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TutorialVMTKCoronariesCenterlinesMRI Winter2010AHM
TutorialVMTKCoronariesCenterlinesMRI Winter2010AHM
TutorialVMTKCoronariesCenterlinesMRI Winter2010AHM
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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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StarttheExtensionWizard
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ClickNext
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SelectallVMTKExtensions
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ClickDownload&Install
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ClickNext
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Restart3DSlicer
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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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Loading Data
Onlytheredsliceviewer(axialview)isdisplayed.
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Usethemodulesselector(1)tostartthe ExtractSubvolumeROI(2)module
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Createanew MRMLROINode
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CreateanewVolume asOutputvolume
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2 Selecttheextractedsubvolume(2)inthered sliceviewerbyusingthevolumeselector(1)
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2
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Aorticarch
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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)
1 2
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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.
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Vesselness Filtering
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SelecttheEnhancedVesselnessOut volume(2)astheInputVolume(1)
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DeactivateUseVolumeRendering becausePolydataisneededlater
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ClickStart!
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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
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Centerline Computation
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Centerline Computation
NowusetheCenterlines Computationpanelforstep2
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Centerline Computation
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Centerline Computation
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Centerline Computation
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Centerline Computation
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Centerline Computation
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Centerline Computation
ClickGetCenterlines!
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Centerline Computation
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Centerline Computation
Thisisagoodtimetosavethelumensegmentation,the generatedVoronoidiagram,theCenterlinesasPolydata andallotherMRMLdatabyusingtheFilemenuand Save.
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Results
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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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Results
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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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