Tools for Processing Medical Images · Automatic Segmentation Measuring Tumor Growth Conclusion....
Transcript of Tools for Processing Medical Images · Automatic Segmentation Measuring Tumor Growth Conclusion....
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Tools for Processing Medical ImagesBy
Kilian Maria Pohl
[email protected] ♦ http://www.csail.mit.edu/~pohl
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Kilian M. Pohl - 2 -
Overview
Motivation
Software for Processing Images
Automatic Segmentation
Measuring Tumor Growth
Conclusion
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Kilian M. Pohl Motivation - 3 -
Neuroscience Studies
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Kilian M. Pohl Motivation - 4 -
Multiple Sclerosis Lesion
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Kilian M. Pohl Motivation - 5 -
Finding Differences
Within SubjectsAcross Subjects
courtesy of Istvan Csapo
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Kilian M. Pohl Motivation - 6 -
Manual vs. Automatic
Manual Segmentation:- Very expensive- High risks related to observer reliability
Automatic segmentation:- Relatively cheap- Quality is often lower than manual segmentations
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Kilian M. Pohl Slicer 3 - 7 -
GoalDevelop tools for processing medical images:- fast and flexible - requiring minimal amount of training effort- include prior information
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Kilian M. Pohl - 8 -
Overview
Motivation
Software for Processing Images
Automatic Segmentation
Measuring Tumor Growth
Conclusion
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Kilian M. Pohl Slicer 3 - 9 -
What is 3D Slicer?
• A platform for exploring novel image analysis and visualization techniques
• A freely-downloadable code and executablesavailable for Windows,Linux,and Mac OS X
• Slicer is a research platform:– NOT FDA approved – NOT finished (work in progress)
Image provided by S. Pieper
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Kilian M. Pohl Slicer 3 - 10 -
3D Slicer
• www.slicer.org• Over 500k lines of
code• 32 active developer• Tutorial:
Google: slicer 101
Image provided by A. Golby, F. Talos, P. Black
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Kilian M. Pohl Slicer 3 - 11 -
Slicer Features
• Visualization • Filtering• Registration• Segmentation• DTI• Quantification• Real-time Integration
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Kilian M. Pohl Slicer 3 - 12 -
Algorithms: DTI
• Automatic extraction of anatomically meaningful fiber bundles
• Advanced Rendering methods for segmentation results using photon mapping
Rendering provided by Banks, Data by Odonnell, Shenton, Westin, et al.
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Kilian M. Pohl Slicer 3 - 13 -
• Active visualization of medical images to aid in decision making.
• Allows physician to– See Beyond the
Surface– Define Targets– Control the
Interventions
• Enables new procedures, decreases invasiveness, optimizes resection
Image Guided Therapy (IGT)
Dimaio SP, Archip N, Hata N, Talos IF, Warfield SK, Majumdar A, Mcdannold N, Hynynen K, Morrison PR, Wells WM 3rd, Kacher DF, Ellis RE, Golby AJ, Black PM, JoleszFA, Kikinis R.: Image-guided neurosurgery at Brigham and Women's Hospital.IEEE Eng Med Biol Mag. 2006 Sep-Oct;25(5):67-73
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Kilian M. Pohl Slicer 3 - 14 -
U Iowa Meshing Project
• VTK/KWWidgetsbased Mesh Quality Viewer (Lisle)
• Migration of Stand Alone Meshing Tool into Slicer Module (Lisle)
• Key Driver for 3D Widgets in Slicer3
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Kilian M. Pohl Slicer 3 - 15 -
Many More Examples
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Kilian M. Pohl Slicer 3 - 16 -
NA-MIC Kit Components
• End User Application–3D Slicer
• Image Analysis, Visualization, and GUI libraries–ITK, VTK, KWWidgets
• Large Scale Data Processing Tools –Batchmake, BIRN GRID tools
• Software Engineering Tools–CMake, Dart, CTest, CPackhttp://www.na-mic.org/Wiki/index.php/SoftwareInventory
Provided by Pieper, Kikinis
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Kilian M. Pohl Motivation - 17 -
Acknowledgments
V E R I TAS
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Kilian M. Pohl - 18 -
Overview
Motivation
Software for Processing Images
Automatic Segmentation
Measuring Tumor Growth
Conclusion
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Kilian M. Pohl Slicer 3 - 19 -
Tissue Classification
Software:-EMWells 96
-EMSVan Leemput 99
-SPMAshburner 03
-MNIZijdenbos 02
-FSLZhang 01
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Cortical + Subcortical Parcellation
Software:-ANIMALCollins 99-EM-MF-LPPohl 02
-FreesurferFischl 02
-BrainSuiteThompson 04
-FANTASMTosun 04
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Kilian M. Pohl Motivation - 21 -
Mission
ToolMRI
Atlas
Label Map
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Kilian M. Pohl Slicer 3 - 22 -
Hierarchical Tree
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Kilian M. Pohl Slicer 3 - 23 -
Design of Algorithm
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Kilian M. Pohl Slicer 3 - 24 -
Level 1Pr
ior
Info
rmat
ion
IMAGE
BG ICC
CSF GM WM
Input
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Level 2C
urre
nt P
aram
eter
Input
IMAGE
ICC
CSF GM WM
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Kilian M. Pohl Slicer 3 - 26 -
Modify the Tree
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Kilian M. Pohl Slicer 3 - 27 -
Segmentation of 31 Structures
Pohl et al., ISBI 04
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Kilian M. Pohl Slicer 3 - 28 -
Software in 3D Slicer
Download: www.slicer.orgTutorial: http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
S. Bouix et al. On evaluating brain tissue classifiers without a ground truth, NeuroImage, Volume 36, Issue 4, pp 1207-1224, 2007
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Kilian M. Pohl Slicer 3 - 29 -
SpecifyInputs
Parameters Target Images Atlas Images
EM Segment Workflow
courtesy of Brad Davis
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Kilian M. Pohl Slicer 3 - 30 -
SpecifyInputs
DefaultPre-
Processing
Parameters Target Images Atlas Images
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
EM Segment Workflow
courtesy of Brad Davis
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Kilian M. Pohl Slicer 3 - 31 -
SpecifyInputs
DefaultPre-
Processing
Parameters Target Images Atlas Images
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
Segmentation EM Segment Algorithm: Pohl et al.
