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Standard and Advanced Tumor Response Analysis using 3D Slicer

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).

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Standard and Advanced Tumor Response Analysis using 3D Slicer

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  1. Standard and Advanced Tumor Response Analysis using 3D Slicer Title change? Images & Acknowledgements…

  2. RECIST and Advanced Tumor Response Analysis in 3D Slicer Clinical relevance: (jeff) Tutorial description: (jeff desc. how addresses clinical needs)

  3. 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

  4. Part 1: Volumetric Analysis using Structural MR (image)

  5. 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??

  6. Learning objective Following Part I of this tutorial, you’ll be able to…

  7. Part I: Volumetric Analysis using structural MR Description of Tutorial Data: Pre-treatment: Post-treatment: Acknowledgement for the data?

  8. Volumetric Analysis: Measurement WorkFlow Standard volumetric measurements • 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

  9. Volumetric Analysis: Loading data • 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…

  10. Volumetric Analysis: Loading data • 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 Post-TX T1 shown in “Four-up” Layout (Axial, Saggital, Coronal, & 3D Views)

  11. Volumetric Analysis: Displaying data • 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

  12. Volumetric Analysis: Changing layouts • 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

  13. Volumetric Analysis: Linear measurement • 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 • Fiducials Module: • Create Fiducial List • Create two fiducials • Click & drag fiducials to endpoints of longest diameter • Record distance readout • Linear Measurement: • D1pre=48.7073mm

  14. Volumetric Analysis: Linear measurement • 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 • Fiducials Module: • Click & drag fiducials to endpoints of orthogonal diameter • Record distance readout • Linear Measurement: • D2pre=48.6839 mm

  15. Volumetric Analysis: Linear measurement • 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 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)

  16. Volumetric Analysis: Linear measurement • 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 Linear Measurement on Post-TX volume: D1post=26.123mm

  17. Volumetric Analysis: Linear measurement • 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 Linear Measurement on Post-TX volume: D2post=17.8873mm

  18. Volumetric Analysis: ROI comparison • 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: Use Threshold Paint Tool, configured to capture the grayscale range within tumor. Paint in a few strokes

  19. Volumetric Analysis: ROI comparison • 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.

  20. Volumetric Analysis: ROI comparison • 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)

  21. Volumetric Analysis: ROI comparison • 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)

  22. Volumetric Analysis: Final volumetric comparisons • 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 48.6839 mm 7877.268 mm3 48.7073mm Post-TX 26.123mm 17.8873mm 38.192 mm3

  23. 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 • Create left breast volume of interest (for both pre- and post-TX) • Mask out background using Editor Tools: • Run MRI bias field correction (10 iterations): • Run histogram matching: input = preTX, ref = post-TX • Run manual, then affine registration with default settings • Step B. Perform Change Tracking Analysis on registered datasets • Use ChangeTracker Wizard

  24. Volumetric Analysis: Pre-processing data • 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)

  25. Volumetric Analysis: Pre-processing data • 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)

  26. Volumetric Analysis: Pre-processing data • 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 pre- and post-TX volumes, to create: • PreTreatSubvol-label • and • PostTreatSubvol-label

  27. Volumetric Analysis: Pre-processing data • 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

  28. Volumetric Analysis: Pre-processing data • 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

  29. Volumetric Analysis: Pre-processing data • 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.

  30. Volumetric Analysis: Pre-processing data • 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.

  31. 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

  32. 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)

  33. 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.

  34. Volumetric Analysis: Analyzing change Advanced volumetric analysis: Building 3D Models

  35. Volumetric Analysis: Analyzing change Advanced volumetric analysis: Visualization

  36. Volumetric Analysis: Analyzing change Advanced volumetric analysis: Computing Changes

  37. Conclusion of Part I What is important to conclude?

  38. Part 2: Perfusion Analysis using DCE-MRI (image)

  39. 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??

  40. Learning objective Following Part II of this tutorial, you’ll be able to…

  41. Part II: Perfusion Analysis using DCE-MRI Description of Tutorial Data: Pre-treatment: Post-treatment: Acknowledgement for the data?

  42. Conclusion of Part II What is important to conclude?

  43. Part 3: Functional Image Analysis using PET/CT (image)

  44. 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??

  45. Learning objective Following Part III of this tutorial, you’ll be able to…

  46. Part II: Functional Image Analysis using PET/CT Description of Tutorial Data: Pre-treatment: Post-treatment: Acknowledgement for the data?

  47. Part II: Functional Image Analysis: Workflow • Load pre- and post-treatment CT, PET, and tumor segmentations • Adjust display of CT studies in Volumes Module • Switch to Four-Up Layout • Set up Display for PET (Volumes & VolumeRendering Modules) • Select pre-treatment CT, PET and label map in PETCTFusion Module • Retrieve values from DICOM or enter parameters manually • Perform analysis, record SUVmax, SUVmean, SUVmaxmean • Repeat for post-treatment CT, PET and label map

  48. Conclusion of Part III What is important to conclude?

  49. Acknowledgements Harvard CTSC NA-MIC NAC (what other?)

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