EMSegmentation EMSegmentation in Slicer 3in Slicer 3

B. Davis, S. Barre, Y. Yuan, W. Schroeder, P. Golland, K. Pohl

OverviewOverview IntroductionIntroduction EM Module Step-By-StepEM Module Step-By-Step Feedback & DiscussionFeedback & Discussion Live DemoLive Demo

MotivationMotivationT1-weighted MRI T2-weighted MRI

Automatic Segmentation

Cortical Spinal Fluid

White Matter SuperiorTemporal Gyrus

MiddleTemporal Gyrus

Hierarchical TreeHierarchical Tree

Applications of EM Applications of EM SegmenterSegmenter

Subcortical SegmentationPsychiatry Neuroimaging LaboratoryBWH, Harvard

White Matter LesionCenter for Neurological Imaging BWH, Harvard

GoalsGoals

Slicer2

Slicer3

Design automatic segmenter thatDesign automatic segmenter that is easy to use is easy to use adapts to variety of scenariosadapts to variety of scenarios works on large data setsworks on large data sets is a research toolis a research tool

OverviewOverview IntroductionIntroduction EM Module Step-By-StepEM Module Step-By-Step Feedback & DiscussionFeedback & Discussion Live DemoLive Demo

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Wizard InterfaceWizard Interface

Separates complex tasks into a Separates complex tasks into a sequence of simpler stepssequence of simpler steps

Checks user input before each Checks user input before each transitiontransition

Provides consistent access to helpProvides consistent access to help

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Create new Create new parameter setparameter set

Apply/modify Apply/modify existing existing parameter setparameter set

Parameter set defines segmentation Parameter set defines segmentation scenario:scenario:

Atlas, Images, Algorithm parametersAtlas, Images, Algorithm parameters

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Defines a hierarchy of anatomical structuresDefines a hierarchy of anatomical structures

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Assign atlas to anatomical structures Assign atlas to anatomical structures

white matter csf

grey matter background

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Choose input channelsChoose input channels

T1

T2

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Define intensity distribution for each structureDefine intensity distribution for each structure

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Specify node-based segmentation parametersSpecify node-based segmentation parameters

Influence of Influence of Input channelsInput channels AtlasAtlas SmoothingSmoothing

Relative Relative weight to other weight to other structuresstructures

Stopping Stopping conditionsconditions

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Specify atlas-to-input channel registrationSpecify atlas-to-input channel registration

white matter csf

grey matter background

T1 T2

Parameter Set

Atlas

Tree

Intensity

Target

Parameters

Registration

Run

Segment input channels using parametersSegment input channels using parameters

PipelinePipeline

2AtlasAlignment 3EM

Segmentation1IntensityNormalization

Observed Data (ROI)

EM

Image Prior

Hierarchy Labelmap

EM SegmenterEM Segmenter

Level 1Level 1P

rior

In

form

atio

n

IMAGE

BG ICC

CSF GM WM

Level 2Level 2

IMAGE

ICC

Cu

rren

t P

aram

eter

CSF GM WM

ROI

Example TreeExample Tree

OverviewOverview IntroductionIntroduction EM Module Step-By-StepEM Module Step-By-Step Feedback & DiscussionFeedback & Discussion Live DemoLive Demo

ResoucesResouces Slicer3 EMSegment Wiki page:Slicer3 EMSegment Wiki page:

http://wiki.na-mic.org/Wiki/index.php/Slicer3:EMhttp://wiki.na-mic.org/Wiki/index.php/Slicer3:EM Project DescriptionProject Description Steps in EMSegment WorkflowSteps in EMSegment Workflow Future WorkFuture Work Implementation DetailsImplementation Details EMSegment TutorialEMSegment Tutorial

Slicer2 Material:Slicer2 Material: Tutorial: http://wiki.na-mic.org/Wiki/index.php/Tutorial: http://wiki.na-mic.org/Wiki/index.php/

Slicer:Workshops:User_Training_101Slicer:Workshops:User_Training_101 PublicationsPublications

K.M. Pohl , S. Bouix, R. Kikinis, W.E.L. Grimson, Anatomical K.M. Pohl , S. Bouix, R. Kikinis, W.E.L. Grimson, Anatomical Guided Segmentation with Non-Stationary Tissue Class Guided Segmentation with Non-Stationary Tissue Class Distributions in an Expectation-Maximization Framework, In Distributions in an Expectation-Maximization Framework, In Proc. ISBI 2004, pp. 81-84,2004Proc. ISBI 2004, pp. 81-84,2004

K.M. Pohl, S. Bouix, M.E. Shenton, W.E.L. Grimson, R. K.M. Pohl, S. Bouix, M.E. Shenton, W.E.L. Grimson, R. Kikinis, Automatic Segmentation Using Non-Rigid Kikinis, Automatic Segmentation Using Non-Rigid Registratio, short communications of MICCAI 2005Registratio, short communications of MICCAI 2005

Feedback & Feedback & DiscussionDiscussion

Priorities for future developmentPriorities for future development Class overview panelClass overview panel Graphical DisplayGraphical Display Controlled vocabularyControlled vocabulary Library of TemplatesLibrary of Templates One-Step-Segmentation One-Step-Segmentation

AcknowledgementAcknowledgementss

Steve PieperSteve Pieper Alex YarmarkovichAlex Yarmarkovich Wendy PlesniakWendy Plesniak Slicer developer communitySlicer developer community Psychiatry Neuroimaging LaboratoryPsychiatry Neuroimaging Laboratory NAMIC NAMIC

AcknowledgementAcknowledgementss

Kitware Developer Kitware Developer

OverviewOverview IntroductionIntroduction EM Module Step-By-StepEM Module Step-By-Step Feedback & DiscussionFeedback & Discussion Live DemoLive Demo

Editing the TreeEditing the Tree

Cortical SubcorticalLevel 3: