MR

Description of Tutorial Data:

Pre-treatment:

Post-treatment:

Acknowledgement for the data?

Volumetric Analysis: 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

Volumetric Analysis: Loading data

1. Load pre- and post-treatment T1s (or Pre/Post GAD) study 2. Adjust display of both studies in Volumes Module3. Switch to Axial (Red) Slice Layout 4. Compare opposing diameters of largest tumor cross section5. Compare region size of largest tumor cross section

…shows a DICOM browser from whichdata can be loadedinto Slicer…

Volumetric Analysis: Loading data


Post-TX T1shown in“Four-up” Layout(Axial,Saggital,Coronal,& 3D Views)

Volumetric Analysis: Displaying data


Volumes Module GUIPre-TX study

Post-TX study

Volumetric Analysis: Changing layouts

1. Load pre- and post-treatment T1s (or Pre/Post GAD) study 2. Adjust display of both studies in Volumes Module3. Switch to Axial (Red) Slice Layout & Display Pre-TX volume4. Compare opposing diameters of largest tumor cross section5. Compare region size of largest tumor cross section

Layout Options

Volumetric Analysis: Linear measurement


Fiducials Module:

• Create Fiducial List• Create two fiducials• Click & drag fiducials to endpoints of longest diameter• Record distance readout

Linear Measurement:D1pre=48.7073mm



Fiducials Module:

•Click & drag fiducials to endpoints of orthogonal diameter

• Record distance readout

Linear Measurement:D2pre=48.6839 mm



Or:

Make only Axial Slice visible in 3D Viewer

Select Four-Up Layout

Use Measurements Module to turn on Ruler Widget; click & drag line & endpoints.

(Currently being extended to work in Slice Viewers too)


Linear Measurementon Post-TX volume:

D1post=26.123mm

1. Load pre- and post-treatment T1s (or Pre/Post GAD) study 2. Adjust display of both studies in Volumes Module3. Switch to Axial (Red) Slice Layout 4. Compare opposing diameters of largest tumor (scar) cross section5. Compare region size of largest tumor cross section


Linear Measurementon Post-TX volume:

D2post=17.8873mm

1. Load pre- and post-treatment T1s (or Pre/Post GAD) study 2. Adjust display of both studies in Volumes Module3. Switch to Axial (Red) Slice Layout 4. Compare opposing diameters of largest tumor (scar) cross section5. Compare region size of largest tumor cross section

Volumetric Analysis: ROI comparison

Editor Module: Use Threshold PaintTool, configuredto capture the grayscale range within tumor.

Paint in a fewstrokes



Editor Module: Rapidly define ROI(more accurate than ellipsoid)

Refine if desired:Dilate, Erode, Remove “islands”,Erase unwanted labels, etc.


View ROI:

as semi-transparent or opaque overlay, or…

…as outline at voxel

boundaries.


Statistics Module: Specify:

• Pre-TX Volume• Label Map• Apply• Save output to file

Volume Measurement:Vpre = 7877.268 mm3

(computed for single slice)



Similar workflow applied to Post-TX volume:

Volume Measurement:Vpost = 38.192 mm3

(computed for single slice)


Volumetric Analysis: Final volumetric comparisons

Pre- and Post-Treatment Comparisons:


Post-TX

Pre-TX

VD2D1

38.192 mm3

7877.268 mm3

17.8873mm26.123mm

48.6839 mm48.7073mm

Volumetric Analysis: Advanced 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 MRI bias field correction (10 iterations):

4. Run histogram matching: input = preTX, ref = post-TX

5. Run manual, then affine registration with default settings

Step B. Perform Change Tracking Analysis on registered datasets

6. Use ChangeTracker Wizard

Advanced analysis, appropriate for assessing small tumor changes.

Step A. Prepare data for registration & register pre- and post-TX

Volumetric Analysis: Pre-processing data

1. Create left breast volume of interest for pre- and post-TX datasets2. Mask out background using Editor Tools3. Run MRI bias field correction4. Run histogram matching: input = preTXbiascorr, ref = postTXbiascorr5. Run manual, then affine registration with default settings

Wizards->ChangeTracker Module:

• Select pre- and post-TX datasets;

• Specify ROI (pre- and post-TX subvolumes should contain anatomy in good correspondence.

