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Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer:

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Presentation on theme: "Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer:"— Presentation transcript:

1 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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

2 Volumetric Analysis using 3D Slicer: 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 File->Add Volume …shows a DICOM browser from which data can be loaded into Slicer… Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

3 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Post-TX T1 shown in Four-up Layout (Axial, Saggital, Coronal, & 3D Views)

4 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumes Module GUIPre-TX study Post-TX study

5 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Layout Options

6 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Fiducials Module: Create Fiducial List Create two fiducials Click & drag fiducials to endpoints of longest diameter Record distance readout Linear Measurement: D1 pre = mm

7 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Fiducials Module: Click & drag fiducials to endpoints of orthogonal diameter Record distance readout Linear Measurement: D2 pre = mm

8 Volumetric Analysis using 3D Slicer: 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 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis 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)

9 Volumetric Analysis using 3D Slicer: Linear Measurement Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Linear Measurement on Post-TX volume: D1 post =26.123mm 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

10 Volumetric Analysis using 3D Slicer: Linear Measurement Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Linear Measurement on Post-TX volume: D2 post = mm 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

11 Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Editor Module: Use Threshold Paint Tool, configured to capture the grayscale range within tumor. Paint in a few strokes 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

12 Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis 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 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 View ROI: as semi-transparent or opaque overlay, or… …as outline at voxel boundaries.

13 Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Statistics Module: Specify: Pre-TX Volume Label Map Apply Save output to file Volume Measurement: V pre = mm 3 (computed for single slice) 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

14 Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Similar workflow applied to Post-TX volume: Volume Measurement: V post = mm 3 (computed for single slice) 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

15 Volumetric Analysis using 3D Slicer: ROI Comparison Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis 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 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 Pre-TX VD2D mm mm mm26.123mm mm mm

16 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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 Pre-process Data & Perform Volume Change Analysis Step A. Prepare data for registration & register pre- and post-TX

17 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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)

18 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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: (subsequently renamed PreTreatSubvol for brevity) Post-Tx subvolume: (subsequently renamed PostTreatSubvol for brevity)

19 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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

20 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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 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

21 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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 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

22 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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.

23 Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Volumetric Analysis using 3D Slicer: 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.

24 Volumetric Analysis using 3D Slicer: Change Tracking Analysis Advanced volumetric analysis: ChangeTracker Module Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Wizards-> ChangeTracker Module: Use default registration parameters. Scan1 = pre-Tx Scan2 = post-Tx Create subvolume around pre-Tx tumor

25 Volumetric Analysis using 3D Slicer: Change Tracking Analysis Advanced volumetric analysis: ChangeTracker Module Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Wizards-> ChangeTracker Module: Select high resolution segmentation (label map) of pre-TX tumor (or specify an intensity threshold)

26 Volumetric Analysis using 3D Slicer: Change Tracking Analysis Advanced volumetric analysis: ChangeTracker Module Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis Wizards-> ChangeTracker Module: Choose growth metric (intensity patterns) Choose not to align data since registration has already been performed.

27 Volumetric Analysis using 3D Slicer: Pre-processing Data Advanced volumetric analysis: Building 3D Models Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

28 Volumetric Analysis using 3D Slicer: Pre-processing Data Advanced volumetric analysis: Visualization Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis

29 Volumetric Analysis using 3D Slicer: Volume Change Analysis Advanced volumetric analysis: Computing Changes Clinical case studies Volumetric Measurements Visualization & Change Tracking Perfusion Analysis PET/CT Image Analysis


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