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Pohl K, Konukoglu E
-1-National Alliance for Medical Image Computing
Measuring Volume Change in Tumors
Kilian M Pohl, PhDEnder Konugolu
Slicer3 Training Compendium
Pohl K, Konukoglu E
-2-National Alliance for Medical Image Computing
Material
This course requires the following installation:
•The current version of Slicer 3 Software, which can be installed from http://www.na-mic.org/Slicer/Download/Snapshots/<OS>/Slicer3-3.3-alpha-2008-09-11-*
•The TumorGrowth-Tutorial-Data.xcat, which can be downloaded from http://www.na-mic.org/Wiki/index.php/Slicer3:Training
•A reliable internet connection for downloading the data
Disclaimer
It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.
The module described in this tutorial was tested on Axial 3D SPGR T1 post Gadolinium scans (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256)
Pohl K, Konukoglu E
-3-National Alliance for Medical Image Computing
Data
This course is built upon two scans of a patient with meningioma:
MR Scan 1 MR Scan 2
Pohl K, Konukoglu E
-4-National Alliance for Medical Image Computing
Learning objective
Following this tutorial, you’ll be able to load two scans into Slicer3, and measure and visualize the change in volume of the meningioma between the two scans.
Pohl K, Konukoglu E
-5-National Alliance for Medical Image Computing
Overview
• Loading a scene
• Measuring volume change in tumors
Pohl K, Konukoglu E
-6-National Alliance for Medical Image Computing
Part 1: Loading the tutorial data
via a scene file
Pohl K, Konukoglu E
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Slicer3 GUI
The Graphical User Interface (GUI) of Slicer3 integrates five components:
•the Menu Toolbar
•the Module GUI Panel
•the 3D Viewer
•the Slice Viewer
•the Slice and 3D View Controller
Slice Viewer
3DViewerModule GUI Panel
Slice and 3D View
Controller
Menu Toolbar
Pohl K, Konukoglu E
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Loading a SceneSelect FileLoad Scene in the Main Menu.
Load the file ChangeTracker-Tutorial-Data.xcat
Data is downloaded from www.xnat.org
Pohl K, Konukoglu E
-9-National Alliance for Medical Image Computing
Loading a Scene
The MRML Tree in the Data module shows the two scans (2006-spgr and 2007-spgr) in this scene.
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Modifying Layout of Viewer
Select and Four-up layout.
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New Layout of Viewer
Slice Viewers
3D Viewer
Modify size of windows as needed
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Part 2: Measuring Volume Change
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New Layout of Viewer
Select Modules
Select ChangeTracker
Pohl K, Konukoglu E
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Workflow Wizard
The Workflow Wizard of Slicer3 guides the user through a sequence of steps and is defined by the following components:
•the Step Panel
•the User Panel
•the Navigation Panel
Step Panel
User Panel
Navigation Panel
Pohl K, Konukoglu E
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Select Scans
Select 2006-spgr and 2007-spgr
Press Next
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Identify Volume of Interest
Move sliders to see tumor
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Identify Volume of Interest
Identify VOI by clicking left mouse button inside tumor
Press Show VOI to view region
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Identify Volume of Interest
VOI is shown in blue
Lower and Upper bound of VOI
Pohl K, Konukoglu E
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Identify Volume of Interest
Move sliders or enter:X: 105 155Y: 76 121Z: 62 90
Press Next
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Segment Tumor
Slice Viewers show VOI with current Segmentation
3D Viewer shows model of tumor with additional structures
Change Segmentation by moving Slider to 125
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Segment TumorPress Grid to view grid with original voxel size
Pohl K, Konukoglu E
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Segment TumorPress Slice to see the first scan in the 3D Viewer
Press Next
Pohl K, Konukoglu E
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Choose Metric TypeChoice of Metric:
• Detect change by analyzing intensity pattern (fast)
• Measure change by analyzing deformation map (slow)
Select fast and press Analyze
Pohl K, Konukoglu E
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Analysis I: Volume Preserving Registration
Before Afterwards
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Analysis II: Normalize Intensities
Scan 1 Scan 2 Scan 2 - Norm
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)(absxI
PDF of Dormant Tissue
Determine probability density function
Analysis III: Detect Change – Intensity
Based
- =
Compute statistics of static tissue:
Subtract Scan2 from Scan1
Define region of static tissue
Pohl K, Konukoglu E
-27-National Alliance for Medical Image Computing
Analysis III: Detect Change – Intensity Based
Mode : Sensitive Moderate Robust False Positive Risk: High Medium LowGrowth (mm3) : 1301 547 100Growth (voxel): 1057 444 81
Ana
lysi
sD
ata
Konukoglu et al. ,“Monitoring Slowly Evolving Tumors”, ISBI, 2008
Pohl K, Konukoglu E
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Analysis III: Detect Change–Deformation Map
=
Determine change via mapping:
Compute diffeomorphic mapping between scans
Compute Jaccobian
Apply mapping to segmentation
or
Mode : Jaccobian Growth (mm3) : 1291 Growth (voxels): 1049
Mode : Segmentation Growth (mm3) : 1386 Growth (voxels): 1126
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Show Change in Pathology
Define sensitivity of analysis
Show change in volume: purple = growthgreen = shrinkage
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Define Working Directory
Press directory button
Select to create directory
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Define Working Directory
Enter tutorial and press OK
Select tutorial and press OK
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Save Screenshot
Press ScreenshotScreenshot is saved to tutorial directory
View TG_Screenshot_001.png
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Save Analysis Result
Press AnalysisOutcome of analysis is saved to tutorial directory
View AnalysisOutcome.log
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Save Intermediate Results
Press Data
Press Save All and Save
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Finish Workflow
Press OK to return to the first step of the workflow
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Overview
• Loading a scene
• Measuring volume change in tumors
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Summary
Conclusion:
• Interactive interface to load scene
• Workflow technology to semi-automatically detect change in pathology
In-depth description of technology:
• Konukoglu et al. ,“Monitoring Slowly Evolving Tumors”, IEEE ISBI, p. 812 – 815, 2008 http://www.spl.harvard.edu/pages/Special:PubDB_View?dspaceid=1430
• Pohl et al. , “Automatic Tumor Growth Detection” in Meningiomas A Comprehensive Text, In Press.
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Information
• We tested the tool on Axial 3D SPGR T1 post Gadolinium scans (Voxel dimension: 0.94mm x 0.94mm x 1.20mm, FOV: 240mm, Matrix: 256 x 256)
• We expect the tool to work also on set of scans that fulfill the following requirements:– same patient was scanned– scans were acquired with the same
acquisition protocol – scans have isotropic resolution
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Acknowledgments
National Alliance for Medical Image ComputingNIH U54EB005149
add nac, ncigt and spl acknowledgements
Brain Science Foundation
INRIA, France