applied chest imaging laboratory
TRANSCRIPT
ParenchymalAnalysisAChestImagingPlatformSlicerExtensionmodule
AppliedChestImagingLaboratoryBoston,Massachusetts.USA
AppliedChestImagingLaboratory
• Goal:TheparenchymaanalysismoduleperformsdensitometryinchestCTscansbyisolatingthelungregionandcomputingdifferentphenotypesbasedonthehistogramofthedensitymeasurements.
• Densitometryisusedtoquantify:• Emphysema:Emphysemaiscomputedinfullinspiratoryscansasthepercentageofvoxelsbelowagiventhreshold,typically-950HUor-910HU.Othersurrogatemetricsofemphysemaaremeanlungdensityandlungmass(meanlungdensity*volume)
• GasTrapping:Gastrappingiscomputedinexpiratoryscansasthepercentageofvoxelsbelow-856HU.
• InterstitialLungDisease:ILDiscomputedinfullinspiratoryscansasthepercentageofvoxelsbetween-600HUand-250HUs.
Overview
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ParenchymaAnalysis
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1- SelectaninputCTimage
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2- Ifavailable,selectthepartialLungLabelMap fortheselectedinputCTTip:IfNone,anewLabelMap wouldbeautomaticallycreatedduringtheanalysis
Note:WhenapartialLungLabelMAp isalreadyselected,optionsforlabelmapcreationaredisabled.
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3- Filteringoptions.Tip:Bydefaultfilteringissetto”off”,turnto“on”toactivatefilter
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ParenchymaAnalysisTip:whenfilteringis”on”anewframeopensup
Selectfilter:non-localmeans(NLM),medianorGaussianfilter
Selectwhethertoapplyfilterin2Dor3D
Selectfilteringstrength:Smooth,medium,Heavy
Check“FilterforphenotypeAnalysis”iffilteringshouldnotbeusedforcreatingthelabelmap
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CreatingpartialLungLabelMap.Selectmethod.Tip:Slowmethodtakesmoretimetofinishbutismoreaccurate.
8- ClickApplytostarttheparenchymaanalysis
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Thelungdensityhistogramiscreatedforeachregion
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Atablewiththemetricsforeachregionisalsocreatedandpresentedontheinterface
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IntheHistogramSection,regionswhosehistogramhastobeshowncanbechecked
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ParenchymaAnalysisViewaChartwiththeobtainedresults
10- Clickon“Chart”toseetheresultsoftheselectedstatistic
9- Selectthedesiredstatistic
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Achartshowingtheselectedstatisticsforeachregioniscreated
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Saveoption:clickon“Save”tosavethecomputedstatistics.
Openoption:Clickon“open”toopenpreviouslydonestatistics
Exportoption:Click“export”toexportthecomputedstatistics
Click“cleancaché”toremoveallsavedstatistics
AppliedChestImagingLaboratory
• TheParenchymalAnalysismoduleispartoftheChestImagingPlatformextensionfor3DSlicer(www.chestimagingplatform.org)
• ThisworkisfundedbytheNationalHeart,Lung,AndBloodInstituteoftheNationalInstitutesofHealthunderAwardNumberR01HL116931.ThecontentissolelytheresponsibilityoftheauthorsanddoesnotnecessarilyrepresenttheofficialviewsoftheNationalInstitutesofHealth.
• Contributors:• Pietro Nardelli• AppliedChestImagingLaboratory• BrighamandWomen'sHospital• HarvardMedicalSchool
ParenchymalAnalysis
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