• Oversample pre-Tx by a factor of 2 (low resolution dataset)


1. Create left breast volume of interest for pre- and post-TX datasets2. Mask out background using Editor Tools3. Run MRI bias field correction4. Run histogram matching: input = preTX, ref = post-TX5. Run manual, then affine registration with default settings

Wizards->ChangeTracker Module:

Pre-Tx-supersampled subvolume:(subsequently renamed “PreTreatSubvol” for brevity)

Post-Tx subvolume:(subsequently renamed “PostTreatSubvol” for brevity)


1. Create left breast volume of interest2. Mask out background using Editor Tools3. Run MRI bias field correction 4. Run histogram matching: input = preTX, ref = post-TX4. Run manual, then affine registration with default settings

Editor Module:

Tools to use:• threshold, • save island, • dilation, • island removal,• erosion

Perform for both pre- and post-TX volumes, to create:

PreTreatSubvol-label andPostTreatSubvol-label


1. Create left breast volume of interest2. Mask out background using Editor Tools3. Run MRI bias field correction4. Run histogram matching: input = preTX, ref = post-TX5. Run manual, then affine registration with default settings

MRI Bias Field Correction Module:

IN parameters = GADParameters

Input Volume =PreTreatSubvol

Mask Volume =PreTreatSubvol-label

Create new volumes for Preview and Output.

Set iterations = 10

Use default parameters for all other options.

Pre-TX prior to bias field correction Pre-TX after bias field correction



Histogram Matching Module:

Default parameters

Input Volume =PreTreatSubvolBias10

Reference Volume =PostTreatSubvolBias10

Create new volumes for Output.

Pre-TX prior to histogram matching Pre-TX after histogram matching



Transforms Module:

Adjust display:Change color LUTs in Volumes Module to use Red/Green or Ocean/Desert, and adjust the FG/BG fade to display both layers simultaneously.

Adjust Translations and Rotations manually to get best possible alignment.



Registration-> Affine Registration Module:

Use default registration parameters.

Initial Transform = linear transform

Fixed image = pre-Tx

Moving image = post-Tx

Create new transform for affine output

Create new volume for output.

Volumetric Analysis: Analyzing changes

Advanced volumetric analysis: ChangeTracker Module

Wizards-> ChangeTracker Module:

Use default registration parameters.

Scan1 = pre-Tx

Scan2 = post-Tx

Create subvolume around pre-Tx tumor

Volumetric Analysis: Analyzing change



Select high resolution segmentation (label map) of pre-TX tumor

(or specify an intensity threshold)




Choose growth metric(intensity patterns)

Choose not to align data since registration has already been performed.


Advanced volumetric analysis: Building 3D Models


Advanced volumetric analysis: Visualization


Advanced volumetric analysis: Computing Changes

Conclusion of Part I

What is important to conclude?

Part 2: Perfusion Analysis using DCE-MRI

(image)

Overview

Part II: Perfusion Analysis using DCE-MRI

In Part II, you will learn how to load, visualize and analyze perfusion sequences using the FourDImage and FourDAnalysis Modules in 3D Slicer.

• Load DICOM DCE-MRI perfusion dataset

• Visualize the timeseries data

• Create a simple ROI using thresholding

• Plot intensity profiles for both tumor and blood pool

• and perform curve fitting using Toft’s Kinetic Model


Learning objective

Following Part II of this tutorial, you’ll be able to…

Part II: Perfusion Analysis using DCE-MRI


Pre-treatment:

Post-treatment:


Conclusion of Part II


Part 3: Functional Image Analysis using PET/CT

(image)

Overview

Part III: Functional image analysis using PET/CT

In Part II, you will learn how to load, visualize and analyze PET/CT studies using the PETCTFusion Module in 3D Slicer.

• Load DICOM and non-DICOM PET/CT datasets

• Visualize the Fused datasets

• Manually enter required nuclear medicine parameters

• and Compute the Standardized Uptake Value (SUV)


Learning objective

Following Part III of this tutorial, you’ll be able to…

Part II: Functional Image Analysis using PET/CT


Pre-treatment:

Post-treatment:


Part II: Functional Image Analysis: Workflow

1. Load pre- and post-treatment CT, PET, and tumor segmentations

2. Adjust display of CT studies in Volumes Module

3. Switch to Four-Up Layout

4. Set up Display for PET (Volumes & VolumeRendering Modules)

5. Select pre-treatment CT, PET and label map in PETCTFusion Module

6. Retrieve values from DICOM or enter parameters manually

7. Perform analysis, record SUVmax, SUVmean, SUVmaxmean

8. Repeat for post-treatment CT, PET and label map

Conclusion of Part III


Acknowledgements

Harvard CTSC

NA-MIC

NAC

(what other?)

Standard and Advanced Tumor Response Analysis using 3D Slicer

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