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Slicer3TrainingCompendium Slicer3 Training Tutorial

CenterlineExtractionof CoronaryArteriesin3DSlicer usingVMTKbasedTools


DanielHhn StudentofMedicalInformatics UniversityofHeidelberg,Germany
Contact:haehn@bwh.harvard.edu

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Learning Objective
Guidingyoustepbystep throughtheprocessof centerlineextractionof CoronaryArteriesinacardiac bloodpoolMRIusingVMTK basedTools.

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Background
Coronary heart disease (CHD) is the leading cause of death in highincome countriesandoneofthemaincausesof deathworldwide*. The primary cause for CHD is atherosclerosis of the coronary arteries and is called coronary artery disease (CAD). The extraction of the central lumen line (centerline)ofcoronaryarteriesishelpful for visualization purposes, stenosis quantification or further processing steps.
HumanHeartwithCoronaries,Author:PatrickJ.Lynch (1999),CreativeCommonsLicense

*WHOFactSheet310:http://www.who.int/mediacentre/factsheets/fs310/en/index.html

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Materials
ThistutorialrequirestheinstallationoftheSlicer3 softwareandthetutorialdataset.Theyareavailableat thefollowinglocations: Slicer3downloadpage(Slicer3.5NightlyBuild*)
http://slicer.org/pages/Special:SlicerDownloads

UnzippedTutorialMRIdata(3files)
http://www.namic.org/Wiki/index.php/File:TutorialVMTKCoronariesCenterlinesMRI_Data_Winter2010AHM.zip

Disclaimer:ItistheresponsibilityoftheuserofSlicertocomplywithboththeterms ofthelicenseandwiththeapplicablelaws,regulations,andrules.
*oraSnapshotafterDecember2009,theSlicer3extensionsystemhastoworkproperly

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Overview
InstallingVMTKin3DSlicer ThePipeline LoadingData ExtractingtheROI VesselnessFiltering LevelSetSegmentation CenterlineComputation Results References Acknowledgements 612 13 1419 2032 3343 4457 5869 7075 76 77

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Installing VMTK in 3D Slicer

StarttheExtensionWizard

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Installing VMTK in 3D Slicer

ClickNext

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Installing VMTK in 3D Slicer

SelectallVMTKExtensions

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Installing VMTK in 3D Slicer

ClickDownload&Install

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Installing VMTK in 3D Slicer

ClickNext

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Installing VMTK in 3D Slicer

Restart3DSlicer

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Installing VMTK in 3D Slicer


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TheVMTKExtensions appearinthemodules selector(1)insidethe categoryVascular ModelingToolkit

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The Pipeline

ThispipelineisusedfortheCenterlineExtraction.
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Loading Data

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Toloadthetutorialdata,choosetheFilemenu (1)andselectAddVolume...(2)
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Loading Data
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Selectthefiletutorial_cardiac_mri_data.nrrd(1) oftheunzippedtutorialdataandpressApply(2)

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Loading Data
1 2 Usethelayoutselector(1)to switchtotheConventional layout(2)

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Loading Data
The2Dsliceviewersshowtheloadedvolume.

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Loading Data
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Usethelayoutselector(1)to switchtotheRedsliceonly layout(2)

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Loading Data

Onlytheredsliceviewer(axialview)isdisplayed.

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Extracting the ROI


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Usethemodulesselector(1)tostartthe ExtractSubvolumeROI(2)module
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Extracting the ROI


Thispanelnowappears. BesurethattheInput volumeistheloaded tutorialdata.

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Extracting the ROI

Createanew MRMLROINode

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Extracting the ROI

CreateanewVolume asOutputvolume

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Extracting the ROI


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Nowclickaroundthehearttoselectthesubvolume. Navigatetothemostinteriorandsuperiorslicesusing thecontrol(1)toselectthecompleteheart.The selectionisshownasablueoverlay.


