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

• 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

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 Module3. Switch to Axial (Red) Slice Layout 4. Compare opposing diameters of largest tumor cross section5. Compare region size of largest tumor cross section

File->Add Volume…shows a DICOM browser from whichdata can be loadedinto Slicer…






Volumetric Analysis using 3D Slicer: Loading Data







Post-TX T1shown in“Four-up” Layout(Axial,Saggital,Coronal,& 3D Views)

Volumetric Analysis using 3D Slicer: Displaying Data







Volumes Module GUIPre-TX study

Post-TX study

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 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 using 3D Slicer: Linear Measurement







Fiducials Module:

• Create Fiducial List• Create two fiducials• Click & drag fiducials to endpoints of longest diameter• Record distance readout

Linear Measurement:D1pre=48.7073mm








Fiducials Module:

•Click & drag fiducials to endpoints of orthogonal diameter

• Record distance readout

Linear Measurement:D2pre=48.6839 mm








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)







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







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 using 3D Slicer: ROI Comparison






Editor Module: Use Threshold PaintTool, configuredto capture the grayscale range within tumor.

Paint in a fewstrokes








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.







Statistics Module: Specify:

• Pre-TX Volume• Label Map• Apply• Save output to file

Volume Measurement:Vpre = 7877.268 mm3

(computed for single slice)








Similar workflow applied to Post-TX volume:

Volume Measurement:Vpost = 38.192 mm3

(computed for single slice)








Pre- and Post-Treatment Comparisons:


Post-TX

Pre-TX

VD2D1

38.192 mm3

7877.268 mm3

17.8873mm26.123mm

48.6839 mm48.7073mm






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






Volumetric Analysis using 3D Slicer: 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)







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)







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







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








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








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.








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 using 3D Slicer: Change Tracking Analysis

Advanced volumetric analysis: ChangeTracker Module






Wizards-> ChangeTracker Module:

Use default registration parameters.

Scan1 = pre-Tx

Scan2 = post-Tx

Create subvolume around pre-Tx tumor









Select high resolution segmentation (label map) of pre-TX tumor

(or specify an intensity threshold)









Choose growth metric(intensity patterns)

Choose not to align data since registration has already been performed.


Advanced volumetric analysis: Building 3D Models







Advanced volumetric analysis: Visualization






Volumetric Analysis using 3D Slicer: Volume Change Analysis

Advanced volumetric analysis: Computing Changes






Documents

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