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Tutorial slides currently under development - 3D Slicer

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					 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.   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




…shows a DICOM
browser from which
data can be loaded
into 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 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




Post-TX T1
shown 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 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


Pre-TX study                                                  Volumes Module GUI




                             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 Module
 3.   Switch to Axial (Red) Slice Layout & Display Pre-TX volume
 4.   Compare opposing diameters of largest tumor cross section
 5.   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 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




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 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




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 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


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

              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 (scar) cross section
              5.     Compare region size of largest tumor cross section



Linear Measurement
on Post-TX volume:

D1post=26.123mm
            Volumetric Analysis: Linear measurement

              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 (scar) cross section
              5.     Compare region size of largest tumor cross section



Linear Measurement
on Post-TX volume:

D2post=17.8873mm
                 Volumetric Analysis: ROI comparison

                  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



Editor Module:

Use Threshold Paint
Tool, configured
to capture the
grayscale
range within tumor.

Paint in a few
strokes
                 Volumetric Analysis: ROI comparison

                     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



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.     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



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.     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



Similar workflow
applied to Post-TX
volume:


Volume Measurement:
Vpost = 38.192 mm3
(computed for single slice)
 Volumetric Analysis: Final volumetric comparisons

  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




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.    Create left breast volume of interest for pre- and post-TX datasets
                 2.    Mask out background using Editor Tools
                 3.    Run MRI bias field correction
                 4.    Run histogram matching: input = preTXbiascorr, ref = postTXbiascorr
                 5.    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 datasets
              2.   Mask out background using Editor Tools
              3.   Run MRI bias field correction
              4.   Run histogram matching: input = preTX, ref = post-TX
              5.   Run manual, then affine registration with default settings



Wizards->ChangeTracker Module:




                   Pre-Tx-supersampled subvolume:                    Post-Tx subvolume:
                   (subsequently renamed                             (subsequently renamed
                   “PreTreatSubvol” for brevity)                     “PostTreatSubvol” for brevity)
             Volumetric Analysis: Pre-processing data
              1.    Create left breast volume of interest
              2.    Mask out background using Editor Tools
              3.    Run MRI bias field correction
              4.    Run histogram matching: input = preTX, ref = post-TX
              4.    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
       and
PostTreatSubvol-label
               Volumetric Analysis: Pre-processing data
                1.    Create left breast volume of interest
                2.    Mask out background using Editor Tools
                3.    Run MRI bias field correction
                4.    Run histogram matching: input = preTX, ref = post-TX
                5.    Run manual, then affine registration with default settings



MRI Bias Field                Pre-TX prior to bias field correction     Pre-TX after bias field correction
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.
              Volumetric Analysis: Pre-processing data
               1.    Create left breast volume of interest
               2.    Mask out background using Editor Tools
               3.    Run MRI bias field correction
               4.    Run histogram matching: input = preTX, ref = post-TX
               5.    Run manual, then affine registration with default settings



Histogram Matching           Pre-TX prior to histogram matching        Pre-TX after histogram matching
Module:

Default parameters

Input Volume =
PreTreatSubvolBias10

Reference Volume =
PostTreatSubvolBias10

Create new volumes for
Output.
              Volumetric Analysis: Pre-processing data
               1.     Create left breast volume of interest
               2.     Mask out background using Editor Tools
               3.     Run MRI bias field correction
               4.     Run histogram matching: input = preTX, ref = post-TX
               5.     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 interest
               2.     Mask out background using Editor Tools
               3.     Run MRI bias field correction
               4.     Run histogram matching: input = preTX, ref = post-TX
               5.     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?)

				
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posted:6/5/2012
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