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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
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
Post-TX T1shown in“Four-up” Layout(Axial,Saggital,Coronal,& 3D Views)
Volumetric Analysis: Displaying 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
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
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
Fiducials Module:
• Create Fiducial List• Create two fiducials• Click & drag fiducials to endpoints of longest diameter• Record distance readout
Linear Measurement:D1pre=48.7073mm
Volumetric Analysis: Linear measurement
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
Fiducials Module:
•Click & drag fiducials to endpoints of orthogonal diameter
• Record distance readout
Linear Measurement:D2pre=48.6839 mm
Volumetric Analysis: Linear measurement
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
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)
Volumetric Analysis: Linear measurement
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
Volumetric Analysis: Linear measurement
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
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
Volumetric Analysis: ROI comparison
Editor Module: Rapidly define ROI(more accurate than ellipsoid)
Refine if desired:Dilate, Erode, Remove “islands”,Erase unwanted labels, etc.
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
View ROI:
as semi-transparent or opaque overlay, or…
…as outline at voxel
boundaries.
Volumetric Analysis: ROI comparison
Statistics Module: Specify:
• Pre-TX Volume• Label Map• Apply• Save output to file
Volume Measurement:Vpre = 7877.268 mm3
(computed for single slice)
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
Volumetric Analysis: ROI comparison
Similar workflow applied to Post-TX volume:
Volume Measurement:Vpost = 38.192 mm3
(computed for single slice)
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
Volumetric Analysis: Final volumetric comparisons
Pre- and Post-Treatment Comparisons:
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
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)
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 = 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)
Volumetric Analysis: Pre-processing data
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
Volumetric Analysis: Pre-processing data
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
Volumetric Analysis: Pre-processing data
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
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
Volumetric Analysis: Pre-processing data
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
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.
Volumetric Analysis: Pre-processing data
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
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
Advanced volumetric analysis: ChangeTracker Module
Wizards-> ChangeTracker Module:
Select high resolution segmentation (label map) of pre-TX tumor
(or specify an intensity threshold)
Volumetric Analysis: Analyzing change
Advanced volumetric analysis: ChangeTracker Module
Wizards-> ChangeTracker Module:
Choose growth metric(intensity patterns)
Choose not to align data since registration has already been performed.
Volumetric Analysis: Analyzing change
Advanced volumetric analysis: Building 3D Models
Volumetric Analysis: Analyzing change
Advanced volumetric analysis: Visualization
Volumetric Analysis: Analyzing change
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
• Approximate time to complete: 20 minutes??
Learning objective
Following Part II of this tutorial, you’ll be able to…
Part II: Perfusion Analysis using DCE-MRI
Description of Tutorial Data:
Pre-treatment:
Post-treatment:
Acknowledgement for the data?
Conclusion of Part II
What is important to conclude?
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)
• Approximate time to complete: 20 minutes??
Learning objective
Following Part III of this tutorial, you’ll be able to…
Part II: Functional Image Analysis using PET/CT
Description of Tutorial Data:
Pre-treatment:
Post-treatment:
Acknowledgement for the data?
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
What is important to conclude?
Acknowledgements
Harvard CTSC
NA-MIC
NAC
(what other?)