FreeSurfer‐Iniated Fully‐Automated Subcorcal Brain Segmentaon … · • FreeSurfer labels to...
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Conclusion • Fully‐automated sub‐cor5cal brain segmenta5on pipeline • Built around exis5ng FreeSurfer workflow • Advantages: • Accurate and robust mapping of deep sub‐cor5cal nuclei • Inherently smooth segmenta5ons • Single template‐based solu5on – can accommodate different segmenta5on protocols • Further valida5on on larger studies is required Introduc5on • Probabilis5c approach to voxel classifica5on for sub‐cor5cal regions • Fully‐automated pipeline for sub‐cor5cal segmenta5on • Limita5ons: • Voxel‐wise labeling – smoothness issues • Requires re‐training to adapt to new segmenta5on protocols • High‐dimensional transforma5on between pair of image volumes • Diffeomorphic mappings inherently smooth and topology preserving • Segmenta5on via label propaga5on • Limita5ons: • High‐dimensional op5miza5on – requires sufficient ini5aliza5on • Many exis5ng methods use manual landmarks • FreeSurfer labels to ini5alize regions of interest (ROI’s) • LDDMM template‐based label propaga5on on each ROI • Provides accurate and smooth sub‐cor5cal segmenta5ons • Can propagate either surfaces or images FreeSurfer‐Ini+ated Fully‐Automated Subcor+cal Brain Segmenta+on in MRI Using Large Deforma+on Diffeomorphic Metric Mapping Ali R. Khan, 1 Lei Wang, 2 and Mirza Faisal Beg 1 1 School of Engineering Science Faculty of Applied Science Simon Fraser University 8888 University Drive Burnaby, BC, Canada V5A 1S6 2 Department of Psychiatry Washington University School of Medicine Box 8134, Renard Hospital, Room 6604 660 South Euclid St. Louis, MO 63110, USA Results Caudate Nucleus & Putamen Pre‐symptoma5c Hun5ngton’s Disease Basal Ganglia Tourege’s Syndrome Hippocampus Schizophrenia Dataset Alzheimer’s Disease Dataset FreeSurfer Manual FS+LDDMM FreeSurfer Manual FS+LDDMM FreeSurfer Manual FS+LDDMM [email protected] www.alikhan.ca [email protected] www.sfu.ca/~m0eg [email protected] • Coarse (affine) registra5on of anatomy using FreeSurfer labels • Bounding box defined by extents of FreeSurfer labels Region of Interest Genera5on • Find median 5ssue intensi5es using FreeSurfer labels • Use these landmarks to linearly transform MR intensi5es Histogram‐based Intensity Normaliza5on • Mul5‐stage mapping procedure: • Each stage ini5alized using velocity flow of previous stage • Cerebro‐spinal Fluid Labels (to aid ventricle mapping) • Smoothed MRI Images (to overcome local minima) • MRI Images • Template surfaces propagated to obtain final target surface LDDMM‐based Registra5on Method CSF Mapping Mul5‐res MRI Mapping FS+LDDMM FS LDDMM Subject Informa+on Scan Parameters N Sex Age Sequence TR/TE/N 16 7/9 37±11 SPGR 18/3/2 Lem Caudate Right Caudate Lem Putamen Right Putamen FreeSurfer 0.80 0.77 0.77 0.78 FS+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. Nucleus Acc. R. Pallidum R. Putamen FreeSurfer 0.73 0.57 0.73 0.80 FS+LDDMM 0.78 0.60 0.78 0.83 0.40 0.50 0.60 0.70 0.80 0.90 1.00 DSC Subject Informa+on Scan Parameters N Sex Age Sequence TR/TE/N 5 3/2 36.5±9.81 MPRAGE 9.7/4/1 Subject Informa+on Scan Parameters N Disease State 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 0.73 FS+LDDMM 0.77 0.75 0.40 0.50 0.60 0.70 0.80 0.90 1.00 DSC R. Hippo. CDR 0 R. Hippo. CDR 0.5 FreeSurfer 0.69 0.70 FS+LDDMM 0.73 0.72 0.40 0.50 0.60 0.70 0.80 0.90 1.00 DSC Subject Informa+on Scan Parameters N Disease State Sex (M/F) Age (min‐max) Sequence TR/TE/N 5 CDR 0 3/2 74.2 ± 5.2 MPRAGE 10/4/1 5 CDR 0.5 3/2 74.0 ± 4.8 MPRAGE 10/4/1 Schizophrenia Dataset Alzheimer’s Disease Dataset Overlap Metric: FreeSurfer LDDMM FS+LDDMM
Transcript of FreeSurfer‐Iniated Fully‐Automated Subcorcal Brain Segmentaon … · • FreeSurfer labels to...
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