EM Segment Workflow
courtesy of Brad Davis
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Kilian M. Pohl Slicer 3 - 32 -
SpecifyInputs
DefaultPre-
Processing
Parameters Target Images Atlas Images
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
Segmentation EM Segment Algorithm: Pohl et al.
ReviewResults
Slicer3 Slice
Views
Slicer3 Model
Maker
External
Program
EM Segment Workflow
courtesy of Brad Davis
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Kilian M. Pohl Slicer 3 - 33 -
Dissemination
• Integration into Slicer 3http://wiki.na-mic.org/Wiki/index.php/Slicer3:EM
• Grid Computing
• Tutorialhttp://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
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Kilian M. Pohl Slicer 3 - 34 -
Morphometry Study TMI ‘07
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Kilian M. Pohl Slicer 3 - 35 -
Lesion Detection
Progression of Multiple Sclerosis lesions
courtesy of Istvan Csapo
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Kilian M. Pohl Slicer 3 - 36 -
Non-Human Primates
Measuring Alcohol and Stress Interactions with Structural and Perfusion MRI
courtesy of Chris Wyatt
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Kilian M. Pohl Slicer 3 - 37 -
CT Hand Bone Segmentation
courtesy of Austin Rammeand Vince Magnotta
Developing patient-specific kinematic models
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Kilian M. Pohl Slicer 3 - 38 -
Segmentation of Microscopy Images
courtesy of Brad Davis
Detecting patterns in biology
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Kilian M. Pohl Slicer 3 - 39 -
Publications • Pohl et al. A hierarchical algorithm for MR brain image parcellation.
IEEE Transactions on Medical Imaging, 26(9), pp 1201-1212, 2007.
• Nakamura et al. Neocortical gray matter volume in first episode schizophrenia and first episode affective psychosis: a cross-sectional and longitudinal MRI study. Biological Psychiatry, 2007. In Press.
• Koo et al. Smaller neocortical gray matter and larger sulcal CSF volumes in neuroleptic-naive females with schizotypal personality disorder. Archives of General Psychiatry, 63, pp. 1090-1100, 2006.
• Zöllei et al. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation, MICCAI 2007
• Pohl et al. Anatomical Guided Segmentation with Non-Stationary Tissue Class Distributions in an Expectation-Maximization Framework, In Proc. ISBI’2004, pp. 81 – 84, 2004.
Papers are accessible through www.csail.mit.edu/~pohl
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Kilian M. Pohl Slicer 3 - 40 -
Alternative Prior Model
Simultaneous Registration and SegmentationPohl et al. A Bayesian Model for Joint Segmentation and Registration. NeuroImage, 31(1), pp. 228-239, 2006
Shape Based Segmentation Pohl et al., “Using the Logarithm of Odds to Define a Vector Space on Probabilistic Atlases", Medical Image Analysis, 2007 MedIA –MICCCAI Best Paper Prize 2006
Pohl et al. Active mean fields: Solving the mean field approximation in the level set framework.IPMI, vol. 4584 of LNCS, pp. 26-37, 2007.
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Kilian M. Pohl - 41 -
Overview
Motivation
Software for Processing Images
Automatic Segmentation
Measuring Tumor Growth
Conclusion
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Kilian M. Pohl - 42 -Tumor Tracking
Meningioma Patient1st Scan 2nd Scan
Monitor evolution of meningioma through periodic MR scanning of patient
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Kilian M. Pohl - 43 -Tumor Tracking
The Problem1st Scan 2nd Scan
Has this tumor changed? Bigger? Smaller?
