freesurfer‐iniated fully‐automated subcorcal brain segmentaon … · • freesurfer labels to...
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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
[email protected] www.alikhan.ca
[email protected] www.sfu.ca/~m0eg
• 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