NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC...
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![Page 1: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/1.jpg)
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Slicer3 EMSegment Tutorial
January 2008 NAMIC All-Hand’s Meeting
Brad Davis, Yuman Yuan, Sebastien Barre, Will Schroeder, Polina Goland, Ron Kikinis, Kilian Pohl
![Page 2: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/2.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Program
• EM Segmenter basics• Algorithm “views” in Slicer3• Slicer3 EM segment under the hood• Tutorial
– Data– Simple Segmentation Interface– Template Builder Interface
• Questions (all week…)
![Page 3: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/3.jpg)
National Alliance for Medical Image Computing http://na-mic.org
EM Segment BasicsT1-weighted MRI T2-weighted MRI
Automatic Segmentation
Cortical Spinal Fluid
White Matter SuperiorTemporal Gyrus
MiddleTemporal Gyrus
Figure: Pohl et al.
![Page 4: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/4.jpg)
National Alliance for Medical Image Computing http://na-mic.org
EM Segment Basics
Figures: Pohl et al.
![Page 5: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/5.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Atlas Images
Target Images
Parameters
Segmentation Result
EM Segment Basics
GM
WM
CSF
Air
Skin/Skull
![Page 6: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/6.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Atlas Images
Parameters
Segmentation Result
EM Segment Basics
• Collection of images (input channels) that will be segmented
T1 T2
Target Images
![Page 7: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/7.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Atlas Images
Target Images
Parameters
Segmentation Result
EM Segment Basics
• Hierarchy of anatomical structures– Intensity distributions, prior probabilities
• Default preprocessing– Intensity normalization, registration
• EM segmentation algorithm– Smoothing, weights, # iterations
• Stored as XML MRML file
Root
ICC Background
Air Skin/Skull
GM WM CSF
![Page 8: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/8.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Target Images
Parameters
Segmentation Result
EM Segment Basics
• Atlas images (spatial priors) – Aligned in common coordinate frame
GM Air Skin/SkullWMCSF
Atlas Images
![Page 9: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/9.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Atlas Images
Target Images
Parameters
Segmentation Result
EM Segment Basics
• Labelmap volume – Voxel values
specified in parameters
Root
ICC Background
Air Skin/Skull
GM WM CSF
![Page 10: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/10.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Algorithm Development
• 12-year history of algorithm development– Wells et al. 1996 (TMI): EM framework for simultaneous
estimation of bias field and label map– Kapur et al. 1999 (PhD Thesis): Model noise via Markov
Random Field – Van Leemput et al. 1999 (TMI): Non-spatial tissue
priors– Pohl et al.
• 2002 (MICCAI): Deformable registration to align atlas• 2004 (ISBI): Hierarchical framework to model anatomical
dependencies• 2007 (TMI): Up-to-date, detailed description
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National Alliance for Medical Image Computing http://na-mic.org
Slicer3
Segmentation Code
Preprocessing
Wizard GUI
Recent Development Effort• Goals:
– Easy to use– Adapts to a variety of
scenarios– Is a research tool– Simplified interfaces– Minimize
preprocessing requirements
– Validation and testing
ITK/VTK
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National Alliance for Medical Image Computing http://na-mic.org
EMSegmenter Logic / Preprocessing / Algorithm
Slicer3 GUIEM Template
BuilderModule
EM SimpleModule
CommandLine
EM CommandLine
Executable
Slicer3 EM segment “views”
• Advanced interface for creating/editing segmentation parameters
• Simple interface for applying parameters to new images
• Command-line interface for script/batch processing
![Page 13: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/13.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder View
• Runs inside Slicer3
• Purpose: Build/Adapt parameter sets
• Run segmentation• Wizard guides
user through interface panels
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National Alliance for Medical Image Computing http://na-mic.org
`One-Click’ View
• Runs inside Slicer3
• Purpose: Simple interface for segmenting new data
• Requires predefined parameter set
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National Alliance for Medical Image Computing http://na-mic.org
Command-line View
• EMSegmentCommandLine executable bundled with Slicer3
• Purpose: Scripted/batch processing• Requires predefined parameter set• Specify new target/atlas images on
command line
Atlas Images
Target Images
Parameters
Segmentation Result
![Page 16: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/16.jpg)
National Alliance for Medical Image Computing http://na-mic.org
SpecifyInputs Parameters Target Images Atlas Images
Slicer3 EM Segment Workflow
![Page 17: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/17.jpg)
National Alliance for Medical Image Computing http://na-mic.org
SpecifyInputs
DefaultPre-
Processing
Parameters Target Images Atlas Images
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
Slicer3 EM Segment Workflow
![Page 18: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/18.jpg)
National Alliance for Medical Image Computing http://na-mic.org
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.
