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StatisticsinImagingWorkshop
July8,2004
ABayesianDeformationModel
forImages
SiningChen
PostdoctoralFellow
BiostatisticsDivision,Dept.ofOncology,SchoolofMedicine
Outline
1.Introducingtheproblem
2.Modeldescription
3.Applicationtomousebrainsegmentation
4.Inter-subjectregistrationofhumanbrains
ProblemstoSolve
•Identifyingabnormaltissuefromaseriesofgatedcardiac
images
•Markingaregionofinterestinalargenumberofhumanbrain
MRIs
•Repeatingthesameoperationonsimilarimages
ImageRegistration
Tobringtwosimilarimagesintospatialalignment,suchthat
“correspondingpointsoftheimagedsceneappearinthesame
positionontheregisteredimages”.
Alsoreferredtoas”spatialnormalization”incertaincontexts.
RegistrationMethods
•Curvedtransformationsusingbasisfunctions(Ashburnerand
Friston1999HumanBrainMapping),implementedinthe
softwarepackageSPM.
•Modelsderivedfromthephysicsofelasticobjects(Bajcsyand
Kovacic1989Comp.Vision,Graphics&ImageProcessing)
•Spatialmodelingindeformabletemplates...
Facets–generalizedlandmarks
Deformationmodelmechanism:placelargenumberoffacetsinthe
volumeoftemplateimage.Thenlocateeachinthetargetimage.
templatetarget
ModelHeuristic
Abalancebetween
•“preservingspatialrelationships”–expressedintheprior
•“matchingimagefeatures”–expressedinthelikelihood
Notation
TemplateTarget
facetlocationµx
facetfeatureφf
Thefeatureofafacetisafunctionoftheimageevaluatedatthat
location:canbeintensity(brightness),gradience(edgeness),
laplacian(medialness),etc.
(a)(b)
(c)(d)
(e)(f)
Figure1:a)Originalimage;b)localrankofintensity;
c)d)directionalderivatives;e)gradientmagnitude;f)
Laplacian
Prior–presevingspatialrelationship
Markovrandomfieldpriorspecifiedonafirst-degreeneighborhood
system.
Thespatialrelationshipamongianditsneighbors∂iinthetarget
imageremainssimilarbeforeandafterdeformation.
ij
PSfragreplacements
γij
µ1
µ2
µ3
µ4
µ5
x1
x2
µ3|x∂3
x4
x5
PSfragreplacements
γij
µ1
µ2µ3µ4
µ5
x1
x2µ3|x∂3
x4
x5
Prior–continued
p(x)=1
Z(γ)exp{−
1
2
∑
〈i,j〉
γij((xi−µi)−(xj−µj))a}
Fullconditional(leta=2):
p(xi|.)∝exp{−1
2
∑
j∈∂i
γij((xi−µi)−(xj−µj))2}
∝exp{−1
2(∑
j∈∂i
γij)(xi−µi−
∑
j∈∂iγij(xj−µj)∑
j∈∂iγij
)2}
Likelihood–matchingfeatures
Foreachfaceti,featureafterdeformationfishouldbesimilarto
templatefeatureφi
p(xi|T,φi)=1
Ci(T,φi)exp{sim(fi,φi)}
where
fi=QT(xi)
MeasureofFeatureSimilarity
sim(fi,φi)=b(ri·ρi)α·cos(ui−νi),α>0
ri,ρi:quantilesofgradientmagnitude,
ui,νi:directionsofgradients.
PSfragreplacements(u,r)
(u,r)
(ν,ρ)(ν,ρ)
θ
MeasureofFeatureSimilarity–continued
Advantages:
•robustunderweakassumptionsonintensity
•abilitytodistinguishbetween“meaningful”and“meaningless”
features
•accomodates“no-match”situations
PosteriorInference
MAP(maximumaposteriori)estimatecanbeobtainedbyICM
(iterativeconditionalmodes,Besag1986).
Toobtainestimatethatisclosertoglobalmaximum,webuilda
hierarchyoffacetsinscale-space.