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Kilian M. Pohl - 44 -Tumor Tracking
Accuracy of Manual Inspectionreal MRI 1% (10mm3) 5% (48mm3) 22% (195mm3)
Expert 0/5 1/5 5/5Konukoglu et al. ,“Monitoring Slowly Evolving Tumors”, ISBI 08
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Kilian M. Pohl - 45 -Tumor Tracking
RECIST
1st Scan 2nd Scan
Infer change from largest diameterD1 >> D2 or D1 << D2
D1 D2
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Kilian M. Pohl - 46 -Tumor Tracking
Manually Determine Volume
1st Scan 2nd Scan
Infer Change from Largest VolumeV1 >> V2 or V1 << V2
V1 V2
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Kilian M. Pohl - 47 -Tumor Tracking
Intra-Rater Reliability Scan 1 Scan 2
−99.8 mm3545.8 mm3883.8 mm3
ThirdSecondFirst
Konukoglu et al. ,“Monitoring Slowly Evolving Tumors”, ISBI 08
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Kilian M. Pohl - 48 -Tumor Tracking
Inconsistency Between Scans
1st Scan 2nd Scan
• Changes in Head Position• Artifacts through Image Acquisition
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Kilian M. Pohl - 49 -Tumor Tracking
Mission
Tool
• semi-automatic quantitative measures derived from MRI
• compatibility with clinical requirements
Scan 1
Scan 2
Growth
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Kilian M. Pohl - 50 -Tumor Tracking
WorkflowThe implementation is based on a workflow approach Step 1: Select scansStep 2: Define tumor region Step 3: Segment tumorStep 4: Chose tumor metric
Automatic change detection is completed in less then 5 minutes
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Kilian M. Pohl - 51 -Tumor Tracking
Step1: Select Scans
Control Window
Navigation Panel
Viewers
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Kilian M. Pohl - 52 -Tumor Tracking
Step 2: Define ROI in Scan 1
Simple mouse click around the tumordefines region
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Kilian M. Pohl - 53 -Tumor Tracking
Step 3: Zoom into ROI
Grid shows original voxel size
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Kilian M. Pohl - 54 -Tumor Tracking
Step 3: Outline Tumor
State of the art semi-automatic segmenter is calibrated by slider
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Kilian M. Pohl - 55 -Tumor Tracking
Step 3: Outline Tumor
Move slider until tumoris correctly identified
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Kilian M. Pohl - 56 -Tumor Tracking
Step 4: Select Metric
Choice of Metric:• Detect growth by analyzing
intensity pattern (fast)• Measure growth by analyzing
deformation map (slow)
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Kilian M. Pohl - 57 -Tumor Tracking
Step 5: Analysis - Registration
Volume Preserving Registration
Before After
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Step 5: Analysis – Normalize Intensities
Scan 1 Scan 2 Scan 2 - Norm
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Statistical Model of Dormant Tissue
- =
)(absxI
PDF of Dormant Tissue
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Kilian M. Pohl - 60 -Tumor Tracking
Step 5: Analysis – Adjust Sensitivity
Mode : Aggressive ConservativeGrowth (mm3) : 2239 868 276Growth (voxel): 1819 705 224
Ana
lysi
sD
ata
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Analyze Deformation Map
=Compute deformation field using diffeomorphic demons
Mode : Segmentation Growth (mm3) : 764 Growth (voxels): 619
Mode : JaccobianGrowth (mm3) : 887 Growth (voxels): 718
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Step 5: Analysis – Adjust Sensitivity
• Growth is shown in blue• Outcome depends on
Sensitivity • Small sensitivity may
include noise in growth
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ImagingDeveloped a protocol that is compatible with clinical work and can be used for image analysis– Axial 3D SPGR T1 post Gadolinium– Voxel dimension: 0.94mm x 0.94mm x 1.20mm– FOV: 240mm Matrix: 256 x 256– Scan time: 8 mins on 1.5TIRB approval was not required
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Synthetic Experiment real MRI 1% 5% 22%
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Test DatabaseOur training data base consists of • 8 subjects scanned twice • 1 subject scanned three times
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Test DatabaseOur training data base consists of • 8 subjects scanned twice • 1 subject scanned three times
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Test DatabaseOur training data base consists of • 8 subjects scanned twice • 1 subject scanned three times
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Dissemination (In Progress)• Tool will be accessible via www.slicer.org• Konukoglu et al. ,“Monitoring Slowly Evolving Tumors”,
ISBI 08 • Pohl et al. , “Automatic Tumor Growth Detection” in
Meningiomas A Comprehensive Text, In Press• Online-Tutorial
www.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101
• Hands-on training http://www.themeningiomaconference2008.org/
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Kilian M. Pohl - 69 -
Overview
Motivation
Software for Processing Images
Automatic Segmentation
Measuring Tumor Growth
Conclusion
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Kilian M. Pohl Discussion & Conclusion - 70 -
Summary• Publicly available software targeted towards
medical imaging
• Automatic segmenter adoptable towards wide range of imaging problems
• Oncology tool for tracking tumor growth
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Kilian M. Pohl Discussion & Conclusion - 71 -
Thank You
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