Standard and Advanced
Tumor 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
(image)
Part 1: Volumetric Analysis
using Structural MR
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
Standard volumetric measurements
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
Volumetric Analysis: Loading data
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
…shows a DICOM
browser from which
data can be loaded
into Slicer…
Volumetric Analysis: Loading data
1.
2.
3.
4.
5.
Post-TX T1
shown in
“Four-up”
Layout
(Axial,
Saggital,
Coronal,
& 3D Views)
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Volumetric Analysis: Displaying data
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Pre-TX study
Volumes Module GUI
Post-TX study
Volumetric Analysis: Changing layouts
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout & Display Pre-TX volume
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Layout Options
Volumetric Analysis: Linear measurement
1.
2.
3.
4.
5.
Fiducials Module:
• Create Fiducial List
• Create two fiducials
• Click & drag fiducials
to endpoints of longest
diameter
• Record distance
readout
Linear Measurement:
D1pre=48.7073mm
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Volumetric Analysis: Linear measurement
1.
2.
3.
4.
5.
Fiducials Module:
•Click & drag fiducials
to endpoints of
orthogonal diameter
• Record distance
readout
Linear Measurement:
D2pre=48.6839 mm
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Volumetric Analysis: Linear measurement
1.
2.
3.
4.
5.
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)
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Volumetric Analysis: Linear measurement
1.
2.
3.
4.
5.
Linear Measurement
on Post-TX volume:
D1post=26.123mm
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor (scar) cross section
Compare region size of largest tumor cross section
Volumetric Analysis: Linear measurement
1.
2.
3.
4.
5.
Linear Measurement
on Post-TX volume:
D2post=17.8873mm
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor (scar) cross section
Compare region size of largest tumor cross section
Volumetric Analysis: ROI comparison
1.
2.
3.
4.
5.
Editor Module:
Use Threshold Paint
Tool, configured
to capture the
grayscale
range within tumor.
Paint in a few
strokes
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Volumetric Analysis: ROI comparison
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
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.
Volumetric Analysis: ROI comparison
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Statistics Module:
Specify:
•
•
•
•
Pre-TX Volume
Label Map
Apply
Save output to file
Volume Measurement:
Vpre = 7877.268 mm3
(computed for single slice)
Volumetric Analysis: ROI comparison
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Similar workflow
applied to Post-TX
volume:
Volume Measurement:
Vpost = 38.192 mm3
(computed for single slice)
Volumetric Analysis: Final volumetric comparisons
1.
2.
3.
4.
5.
Load pre- and post-treatment T1s (or Pre/Post GAD) study
Adjust display of both studies in Volumes Module
Switch to Axial (Red) Slice Layout
Compare opposing diameters of largest tumor cross section
Compare region size of largest tumor cross section
Pre- and Post-Treatment Comparisons:
D1
D2
V
Pre-TX
48.7073mm
48.6839 mm
7877.268 mm3
Post-TX
26.123mm
17.8873mm
38.192 mm3
Volumetric Analysis: Advanced volume change analysis
Advanced analysis, appropriate for assessing small tumor
changes.
Step A. Prepare data for registration & register pre- and post-TX
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
Volumetric Analysis: Pre-processing data
1.
2.
3.
4.
5.
Create left breast volume of interest for pre- and post-TX datasets
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTXbiascorr, ref = postTXbiascorr
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.
2.
3.
4.
5.
Create left breast volume of interest for pre- and post-TX datasets
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
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.
2.
3.
4.
4.
Create left breast volume of interest
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
Run manual, then affine registration with default settings
Editor Module:
Tools to use:
• threshold,
• save island,
• dilation,
• island removal,
• erosion
Perform for both preand post-TX
volumes, to create:
PreTreatSubvol-label
and
PostTreatSubvol-label
Volumetric Analysis: Pre-processing data
1.
2.
3.
4.
5.
Create left breast volume of interest
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
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.
2.
3.
4.
5.
Create left breast volume of interest
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
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.
2.
3.
4.
5.
Create left breast volume of interest
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
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.
2.
3.
4.
5.
Create left breast volume of interest
Mask out background using Editor Tools
Run MRI bias field correction
Run histogram matching: input = preTX, ref = post-TX
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?
(image)
Part 2: Perfusion Analysis using
DCE-MRI
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?
(image)
Part 3: Functional Image
Analysis using PET/CT
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?)