Slicer3 EM Segment Workflow
![Page 19: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/19.jpg)
National Alliance for Medical Image Computing http://na-mic.org
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
Slicer3 EM Segment Workflow
![Page 20: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/20.jpg)
National Alliance for Medical Image Computing http://na-mic.org
DefaultPre-
Processing
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
New Development: Default Preprocessing
• Lower bar for entry• Starting point for building effective pipeline• Not intended for all scenarios• No interface for complex parameter
tweaking• Easily bypassed by advanced users
![Page 21: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/21.jpg)
National Alliance for Medical Image Computing http://na-mic.org
DefaultPre-
Processing
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
New Development: Default Preprocessing
• VTK filter by Kilian Pohl
• Scale intensities to achieve predefined mean– Heuristics determine histogram cutoffs
• Default settings for T1, T2 images
![Page 22: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/22.jpg)
National Alliance for Medical Image Computing http://na-mic.org
DefaultPre-
Processing
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
New Development: Default Preprocessing
• Target image 1 is fixed image• Perform registration for each additional
target image– Align image centers– Rigid registration, mutual information, gradient
descent optimization (ITK)– Coarse-to-fine
![Page 23: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/23.jpg)
National Alliance for Medical Image Computing http://na-mic.org
DefaultPre-
Processing
Target Image
Normalization
Target-to-target
Registration
Atlas-to-target
Registration
New Development: Default Preprocessing
• Target image 1 is fixed image• Perform registration with selected atlas image
– Align image centers, Rigid registration, B-Spline registration– Mutual information, (normalized cross-correlation, sse, not yet tested)– Rigid: gradient descent, B-Spline: ITK LBFGSB optimizer, 5x5x5 knot
points – Coarse-to-fine– Fast/Standard/Slow: sample points, max iterations– Resample all atlas images via transform; guess background value
![Page 24: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/24.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Default Registration Results
![Page 25: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/25.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Tutorial Data Walkthrough 1/3
• README: extra release notes• Predefined parameter file
– MR T1 & T2 brain segmentation: White matter, gray matter, CSF
• Target Images– ImageData_Input sub directory– Target: T1 & T2 images used in parameter file– Target_NewPatient1, Target_NewPatient2:
New data to try with the parameter file
![Page 26: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/26.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Tutorial Data Walkthrough 2/3
• Atlas Images– ImageData_Input sub directory– Atlas: atlas images used in parameter file– Atlas_NewAtlas: Extra atlas data for
demonstration purposes (currently a copy of first atlas)
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National Alliance for Medical Image Computing http://na-mic.org
Tutorial Data Walkthrough 3/3
• Low resolution data for testing – Full sized data: 30
minutes– Low resolution
data: 1 minute
• Data, parameters have “_small” appended to filename
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National Alliance for Medical Image Computing http://na-mic.org
`One-Click’ Module Tutorial 1/3
• EMSegment tutorial data is required
• Within Slicer3, open EMSegment Simple Module
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National Alliance for Medical Image Computing http://na-mic.org
`One-Click’ Module Tutorial 2/3
• MRML Scene: Select the tutorial parameter set
• Result Labelmap: Select a new image filename
• Target Volumes: Select input target volumes from one of the target directories (e.g., Target_NewPatient1)
• Note: target volume order is important
• Click `Apply’, wait (~30 minutes for full size images)…
![Page 30: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/30.jpg)
National Alliance for Medical Image Computing http://na-mic.org
`One-Click’ Module Tutorial 3/3
• Review the results in Slicer3– Load target images– Load result labelmap– Use slice views to review
segmentation results
• Apply Model Maker to generate surfaces
![Page 31: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/31.jpg)
National Alliance for Medical Image Computing http://na-mic.org
EMSegment Command-line Examples
• Script examples available in tutorial directory – New images– New atlas– New image and atlas– See README
