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BRAINS Development. Vincent A. Magnotta Associate Professor Department of Radiology March 15, 2011. Acknowledgements. Hans Johnson Ronald Pierson Kent Williams Mark Scully Eun Young Kim Wen Li Steve Dunn Wei Lu. Design of Version 3. BRAINS Tracer. BRAINS Command Line. - PowerPoint PPT Presentation

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BRAINS DevelopmentVincent A. MagnottaAssociate ProfessorDepartment of Radiology

March 15, 2011AcknowledgementsHans JohnsonRonald PiersonKent WilliamsMark ScullyEun Young KimWen LiSteve DunnWei Lu

Design of Version 3BRAINS Command LineTCLITKVTKQtGenerateCLPCommand Line Programs BRAINSFit, BRAINSCortex, etcBRAINS TracerBRAINS - LibraryBRAINS TracerVisualization toolImages, traces, landmarks, and surfacesGenerates surfaces from ROIsTracing toolNow includes measurementsLandmark operationsGUI Interface for command line toolsAutomated discovery of BRAINS toolsBRAINS TCL interfaceCommand line results sent to viewer

BRAINSTracerQt

BRAINSTracer Putamen Trace

BRAINSTracer Talairach and Points

BRAINSTracer Other Features

BRAINS3 AutoWorkupFile format conversionSpatial AlignmentBias Field Correction and NormalizationDefine Talairach Coordinate SystemTissue ClassificationNeural NetworkVolume MeasurementsSurface GenerationSurface MeasurementsDiffusion Tensor Analysis

Running AutoWorkupTCL Script required to run AutoWorkupset baseDir /Users/vince/images/brainstestdata/trunk/MR/DICOM-GE-B2/TESTset T1 $baseDir/T1_002set T2 $baseDir/T2_003set result [Brains::AutoWorkup::WorkupT1T2 $baseDir $T1 $T2]Result is stored saved in baseDir/10_AUT0.VersionExecute scriptbrains3 b workup.tcl

File Format ConversionConvert DICOM images into NIFTIBRAINSImageConversionResults are saved in Stage0 directory within 10_AUTO directorySpatial AlignmentAC-PC alignment of T1 and T2 weighted imagesBRAINSConstellationDetectorAutomated detection of several landmarks including mid-sagittal plane, AC, PC, 4V, eyesRun separately on each T1 and T2 weighted imageResults are saved in Stage1 directory within 10_AUTO directoryAligned imageLandmarksTransformsShould register all other images to the T1 weighted scan

Bias Field CorrectionEM SegmentationBRAINSABCPerforms discrete classification, image registration, bias field correction, brain extraction, and image averagingB-Spline registration aligns atlas with subjectFinal results are saved in 10_AUTO directory and intermediate results saved in BSITKBRAINSABCAverage T1 weighted imageAverage T2 weighted imageBrain maskLabel image

Image NormalizationTCL ScriptBrains::WorkupUtils::StandardizeImageIntensityClips top and bottom 0.05% of histogram within the brain and scales to 0-255 for the T1 and T2 weighted imagesFinal results are saved in 10_AUTO directoryNormalized T1 weighted imageNormalized T2 weighted imageDefine Talairach ParametersTCL Script and External ProgramBrains::WorkupUtils::AutoTalairachParametersBRAINSTalairachReads AC and PC points from the constellation detector programGet bounding box from the brain maskFinal results are saved in 10_AUTO directoryTalairach parameter fileTalairach grid file

Tissue ClassificationTCL Script and External ProgramBrains::WorkupUtils::PickBloodPlugsFromMarginBRAINSClassPlugsBRAINSClassifyExtract blood from edge of brain mask generated by BRAINSABCClassic BRAINS tissue classificationFinal results are saved in 10_AUTO directoryClass plugsContinuous tissue classified Discrete tissue classified image

Neural Network LabelingExternal ProgramBRAINSCutAlign atlas to subject image using B-Spline registration and label based on T1 and T2 weighted imagesFinal results are saved in 10_AUTO directory and intermediate results in ANN directoryLabel images for caudate, putamen, thalamus, hippocampus, globus pallidus

Volume MeasurementsExternal ProgramBrains::Measure::ClassTalairachVolumesBRAINSTalairachMaskStandard BRAINS Measurements based on tissue typesANN VolumesFinal results are saved in 10_AUTO directory and intermediate results in Talairach directoryCSV file for ANN and Class VolumesTalairach masks are in the Talairach directorySurface GenerationExternal ProgramGenusZeroImageFilterOriginalGenerate Genus Zero SurfaceWarp definitions of midline, brainstem and cerebellum to the subject (Diffeomorphic Demons)Use definitions of caudate, putamen, thalamus and ventricles to fill in white matterLow pass filter white matter imageSurface generationDecimate and smooth surfaceFinal results are saved in 10_AUTO directory and intermediate results in Genus0 directoryLeft and right surfacesSurface Labeling and MeasurementsExternal ProgramRegister atlas surface with subject surfaceSpherical diffeomorphic demonsLabel surface using a Bayesian frameworkSurface Features

Surface Inflation

Surface Labeling

Command Line ProgramsVisualizationBRAINSTracerQt Visualization and Tracer for BRAINSRegistrationBRAINSFit Rigid and affine registrationBRAINSDemonsWarp Non-rigid registrationBRAINSConstellationDetector ACPC finderTissue ClassificationBRAINSABC -Tissue classification / bias field correction moduleBRAINSKmeansClusterSamples K-means classificationBayesianClassifier Bayesian classificationBRAINSClassPlugs Plug estimationBRAINSClassify Multi-modal tissue classificationBRAINSDiscreteClass Continuous to discrete conversionLabelingBRAINSMush Brain mask creationBRAINSTalairach Create Talaiarch Parameters and atlas based binary imagesBRAINSCut Automated labelerBRAINSTalairachMask Create a Talairach mask based on atlas definitionSurfaceBRAINSCortex Surface generationGenusZeroFilterOriginal Surface topology correctionDifusion Tensor ImagingGTRACT Diffusion Tensor Imaging