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BRAINS Development Vincent A. Magnotta Associate Professor Department of Radiology March 15, 2011

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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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Page 1: BRAINS Development

BRAINS Development

Vincent A. MagnottaAssociate Professor

Department of Radiology

March 15, 2011

Page 2: BRAINS Development

Acknowledgements

• Hans Johnson• Ronald Pierson• Kent Williams• Mark Scully• Eun Young Kim• Wen Li• Steve Dunn• Wei Lu

Page 3: BRAINS Development

Design of Version 3

BRAINS Command Line

TCL

ITK VTK Qt

GenerateCLP

Command Line Programs – BRAINSFit, BRAINSCortex, etc

BRAINS Tracer

BRAINS - Library

Page 4: BRAINS Development

BRAINS Tracer• Visualization tool– Images, traces, landmarks, and surfaces– Generates surfaces from ROIs

• Tracing tool– Now includes measurements

• Landmark operations• GUI Interface for command line tools– Automated discovery of BRAINS tools

• BRAINS TCL interface– Command line results sent to viewer

Page 5: BRAINS Development

BRAINSTracerQt

Page 6: BRAINS Development

BRAINSTracer – Putamen Trace

Page 7: BRAINS Development

BRAINSTracer – Talairach and Points

Page 8: BRAINS Development

BRAINSTracer Other Features

Page 9: BRAINS Development

BRAINS3 AutoWorkup• File format conversion• Spatial Alignment• Bias Field Correction and Normalization• Define Talairach Coordinate System• Tissue Classification• Neural Network• Volume Measurements• Surface Generation• Surface Measurements• Diffusion Tensor Analysis

Page 10: BRAINS Development

Running AutoWorkup

• TCL Script required to run AutoWorkup– set baseDir /Users/vince/images/brainstestdata/trunk/MR/DICOM-GE-B2/TEST– set T1 $baseDir/T1_002– set T2 $baseDir/T2_003– set result [Brains::AutoWorkup::WorkupT1T2 $baseDir $T1 $T2]

• Result is stored saved in baseDir/10_AUT0.Version

• Execute script– brains3 –b workup.tcl

Page 11: BRAINS Development

File Format Conversion

• Convert DICOM images into NIFTI• BRAINSImageConversion• Results are saved in Stage0 directory within

10_AUTO directory

Page 12: BRAINS Development

Spatial Alignment• AC-PC alignment of T1 and T2 weighted images• BRAINSConstellationDetector• Automated detection of several landmarks including mid-

sagittal plane, AC, PC, 4V, eyes• Run separately on each T1 and T2 weighted image• Results are saved in Stage1 directory within 10_AUTO directory

– Aligned image– Landmarks– Transforms

• Should register all other images to the T1 weighted scan

Page 13: BRAINS Development

Bias Field Correction• EM Segmentation• BRAINSABC• Performs discrete classification, image registration, bias field

correction, brain extraction, and image averaging• B-Spline registration aligns atlas with subject• Final results are saved in 10_AUTO directory and

intermediate results saved in BSITKBRAINSABC– Average T1 weighted image– Average T2 weighted image– Brain mask– Label image

Page 14: BRAINS Development

Image Normalization

• TCL Script– Brains::WorkupUtils::StandardizeImageIntensity

• Clips top and bottom 0.05% of histogram within the brain and scales to 0-255 for the T1 and T2 weighted images

• Final results are saved in 10_AUTO directory– Normalized T1 weighted image– Normalized T2 weighted image

Page 15: BRAINS Development

Define Talairach Parameters

• TCL Script and External Program– Brains::WorkupUtils::AutoTalairachParameters– BRAINSTalairach

• Reads AC and PC points from the constellation detector program

• Get bounding box from the brain mask• Final results are saved in 10_AUTO directory– Talairach parameter file– Talairach grid file

Page 16: BRAINS Development

Tissue Classification• TCL Script and External Program

– Brains::WorkupUtils::PickBloodPlugsFromMargin– BRAINSClassPlugs– BRAINSClassify

• Extract blood from edge of brain mask generated by BRAINSABC• Classic BRAINS tissue classification• Final results are saved in 10_AUTO

directory– Class plugs– Continuous tissue classified – Discrete tissue classified image

Page 17: BRAINS Development

Neural Network Labeling• External Program

– BRAINSCut• Align atlas to subject image using B-Spline registration

and label based on T1 and T2 weighted images• Final results are saved in

10_AUTO directory and intermediate results in ANN directory– Label images for caudate,

putamen, thalamus, hippocampus, globus pallidus

Page 18: BRAINS Development

Volume Measurements

• External Program– Brains::Measure::ClassTalairachVolumes– BRAINSTalairachMask

• Standard BRAINS Measurements based on tissue types

• ANN Volumes• Final results are saved in 10_AUTO directory and

intermediate results in Talairach directory– CSV file for ANN and Class Volumes– Talairach masks are in the Talairach directory

Page 19: BRAINS Development

Surface Generation• External Program

– GenusZeroImageFilterOriginal• Generate Genus Zero Surface

– Warp definitions of midline, brainstem and cerebellum to the subject (Diffeomorphic Demons)

– Use definitions of caudate, putamen, thalamus and ventricles to fill in white matter

– Low pass filter white matter image– Surface generation– Decimate and smooth surface

• Final results are saved in 10_AUTO directory and intermediate results in Genus0 directory– Left and right surfaces

Page 20: BRAINS Development

Surface Labeling and Measurements

• External Program• Register atlas surface with subject surface– Spherical diffeomorphic demons

• Label surface using a Bayesian framework

Page 21: BRAINS Development

Surface Features

Page 22: BRAINS Development

Surface Inflation

Page 23: BRAINS Development

Surface Labeling

Page 24: BRAINS Development

Command Line Programs• Visualization

– BRAINSTracerQt – Visualization and Tracer for BRAINS• Registration

– BRAINSFit – Rigid and affine registration– BRAINSDemonsWarp – Non-rigid registration– BRAINSConstellationDetector – ACPC finder

• Tissue Classification– BRAINSABC -Tissue classification / bias field correction module– BRAINSKmeansClusterSamples – K-means classification– BayesianClassifier – Bayesian classification– BRAINSClassPlugs – Plug estimation– BRAINSClassify – Multi-modal tissue classification– BRAINSDiscreteClass – Continuous to discrete conversion

• Labeling– BRAINSMush – Brain mask creation– BRAINSTalairach – Create Talaiarch Parameters and atlas based binary images– BRAINSCut – Automated labeler– BRAINSTalairachMask – Create a Talairach mask based on atlas definition

• Surface– BRAINSCortex – Surface generation– GenusZeroFilterOriginal – Surface topology correction

• Difusion Tensor Imaging– GTRACT – Diffusion Tensor Imaging