Conclusion

• Fully‐automatedsub‐cor5calbrainsegmenta5onpipeline• Builtaroundexis5ngFreeSurferworkflow

• Advantages:• Accurateandrobustmappingofdeepsub‐cor5calnuclei• Inherentlysmoothsegmenta5ons• Singletemplate‐basedsolu5on–canaccommodatedifferentsegmenta5onprotocols

• Furthervalida5ononlargerstudiesisrequired

Introduc5on

• Probabilis5capproachtovoxelclassifica5onforsub‐cor5calregions

• Fully‐automatedpipelineforsub‐cor5calsegmenta5on• Limita5ons:• Voxel‐wiselabeling–smoothnessissues• Requiresre‐trainingtoadapttonewsegmenta5onprotocols

• High‐dimensionaltransforma5onbetweenpairofimagevolumes

• Diffeomorphicmappingsinherentlysmoothandtopologypreserving

• Segmenta5onvialabelpropaga5on• Limita5ons:• High‐dimensionalop5miza5on–requiressufficientini5aliza5on• Manyexis5ngmethodsusemanuallandmarks

• FreeSurferlabelstoini5alizeregionsofinterest(ROI’s)• LDDMMtemplate‐basedlabelpropaga5ononeachROI• Providesaccurateandsmoothsub‐cor5calsegmenta5ons• Canpropagateeithersurfacesorimages

FreeSurfer‐Ini+atedFully‐AutomatedSubcor+calBrainSegmenta+oninMRIUsingLargeDeforma+onDiffeomorphicMetricMapping

AliR.Khan,1LeiWang,2andMirzaFaisalBeg11SchoolofEngineeringScienceFacultyofAppliedScienceSimonFraserUniversity8888UniversityDrive

Burnaby,BC,CanadaV5A1S6

2DepartmentofPsychiatryWashingtonUniversitySchoolofMedicineBox8134,RenardHospital,Room6604

660SouthEuclidSt.Louis,MO63110,USA

Results

CaudateNucleus&PutamenPre‐symptoma5cHun5ngton’sDisease

BasalGangliaTourege’sSyndrome

HippocampusSchizophrenia

Dataset

Alzheimer’sDisease

Dataset

FreeSurferManual FS+LDDMM

FreeSurferManual FS+LDDMM

FreeSurferManual FS+LDDMM

akhanf@sfu.ca   www.alikhan.ca 

m0eg@ensc.sfu.ca www.sfu.ca/~m0eg 

lei@wustl.edu 

• Coarse(affine)registra5onofanatomyusingFreeSurferlabels• BoundingboxdefinedbyextentsofFreeSurferlabels

RegionofInterestGenera5on

• Findmedian5ssueintensi5esusingFreeSurferlabels• UsetheselandmarkstolinearlytransformMRintensi5es

Histogram‐basedIntensityNormaliza5on

• Mul5‐stagemappingprocedure:• Eachstageini5alizedusingvelocityflowofpreviousstage• Cerebro‐spinalFluidLabels(toaidventriclemapping)• SmoothedMRIImages(toovercomelocalminima)• MRIImages

• Templatesurfacespropagatedtoobtainfinaltargetsurface

LDDMM‐basedRegistra5on

Method

CSFMapping

Mul5‐resMRIMapping

FS+LDDMM

FS

LDDMM

SubjectInforma+on ScanParameters

N Sex Age Sequence TR/TE/N

16 7/9 37±11 SPGR 18/3/2

LemCaudate

RightCaudate

LemPutamen

RightPutamen

FreeSurfer 0.80 0.77 0.77 0.78FS+LDDMM 0.84 0.81 0.84 0.85

0.40

0.50

0.60

0.70

0.80

0.90

1.00

DSC

R.Caudate

R.NucleusAcc.

R.Pallidum

R.Putamen

FreeSurfer 0.73 0.57 0.73 0.80FS+LDDMM 0.78 0.60 0.78 0.83

0.400.500.600.700.800.901.00

DSC

SubjectInforma+on ScanParameters

N Sex Age Sequence TR/TE/N

5 3/2 36.5±9.81 MPRAGE 9.7/4/1

SubjectInforma+on ScanParameters

N DiseaseState Sex(M/F) Age(min‐max) Sequence TR/TE/N

5 Schiz. 5/0 33.0(23‐44) MPRAGE 10/4/1

5 Healthy 5/0 32.4(24‐42) MPRAGE 10/4/1

R.Hippo.Schiz.

R.Hippo.Healthy

FreeSurfer 0.72 0.73FS+LDDMM 0.77 0.75

0.400.500.600.700.800.901.00

DSC

R.Hippo.CDR0

R.Hippo.CDR0.5

FreeSurfer 0.69 0.70FS+LDDMM 0.73 0.72

0.400.500.600.700.800.901.00

DSC

SubjectInforma+on ScanParameters

N DiseaseState Sex(M/F) Age(min‐max) Sequence TR/TE/N

5 CDR0 3/2 74.2±5.2 MPRAGE 10/4/1

5 CDR0.5 3/2 74.0±4.8 MPRAGE 10/4/1

SchizophreniaDataset

Alzheimer’sDiseaseDataset

OverlapMetric:

FreeSurfer

LDDMM

FS+LDDMM