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Extracting the ROI


2 1 ClickDoROIresample(1)toextractthe subvolumeandclicktoggletheROIvisibility (2)tohidetheblueoverlay

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Extracting the ROI

Youcanalsodirectlyloadtheprepared tutorial_cardiac_mri_dataSubvolume resample_scale1.0.nrrdfileoftheunzipped tutorialdatatogettheextractedsubvolume (seetheLoadingDatasection).

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Extracting the ROI

2 Selecttheextractedsubvolume(2)inthered sliceviewerbyusingthevolumeselector(1)

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Extracting the ROI


1 2 Fitthevolumetothewindow byusingtheoptionsicon(1) andselectingFittowindow (2)

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Extracting the ROI


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2 Usethemodulesselector(1) tonavigatetotheVolumes module(2)

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Extracting the ROI

Besuretheextractedsubvolume tutorial_cardiac_mri_dataSubvolume resample_scale1.0istheactive Volume(1)andadjusttheWindow/Level settingto1082and1257(2)forbetter visualization

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Extracting the ROI


1 Left Coronary Artery

Aorticarch

Atslicelocation0.80(1)the aorticarchandtheleftcoronary artery(LCA)arevisible


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Extracting the ROI


1 Right Coronary Artery Aorticarch

Atslicelocation15(1)theaortic archandtherightcoronaryartery (RCA)arevisible


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Vesselness Filtering
Navigatetothe VMTKVesselEnhancement moduleinsidethecategory VascularModelingToolkitusing themodulesselector

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Vesselness Filtering
Thispanelappears.Switchto FrangiVesselness.

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Vesselness Filtering
Selecttheextractedsubvolume (2)astheInputVolume(1)

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Vesselness Filtering
Enter0.1(unit:mm)asthe minimaldiameteroftubular structurestodetect

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Vesselness Filtering
Enter2.0(unit:mm)asthe maximumdiameteroftubular structurestodetect

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Vesselness Filtering
Choosealowthresholdof0.3to detectlinelikeratherthanplate likestructures

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Vesselness Filtering
Ahigherthresholdof500limits thedetectionofbloblike structures

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Vesselness Filtering
Thecontrastofthevesselsin comparisiontothebackgroundin thetutorialdataisveryhigh,so setahigherthresholdof500to detectonlywellvisiblestructures

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Vesselness Filtering

ClickStart!

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Vesselness Filtering
Thefilteringproceduretakes approx.610minutes.

Youcanalsodirectlyloadtheprepared EnhancedVesselnessOut.nrrdfileofthe unzippedtutorialdatatogetthevesselness filteredvolume(seetheLoadingData section).

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Vesselness Filtering

Right Coronary Artery

Theredsliceviewershowsthevesselness filteredvolume.Theenhancedtubesare visible(f.e.atslicelocation15).


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Level Set Segmentation


Navigatetothe VMTKEasyLevelSetSegmentation moduleinsidethecategory VascularModelingToolkitusing themodulesselector

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Level Set Segmentation


Thispanelnowappears. TheLevelSetSegmentation processconsistsoftwo steps:Initializationand Evolution

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Level Set Segmentation


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SelecttheEnhancedVesselnessOut volume(2)astheInputVolume(1)

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Level Set Segmentation


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UsetheSourceSeedsselector(1)to createanewFiducialList(2)which automaticallybecomesactive 3 SwitchtoPlacemodebyusingthe icon(3)onthetoolbar

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Level Set Segmentation

ClickinsidetheRCAontheredslice viewertoplaceoneseedpoint(f.e.at slicelocation15)


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Level Set Segmentation

ClickinsidetheLCAontheredslice viewertoplaceoneseedpoint(f.e.at slicelocation0.80)


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Level Set Segmentation

DeactivateUseVolumeRendering becausePolydataisneededlater

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Level Set Segmentation


Setalowerthresholdof 0.143 Thisresultsinimmediate visualizationfeedbackat thesliceviewers

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Level Set Segmentation


1 2 Usethelayoutselector(1)to switchtotheConventional layout(2)

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Level Set Segmentation

ClickStart!