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• EMSegment tutorial data is required
• Within Slicer3, open EMSegment Module
![Page 33: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/33.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Load tutorial parameters– File->Load Scene– Select ‘mrml’ file included
with tutorial
• Explore volumes included with scene– Target volumes, atlas
volumes– An old segmentation result
is also included
![Page 34: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/34.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Step 1: Choose EMSegmenter parameter set
• For now, use tutorial set• Later use this interface
to create a new parameter set
![Page 35: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/35.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Define anatomical structures
• Right click to add or delete nodes
• Label corresponds to eventual voxel values in segmentation result
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Choose an atlas volume for each leaf node
• To change or add new atlas volumes– Load new volumes into
Slicer3– Select new volumes at
this step
![Page 37: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/37.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Choose target images• To change or add target
images– Load new volumes into
Slicer3
– Select new volumes at this step
• You can reorder target images; order is important
![Page 38: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/38.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• You can choose to align target images
• First target is fixed image
• Rigid, mutual information registration
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• You can choose to normalize target images
• Simple, default strategy• Default parameter sets
available from pulldown
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Intensity distributions define appearance of each leaf structure
• Gaussian• Dimensionality equal to
number of target images• Two methods
– Sample voxels from images– Specify mean and covariance
manually• Tip: sample first, then fine
tune manually
![Page 41: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/41.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Sample voxels from images– Load first target image
into Slicer3 slicer view– Choose anatomical
structure– Choose `manual
sampling’– Ctrl-left-click on image
to add voxels
![Page 42: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/42.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Sample voxels from images (continued)– To remove an unwanted
sample right-click on it and choose “remove”
– Change back to “manual” mode to tweak distribution
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Segmentation parameters for every tree node
• Influence– Prior weight relative to
other structures– Atlas– Input channels– Smoothing (parent nodes
only)
• Stopping Conditions
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National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Atlas-to-target registration parameters
• Moving image registered to first target image– You can choose any image
loaded into Slicer3
• Same transformation applied to all atlas images before segmentation begins
![Page 45: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/45.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Template Builder Tutorial
• Select output and run registration
• You can troubleshoot preprocessing by saving intermediate results
• Choose an output labelmap• ROI governs segmentation
processing (one-based, not zero-based)
![Page 46: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/46.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Acknowledgements
• Wendy Plesniak, SPL BWH
• Steve Pieper, Isomics
• Luis Ibáñez, Kitware
• Sylvain Bouix, PNL BWH
• William Wells, BWH
• Funding provided by NAMIC
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NA-MICNational Alliance for Medical Image Computing http://na-mic.org
Questions…
![Page 48: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/48.jpg)
National Alliance for Medical Image Computing http://na-mic.org
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
Slicer3 EM Segment Workflow
![Page 49: NA-MIC National Alliance for Medical Image Computing Slicer3 EMSegment Tutorial January 2008 NAMIC All-Hands Meeting Brad Davis, Yuman.](https://reader036.fdocuments.net/reader036/viewer/2022070305/5514ecea550346935c8b5b93/html5/thumbnails/49.jpg)
National Alliance for Medical Image Computing http://na-mic.org
Atlas Images
Target Images
Parameters
Segmentation Result
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