FacetTreeinScale-Space
AugmentedFull-Conditional
Spatialpartonly
p(xi|xs,s∈∂i,xp)∝exp{−γp((xi−µi)−(xp−µp))2
+∑
s∈∂i
γis((xi−µi)−(xs−µs))2}
Faceti,
facettargetlocationxi,
facettemplatelocationµi,
i’ssiblingss∈∂i,
i’sparentp,
pre-selectedparametersγpandγis
AutomatedSegmentationofMouseBrainImages
ManualSegmentationofMouseHippocampus
Goal:toinvestigatetherelationshipofAlzheimer’sdiseaseto
changesinthevolumeofthehippocampus.
AutomaticsegmentationofanothermouseMRI
TemplateImage
5010
015
020
025
0
50 100
150
200
250
Figure2:Threeregionsofinterestaremarkedonthetemplateimage
withrectangles.
12
01
40
16
01
80
12
0
13
0
14
0
15
0
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0
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0
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40
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0
80
100
120
140
60
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100
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100
120
140
60
70
80
90
100
110
160
180
200
30
40
50
60
70
80
150
160
170
180
190
200
30
40
50
60
70
80
Figure3:Facetsbeforeandafterdeformation.
QuantitativeAssessmentofAuto-segmentation
PSfragreplacementsmi
ticiI
tI
logm(k)i=logti+ε
(k)i,ε∼N(0,∆
2)
logc(k)iI=logtI+(logm
(k)i−logti)+e
(k)iI,e∼N(0,δ
2)
00.010.020.030.040.050.060.070
2000
4000
6000
8000
10000
12000
00.010.020.030.040.050.060.070
2000
4000
6000
8000
10000
12000
Figure4:a)∆2,b)δ
2
Inourdataset,theinconsistencyofauto-segmentationis
approximatelythesameashumansegmentation.
Inter-subjectRegistrationofHumanBrainMRIs
Areallbrainsalike?
Issuesinevaluatinginter-subjectregistration
Problematicduetolackofinformationongroundtruth.
Whatwasdone:
•Qualitativeassessment:visualinspection,mosaic,facet
movement;
•Quantitativeevaluation:segmentationbased,cross-correlation;
•DoneincomparisontotheindustrialstandardSPM.
Mosaic
beforeregistrationafterfacetreg.afterSPMreg.
Facetmovement
Figure5:Locatingfacetsonsubject3
HumanbrainMRIsegmentation
originalMRIwhitemattergraymatter(a)(b)(b)
(a)(b)(c)
Overlap,misclassification
Figure6:Comparisonofgraymattersegmentationof“warpedtem-
plate”andmanuallysegmentedtarget
Segmentationbasedevaluation
misclassify(%)facetSPM
subject117.420.7
subject224.424.4
subject316.515.8
Table1:Percentmisclassifiedforwhitematter
overlap(%)facetSPM
subject187.881.0
subject279.070.1
subject379.773.0
Table2:Percentageoverlapforwhitematter
misclassify(%)facetSPM
subject116.223.3
subject237.054.0
subject326.947.3
Table3:Percentmisclassifiedforgraymatter
overlap(%)facetSPM
subject272.767.8
subject565.960.2
subject666.262.7
Table4:Percentageoverlapforgraymatter
NormalizedCross-covarianceMap
C(f,g)=n·
∑
Afij·gij−∑
Afij·∑
Agij
n√
(∑
Af2+n−2n
2(∑
Af)2)(∑
Ag2+n−2n
2(∑
Ag)2)
(1)
facetSPM
Conclusion
•UsedMarkovrandomfieldtomodelpriorbeliefoffacet
locations;
•proposedanew,robustmeasureofsimilarity;
•successfullyperformedauto-segmentationofmousebrain
hippocampigivenasegmentedtemplate;
•registeredbrainMRIofdifferentindividuals;
•quantitativeevaluatedperformanceofregistration;
•themodelperformsmarginallybetterthanSPM.
Thankyou!
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