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Level Set Segmentation


Thesegmentationisshownasa modelinthe3Drenderingwindow (1)andasanoverlayedlabelmap inthe2Dsliceviewers(2)

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Level Set Segmentation

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UsetheInputVolumeselector(1)to settheextractedsubvolume(2)asthe inputfortheevolutionstage


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Level Set Segmentation


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Specifythebehavioroftheevolutionbyusingthesliders. Theinitializationisalreadyclosetotheedgesofthevesselssono inflationisneeded(1). Togetasmoothsurfaceahighercurvatureweightof70isimportant (2). Toattractthesegmentationtothegradientridgesahighattractionweight of100isnecessary(3).
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Level Set Segmentation


Theresultisshownasablue modelinthe3Drenderingwindow (1)andasanoverlayedlabelmap inthe2Dsliceviewers(2)

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Centerline Computation
NavigatetotheVMTKCenterlines moduleinsidethecategory VascularModelingToolkitusing themodulesselector

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Centerline Computation
Thispanelnowappears. TheCenterlinesextraction consistsoftwosteps:Model preparationandCenterline Computation

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Centerline Computation

1 2 UsetheInputModel selector(1)tosetthe VMTKEvolutionModel(2) astheinput

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Centerline Computation

ClickPrepareModel! Thebluemodelinthe3D RenderingWindowturns green

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Centerline Computation

NowusetheCenterlines Computationpanelforstep2

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Centerline Computation
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UsetheSourceSeeds selector(1)tocreateanew Fiduciallist(2)


Note:ItisrecommendedtousetheFiducialsmoduletohidetheFiducial listsoftheLevelSetSegmentationprocess
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PlacetwoSeedsinthe3DRendering Windowdirectlyonthegreenmodelwhere theCoronariesstart

Centerline Computation

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Centerline Computation
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UsetheTargetSeeds selector(1)tocreateanew Fiduciallist(2)


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Centerline Computation
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ToplacetheTargetSeedscorrectly,itis recommendedtofirstusetheTransformmode(1)to rotatethemodelandthenthePlacemode(2)toset thefiducials

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PlacefourSeedsinthe3DRendering Windowdirectlyonthegreenmodelwhere theCoronariesend

Centerline Computation

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Centerline Computation

ClickGetCenterlines!

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Centerline Computation

TheVoronoidiagramandthecorrespondingCenterlines appearinthe3DRenderingWindow.Usetheright mousebuttontoZoomintothe3Dview


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Centerline Computation
Thisisagoodtimetosavethelumensegmentation,the generatedVoronoidiagram,theCenterlinesasPolydata andallotherMRMLdatabyusingtheFilemenuand Save.

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Results

Allsegmentationpartsare availableasMRMLnodes inthecurrentscene.The Datamoduleshowsthe MRMLtree.

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Results
DeactivatetheVMTKCenterlinesPrepOutmodelto hidethesegmentedlumen(1). The3DRenderingWindowthen showstheVoronoidiagramandthe correspondingCenterlinesonly.

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Results
HidetheVMTKVoronoiOutmodel (1)toshowtheCenterlinesinthe 3DRenderingWindowonly.

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Results
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TheVMTKCenterlinesmodulesupportstheexportof extractedCenterlinesascloudsofpointstothe filesystem. Toexportdetailslikethemaximuminscribedsphere radiusactivatethecheckbox(1),choosea destination(2)andclickExport!(3).


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Results
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Theexportedfileincludestheworld coordinates(1)oftheCenterlinesand alsotheMaximumInscribedSphere Radius(2)foreachpoint.


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Conclusion
VMTKextensionsinstallableusingtheextensionwizard VesselnessFilteringusingVMTKVesselEnhancement LumenSegmentationusingVMTKEasyLevelSetSegmentation CenterlineComputationusingVMTKCenterlines 3DSlicerIntegrationforfurtherprocessingofthedata(MRML nodes) OpenSourceEnvironment

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References

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Acknowledgements
NationalAllianceforMedicalImageComputing SurgicalPlanningLaboratory(BWH) StevePieper,RonKikinis MarioNegriInstitute LucaAntiga

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Thankyouforusingthis tutorial!

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